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EX-10.1

 EXHIBIT 10.1 

ZAFGEN, INC. 

AMENDED AND RESTATED 2006 STOCK OPTION
PLAN 
  

	SECTION 1.	GENERAL PURPOSE OF THE PLAN; DEFINITIONS 

 The name of the plan is the Zafgen, Inc.
Amended and Restated 2006 Stock Option Plan (the “Plan”). The purpose of the Plan is to encourage and enable the officers, employees, directors and other key persons (including consultants and prospective employees) of Zafgen, Inc.,
a Delaware corporation (including any successor entity, the “Company”), and its Subsidiaries upon whose judgment, initiative and efforts the Company largely depends for the successful conduct of its business to acquire a proprietary
interest in the Company. It is anticipated that providing such persons with a direct stake in the Company’s welfare will assure a closer identification of their interests with those of the Company, thereby stimulating their efforts on the
Company’s behalf and strengthening their desire to remain with the Company. 
 The following terms shall be defined as set forth below:

 “Affiliate” of any Person means a Person that directly or indirectly, through one or more intermediaries, controls, is
controlled by or is under common control with the first mentioned Person. A Person shall be deemed to control another Person if such first Person possesses directly or indirectly the power to direct, or cause the direction of, the management and
policies of the second Person, whether through the ownership of voting securities, by contract or otherwise. 
 “Award” or
“Awards,” except where referring to a particular category of grant under the Plan, shall include Incentive Stock Options, Non-Qualified Stock Options, Restricted Stock Awards, Unrestricted Stock Awards or any combination of the
foregoing. 
 “Bankruptcy” shall mean (i) the filing of a voluntary petition under any bankruptcy or insolvency law,
or a petition for the appointment of a receiver or the making of an assignment for the benefit of creditors, with respect to the Holder, or (ii) the Holder being subjected involuntarily to such a petition or assignment or to an attachment or
other legal or equitable interest with respect to the Holder’s assets, which involuntary petition or assignment or attachment is not discharged within sixty (60) days after its date, and (iii) the Holder being subject to a transfer of
its Issued Shares by operation of law (including by divorce, even if not insolvent), except by reason of death. 
 “Board”
means the Board of Directors of the Company. 
 “Code” means the Internal Revenue Code of 1986, as amended, and any
successor Code, and related rules, regulations and interpretations. 
 “Committee” means the Committee of the Board
referred to in Section 2. 
 “Effective Date” means the date on which the Plan is approved by stockholders as set
forth at the end of this Plan. 

 “Exchange Act” means the Securities Exchange Act of 1934, as amended, and the
rules and regulations thereunder. 
 “Fair Market Value” of the Stock on any given date means the fair market value of the
Stock determined in good faith by the Committee. 
 “Holder” means, with respect to an Award or any Issued Shares, the
Person holding such Award or Issued Shares, including the initial recipient of the Award or any Permitted Transferee. 
 “Incentive
Stock Option” means any Stock Option designated and qualified as an “incentive stock option” as defined in Section 422 of the Code. 

“Issued Shares” means, collectively, all outstanding Shares issued pursuant to Restricted Stock Awards, all outstanding
Shares issued pursuant to Unrestricted Stock Awards, and all Option Shares. 
 “Non-Qualified Stock Option” means any Stock
Option that is not an Incentive Stock Option. 
 “Option” or “Stock Option” means any option to purchase
shares of Stock granted pursuant to Section 6. 
 “Option Shares” means outstanding shares of Stock that were issued
to a Holder upon the exercise of a Stock Option. 
 “Permitted Transferees” shall mean any of the following to whom a
Holder may transfer Issued Shares hereunder (as set forth in Section 9(a)(ii)(A)): the Holder’s spouse, children (natural or adopted), stepchildren, grandchildren or a trust for their sole benefit of which the Holder is the settlor;
provided, however, that any such trust does not require or permit distribution of any Issued Shares during the term of this Agreement unless subject to its terms. Upon the death of the Holder, the term Permitted Transferees shall also include
such deceased Holder’s estate, executions, administrations, personal representations, heirs, legatees and distributees, as the case may be. 

“Person” shall mean any individual, corporation, partnership (limited or general), limited liability company, limited
liability partnership, association, trust, joint venture, unincorporated organization or any similar entity. 
 “Repurchase
Event” means the termination of the Award recipient’s employment or service relationship with the Company and its Subsidiaries for Cause (as defined in the Award agreement). 

“Restricted Stock Award” means Awards granted pursuant to Section 7 and “Restricted Stock” means Shares
granted pursuant to such Awards. 
 “Sale Event” means the consummation of (i) the dissolution or liquidation of the
Company, (ii) the sale of all or substantially all of the assets of the Company and its Subsidiaries on a consolidated basis to an unrelated person or entity, or (iii) a merger, reorganization or

 
consolidation in which the outstanding shares of Stock are converted into or exchanged for securities of the successor entity and the holders of the Company’s outstanding voting power
immediately prior to such transaction do not own at least a majority of the outstanding voting power of the successor entity immediately upon completion of such transaction (taking into account only ownership interests resulting from pre-transaction
interests in the Company). 
 “Securities Act” means the Securities Act of 1933, as amended, and the rules and regulations
thereunder. 
 “Shares” means shares of Stock. 

“Stock” means the Common Stock, par value $0.001 per share, of the Company, subject to adjustments pursuant to
Section 3. 
 “Subsidiary” means any corporation or other entity (other than the Company) in which the Company has a
controlling interest, either directly or indirectly. 
 “Unrestricted Stock Award” means any Award granted pursuant to
Section 8 and “Unrestricted Stock” means Shares granted pursuant to such Awards. 
  

	SECTION 2.	ADMINISTRATION OF PLAN; COMMITTEE AUTHORITY TO SELECT GRANTEES AND DETERMINE AWARDS 

 (a)
Administration of Plan. The Plan shall be administered by the Board, or at the discretion of the Board, by a committee of the Board, comprised of not less than two Directors. All references herein to the Committee shall be deemed to refer to
the group then responsible for administration of the Plan at the relevant time (i.e., either the Board or a committee or committees of the Board, as applicable). 

(b) Powers of Committee. The Committee shall have the power and authority to grant Awards consistent with the terms of the Plan,
including the power and authority: 
 (i) to select the Persons to whom Awards may from time to time be granted; 

(ii) to determine the time or times of grant, and the extent, if any, of Incentive Stock Options, Non-Qualified Stock Options, Restricted Stock
Awards, Unrestricted Stock Awards or any combination of the foregoing, granted to any one or more grantees; 
 (iii) to determine the number
of shares of Stock to be covered by any Award; 
 (iv) to determine and modify from time to time the terms and conditions, including
restrictions, not inconsistent with the terms of the Plan, of any Award, which terms and conditions may differ among individual Awards and grantees, and to approve the form of written instruments evidencing the Awards; 

(v) to accelerate at any time the exercisability or vesting of all or any portion of any Award (whether or not expressly provided in any such
Award); 

 (vi) to impose any limitations on Awards granted under the Plan, including limitations on
transfers, repurchase provisions and the like and to exercise repurchase rights or obligations; 
 (vii) subject to any restrictions
applicable to Incentive Stock Options, to extend at any time the period in which Stock Options may be exercised; and 
 (viii) at any time to
adopt, alter and repeal such rules, guidelines and practices for administration of the Plan and for its own acts and proceedings as it shall deem advisable; to interpret the terms and provisions of the Plan and any Award (including related written
instruments); to make all determinations it deems advisable for the administration of the Plan; to decide all disputes arising in connection with the Plan; and to otherwise supervise the administration of the Plan. 

All decisions and interpretations of the Committee shall be binding on all persons, including the Company and Plan grantees. 

(c) Indemnification. Neither the Board nor the Committee, nor any member of either or any delegatee thereof, shall be liable for any
act, omission, interpretation, construction or determination made in good faith in connection with the Plan, and the members of the Board and the Committee (and any delegatee thereof) shall be entitled in all cases to indemnification and
reimbursement by the Company in respect of any claim, loss, damage or expense (including reasonable attorneys’ fees) arising or resulting therefrom to the fullest extent permitted by law and/or under any directors’ and officers’
liability insurance coverage which may be in effect from time to time. 
  

	SECTION 3.	STOCK ISSUABLE UNDER THE PLAN; CHANGES IN STOCK; SUBSTITUTION 

 (a) Stock
Issuable. The maximum number of Shares reserved and available for issuance under the Plan shall be 3,513,864 Shares, subject to adjustment as provided in Section 3(b). For purposes of this limitation, the Shares underlying any Awards which
are forfeited, canceled, reacquired by the Company, satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added back to the Shares available for issuance under the Plan. Subject to such overall limitation,
Shares may be issued up to such maximum number pursuant to any type or types of Award. The Shares available for issuance under the Plan may be authorized but unissued Shares or Shares reacquired by the Company and held in its treasury. 

(b) Changes in Stock. Subject to Section 4, if, as a result of any reorganization, recapitalization, reclassification, stock
dividend, stock split, reverse stock split or other similar change in the Company’s capital stock, the outstanding shares of Stock are increased or decreased or are exchanged for a different number or kind of shares or other securities of the
Company, or additional shares or new or different shares or other securities of the Company or other non-cash assets are distributed with respect to such shares of Stock or other securities, or, if, as a result of any merger, consolidation or sale
of all or substantially all of the assets of the Company, the outstanding shares of Stock are converted into or exchanged for a different number or kind of securities of the Company or any successor entity (or a parent or subsidiary

 
thereof), the Committee shall make an appropriate or proportionate adjustment in (i) the maximum number of shares reserved for issuance under the Plan, (ii) the number and kind of
shares or other securities subject to any then outstanding Awards under the Plan, (iii) the repurchase price per share subject to each outstanding Award, if any, and (iv) the exercise price and/or exchange price for each share subject to
any then outstanding Stock Options under the Plan, without changing the aggregate exercise price (i.e., the exercise price multiplied by the number of Stock Options) as to which such Stock Options remain exercisable. The adjustment by the Committee
shall be final, binding and conclusive. No fractional shares of Stock shall be issued under the Plan resulting from any such adjustment, but the Committee in its discretion may make a cash payment in lieu of fractional shares. 

The Committee may also adjust the number of shares subject to outstanding Awards and the exercise price and the terms of outstanding Awards to
take into consideration material changes in accounting practices or principles, extraordinary dividends, acquisitions or dispositions of stock or property or any other event if it is determined by the Committee that such adjustment is appropriate to
avoid distortion in the operation of the Plan, provided that no such adjustment shall be made in the case of an Incentive Stock Option, without the consent of the grantee, if it would constitute a modification, extension or renewal of the Option
within the meaning of Section 424(h) of the Code. 
 (c) Substitute Awards. The Committee may grant Awards under the Plan in
substitution for stock and stock based awards held by employees, directors or other key persons of another corporation in connection with a merger or consolidation of the employing corporation with the Company or a Subsidiary or the acquisition by
the Company or a Subsidiary of property or stock of the employing corporation. The Committee may direct that the substitute awards be granted on such terms and conditions as the Committee considers appropriate in the circumstances. Any substitute
Awards granted under the Plan shall not count against the share limitation set forth in Section 3(a). 
 SECTION 4. TREATMENT UPON SALE EVENT

 (a) Options. Subject to the powers of the Committee identified in Section 2(b): 

(i) In the case of and subject to the consummation of a Sale Event, the Plan and all Options issued hereunder shall terminate upon the
effective time of any such Sale Event unless provision is made in connection with the Sale Event in the sole discretion of the parties thereto for the assumption or continuation by the successor entity of Options theretofore granted, or the
substitution of such Options with new Options of the successor entity or parent thereof, with appropriate adjustment as to the number and kind of shares and, if appropriate, the per share exercise prices, as such parties shall agree. 

(ii) In the event of the termination of the Plan and all Options issued hereunder, each Holder of Options shall be permitted, within a
specified period of time, not to be less than fifteen (15) days, prior to the consummation of the Sale Event as determined by the Committee, to exercise all such Options which are then exercisable or will become exercisable as of the effective
time of the Sale Event; provided, however, that the exercise of Options not exercisable prior to the Sale Event shall be subject to the consummation of the Sale Event. 

 (iii) Notwithstanding anything to the contrary in Section 4(a)(i), in the event of a Sale
Event pursuant to which holders of the Stock of the Company will receive upon consummation thereof a cash payment for each share surrendered in the Sale Event, the Company shall have the right, but not the obligation, to make or provide for a cash
payment to the grantees holding vested Options in exchange for the cancellation thereof, in an amount equal to the difference between (A) the value as determined by the Committee of the consideration payable per share of Stock pursuant to the
Sale Event (the “Sale Price”) times the number of shares of Stock subject to outstanding vested Options (to the extent then exercisable at prices not in excess of the Sale Price) and (B) the aggregate exercise price of all such
outstanding vested Options. 
 (b) Option Shares and Restricted Stock Awards. Unless otherwise provided in an Award agreement, in the
case of and subject to the consummation of a Sale Event, Option Shares and shares of Restricted Stock shall be subject to the repurchase right set forth in Section 9(c)(i) and 9(c)(ii), respectively. 

(c) Unrestricted Stock Awards. Unless otherwise provided in an Award agreement, any shares of Unrestricted Stock shall be treated in a
Sale Event the same as all other Shares then outstanding. 
  

	SECTION 5.	ELIGIBILITY 

 Grantees under the Plan will be such full or part-time officers and other
employees, directors and key persons (including consultants and prospective employees) of the Company and its Subsidiaries as are selected from time to time by the Committee in its sole discretion. 

 

	SECTION 6.	STOCK OPTIONS 

 (a) Nature of Stock Options. A Stock Option is an Award entitling
the recipient to acquire, at such exercise price as determined by the Committee, shares of Stock subject to such restrictions and conditions as the Committee may determine at the time of grant. Conditions may be based on continuing employment (or
other service relationship) and/or achievement of pre-established performance goals and objectives. The grant of a Stock Option is contingent on the grantee executing the Stock Option agreement. The terms and conditions of each such agreement shall
be determined by the Committee, and such terms and conditions may differ among individual Awards and grantees. 
 Stock Options granted
under the Plan may be either Incentive Stock Options or Non-Qualified Stock Options. Incentive Stock Options may be granted only to employees of the Company or any Subsidiary that is a “subsidiary corporation” within the meaning of
Section 424(f) of the Code. To the extent that any Option does not qualify as an Incentive Stock Option, it shall be deemed a Non-Qualified Stock Option. 

No Incentive Stock Option shall be granted under the Plan after the date which is ten (10) years from the date the Plan is approved by
Board of Directors. 

 (b) Grants of Stock Options. The Committee in its discretion may grant Stock Options to
eligible directors, officers, employees and key persons of the Company or any Subsidiary. Stock Options granted under the Plan shall be subject to the following terms and conditions and shall contain such additional terms and conditions, not
inconsistent with the terms of the Plan, as the Committee shall deem desirable. If the Committee so determines, Stock Options may be granted in lieu of cash compensation at the optionee’s election, subject to such terms and conditions as the
Committee may establish. 
 (i) Exercise Price. The exercise price per share for the Stock covered by a Stock Option granted under the
Plan shall be determined by the Committee at the time of grant but shall not be less than one hundred percent (100%) of the Fair Market Value on the date of grant. If an employee owns or is deemed to own (by reason of the attribution rules of
Section 424(d) of the Code) more than ten percent (10%) of the combined voting power of all classes of stock of the Company or any parent or subsidiary corporation and an Incentive Stock Option is granted to such employee, the option price
of an Incentive Stock Option shall be not less than one hundred ten percent (110%) of the Fair Market Value on the grant date. 
 (ii)
Option Term. The term of each Stock Option shall be fixed by the Committee, but no Stock Option shall be exercisable more than ten (10) years after the date the Stock Option is granted. If an employee owns or is deemed to own (by reason
of the attribution rules of Section 424(d) of the Code) more than ten percent (10%) of the combined voting power of all classes of stock of the Company or any parent or subsidiary corporation and an Incentive Stock Option is granted to
such employee, the term of such Stock Option shall be no more than five (5) years from the date of grant. 
 (iii) Exercisability;
Rights of a Stockholder. Stock Options shall become exercisable at such time or times, whether or not in installments, as shall be determined by the Committee at or after the grant date. The Committee may at any time accelerate the
exercisability of all or any portion of any Stock Option. An optionee shall have the rights of a stockholder only as to shares acquired upon the exercise of a Stock Option and not as to unexercised Stock Options. An optionee shall not be deemed to
have acquired any such shares unless and until a Stock Option shall have been exercised pursuant to the terms hereof, the Company shall have issued and delivered the shares to the optionee, and the optionee’s name shall have been entered on the
books of the Company as a stockholder. 
 (iv) Method of Exercise. Stock Options may be exercised in whole or in part, by giving
written notice of exercise to the Company, specifying the number of shares to be purchased. Payment of the purchase price may be made by one or more of the following methods or as otherwise provided by the Committee: 

(A) In cash, by certified or bank check or other instrument acceptable to the Committee in U.S. funds payable to the order of
the Company in an amount equal to the purchase price of such Option Shares; 
 (B) By the optionee delivering to the Company
a promissory note if the Board has expressly authorized the loan of funds to the optionee for the purpose of enabling or assisting the optionee to effect the exercise of his or her Stock Option; provided that at least so much of the exercise price
as represents the par value of the Stock shall be paid other than with a promissory note if otherwise required by state law; or 

 (C) If permitted by the Committee, through the delivery (or attestation to the
ownership) of shares of Stock that have been beneficially owned by the optionee for at least six (6) months and are not then subject to restrictions under any Company plan. Such surrendered shares shall be valued at Fair Market Value on the
exercise date. 
 Payment instruments will be received subject to collection. No certificates for shares of Stock so purchased will be
issued to optionee until the Company has completed all steps required by law to be taken in connection with the issuance and sale of the shares, including (i) receipt of a representation from the optionee at the time of exercise of the Option
that the optionee is purchasing the shares for the optionee’s own account and not with a view to any sale or distribution thereof, (ii) the legending of any certificate representing the shares to evidence the foregoing representations and
restrictions, and (iii) obtaining from optionee payment or provision for all withholding taxes due as a result of the exercise of the Option. The delivery of certificates representing the shares of Stock to be purchased pursuant to the exercise
of a Stock Option will be contingent upon receipt from the optionee (or a purchaser acting in his stead in accordance with the provisions of the Stock Option) by the Company of the full purchase price for such shares and the fulfillment of any other
requirements contained in the Option Award agreement or applicable provisions of laws. In the event an optionee chooses to pay the purchase price by previously-owned shares of Stock through the attestation method, the number of shares of Stock
transferred to the optionee upon the exercise of the Stock Option shall be net of the number of shares attested to. 
 (c) Annual Limit on
Incentive Stock Options. To the extent required for “incentive stock option” treatment under Section 422 of the Code, the aggregate Fair Market Value (determined as of the time of grant) of the shares of Stock with respect to
which Incentive Stock Options granted under this Plan and any other plan of the Company or its parent and subsidiary corporations become exercisable for the first time by an optionee during any calendar year shall not exceed $100,000. To the extent
that any Stock Option exceeds this limit, it shall constitute a Non-Qualified Stock Option. 
 SECTION 7. RESTRICTED STOCK AWARDS 

(a) Nature of Restricted Stock Awards. A Restricted Stock Award is an Award pursuant to which the Company may, in its sole discretion,
grant or sell, at such purchase price as determined by the Committee, in its sole discretion, shares of Stock subject to such restrictions and conditions as the Committee may determine at the time of grant, which purchase price shall be payable in
cash or other form of consideration acceptable to the Committee. Conditions may be based on continuing employment (or other service relationship) and/or achievement of pre-established performance goals and objectives. The grant of a Restricted Stock
Award is contingent on the grantee executing the Restricted Stock Award agreement. The terms and conditions of each such agreement shall be determined by the Committee, and such terms and conditions may differ among individual Awards and grantees.

 (b) Rights as a Stockholder. Upon execution of a written instrument setting forth the
Restricted Stock Award and payment of any applicable purchase price, a grantee shall have the rights of a stockholder with respect to the voting of the Restricted Stock, subject to such conditions contained in the written instrument evidencing the
Restricted Stock Award. 
 (c) Vesting of Restricted Stock. The Committee at the time of grant shall specify the date or dates and/or
the attainment of pre-established performance goals, objectives and other conditions on which Restricted Stock shall become vested, subject to such further rights of the Company or its assigns as may be specified in the instrument evidencing the
Restricted Stock Award. 
 (d) Record Owner; Dividends. The Holder of Restricted Stock shall be considered the record owner of and
shall be entitled to vote the Shares of Restricted Stock if and to the extent such Shares are entitled to voting rights. The Holder shall be entitled to receive all dividends and any other distributions declared on the Shares; provided,
however, that the Company is under no duty to declare any such dividends or to make any such distribution. The Restricted Stock Award agreement may require or permit the immediate payment, waiver, deferral or investment of dividends paid on the
Restricted Stock. 
  

	SECTION 8.	UNRESTRICTED STOCK AWARDS 

 (a) Grant or Sale of Unrestricted Stock. The Committee
may, in its sole discretion, grant (or sell at par value or such higher purchase price determined by the Committee) an Unrestricted Stock Award to any grantee, pursuant to which such grantee may receive shares of Stock free of any vesting
restrictions under the Plan. Unrestricted Stock Awards may be granted or sold as described in the preceding sentence in respect of past services or other valid consideration, or in lieu of any cash compensation due to such individual. 

(b) Elections to Receive Unrestricted Stock In Lieu of Compensation. Upon the request of a grantee and with the consent of the
Committee, each such grantee may, pursuant to an advance written election delivered to the Company no later than the date specified by the Committee, receive a portion of the cash compensation otherwise due to such grantee in the form of shares of
Unrestricted Stock either currently or on a deferred basis. 
  

	SECTION 9.	TRANSFER RESTRICTIONS; COMPANY RIGHT OF FIRST REFUSAL; COMPANY REPURCHASE RIGHTS 

 (a)
Restrictions on Transfer. 
 (i) Options. No Stock Option shall be transferable by the optionee otherwise than by will or by
the laws of descent and distribution and all Stock Options shall be exercisable, during the optionee’s lifetime, only by the optionee, or by the optionee’s legal representative or guardian in the event of the optionee’s incapacity.
The Optionee may elect to designate a beneficiary by providing written notice of the name of such beneficiary to the Company, and may revoke or change such designation at any time by filing written notice of revocation or change with the Company,
and any such beneficiary may exercise the Optionee’s Stock Option in the event of the Optionee’s death to the extent provided herein. If the Optionee does not designate a beneficiary, or if the designated beneficiary predeceases the
Optionee, the legal 

 
representative of the Optionee may exercise this Stock Option in the event of the Optionee’s death to the extent provided herein. Notwithstanding the foregoing, the Committee, in its sole
discretion, may provide in the Award agreement regarding a given Option that the optionee may transfer, without consideration for the transfer, his or her Non-Qualified Stock Options to members of his or her immediate family, to trusts for the
benefit of such family members, or to partnerships in which such family members are the only partners, provided that the transferee agrees in writing with the Company to be bound by all of the terms and conditions of this Plan and the applicable
Option. 
 (ii) Issued Shares. No Issued Shares shall be sold, assigned, transferred, pledged, hypothecated, given away or in any
other manner disposed of or encumbered, whether voluntarily or by operation of law, unless (i) such transfer is in compliance with the terms of the applicable Award, all applicable securities laws (including the Securities Act), and with the
terms and conditions of this Section 9, (ii) such transfer does not cause the Company to become subject to the reporting requirements of the Exchange Act, and (iii) the transferee consents in writing to be bound by the provisions of
the Plan, including this Section 9. In connection with any proposed transfer, the Committee may require the transferor to provide at the transferor’s own expense an opinion of counsel to the transferor, satisfactory to the Committee, that
such transfer is in compliance with all foreign, federal and state securities laws (including the Securities Act). Any attempted disposition of Issued Shares not in accordance with the terms and conditions of this Section 9 shall be null and
void, and the Company shall not reflect on its records any change in record ownership of any Issued Shares as a result of any such disposition, shall otherwise refuse to recognize any such disposition and shall not in any way give effect to any such
disposition of Issued Shares. 
 (iii) Permitted Transfers. Unless otherwise provided in the agreement with respect to a particular
Award, and subject to the terms of Section 9(a)(ii), Issued Shares may be transferred pursuant to the following specific terms and conditions (provided that with respect to any transfer of Restricted Stock, all vesting and forfeiture provisions
shall continue to apply only with respect to the original recipient): 
 (A) Transfers to Permitted Transferees. The
Holder may sell, assign, transfer or give away any or all of the Issued Shares to Permitted Transferees; provided, however, that following such sale, assignment, or other transfer, such Issued Shares shall continue to be subject to the terms
of this Plan (including this Section 9) and such Permitted Transferee(s) shall, as a condition to any such transfer, deliver a written acknowledgment to that effect to the Company. 

(B) Transfers Upon Death. Upon the death of the Holder, any Issued Shares then held by the Holder at the time of such
death and any Issued Shares acquired thereafter by the Holder’s legal representative shall be subject to the provisions of this Plan, and the Holder’s estate, executors, administrators, personal representatives, heirs, legatees and
distributees shall be obligated to convey such Issued Shares to the Company or its assigns under the terms contemplated hereby. 

 (b) Right of First Refusal. Subject to Section 9(a)(ii), in the event that a Holder
desires at any time to sell, assign, transfer, pledge, hypothecate, give away or in any other manner dispose of or encumber, whether voluntarily or by operation of law, all or any part of such Holder’s Issued Shares to any Person, other than to
a Permitted Transferee in accordance with Section 9(a)(iii), the Holder first shall give written notice to the Company of the Holder’s intention to make such transfer. Such notice shall state the number of Issued Shares which the Holder
proposes to sell (the “Offered Shares”), the price and the terms at which the proposed sale is to be made and the name and address of the proposed transferee. At any time within forty-five (45) days after the receipt of such
notice by the Company, the Company or its assigns may elect to purchase all or any portion of the Offered Shares at the price and on the terms offered by the proposed transferee and specified in the notice. The Company or its assigns shall exercise
this right by mailing or delivering written notice to the Holder within the foregoing 45-day period (the “Company Exercise Notice”). If the Company or its assigns elect to exercise its purchase rights under this Section 9(b),
the closing for such purchase shall, in any event, take place on or prior to the thirtieth (30th) day following the date of the Company Exercise Notice. In the event that the Company or its
assigns do not elect to exercise such purchase right, or in the event that the Company or its assigns do not pay the full purchase price within such 30-day period, the Holder may, within ninety (90) days thereafter, sell the Offered Shares to
the proposed transferee and at the same price and on the same terms as specified in the Holder’s notice. Any Shares purchased by such proposed transferee shall no longer be subject to the terms of the Plan, subject to the provisions of
Section 13(c) hereof. Any Shares not sold to the proposed transferee shall remain subject to the Plan. In the event that the Company has a right of first refusal to which the Holder is subject and is akin to the right of first refusal contained
herein, that right of first refusal shall control. 
 (c) Company’s Right of Repurchase. 

(i) Right of Repurchase for Option Shares. The Company or its assigns shall have the right and option upon a Repurchase Event to
repurchase from a Holder of Option Shares some or all (as determined by the Company) of the Option Shares held or subsequently acquired upon exercise of a Stock Option by such Holder at the price per share specified below. Such repurchase right may
be exercised by the Company within the later of (A) six (6) months following the date of such Repurchase Event or (B) seven (7) months after the acquisition of such Option Shares upon exercise of a Stock Option (the
“Option Shares Repurchase Period”). The “Option Shares Repurchase Price” shall be equal to the Fair Market Value of the Option Shares, determined as of the date the Committee elects to exercise its repurchase rights
in connection with a Repurchase Event. 
 (ii) Right of Repurchase With Respect to Restricted Stock and Unrestricted Stock. Unless
otherwise set forth in the agreement entered into by the recipient and the Company in connection with a Restricted Stock Award or Unrestricted Stock Award, the Company or its assigns shall have the right and option upon a Repurchase Event to
repurchase from a Holder of Issued Shares received pursuant to a Restricted Stock Award or Unrestricted Stock Award some or all (as determined by the Company) of such Issued Shares at the price per share specified below. Such repurchase right may be
exercised by the Company within six (6) months following the date of such Repurchase Event (the “Non-Option Shares Repurchase Period”). The “Non-Option Shares Repurchase Price” shall be (i) in the case of
Issued Shares which are vested as of the date of the Repurchase Event, the Fair Market Value of such Issued Shares as of the date the Committee elects to exercise its repurchase rights in connection with a Repurchase Event and (ii) in the case
of Issued Shares which have not vested as of the date of the Repurchase Event, subject to adjustment as provided in Section 3(b), the original per share purchase price paid by the recipient. 

 (iii) Procedure. Any repurchase right of the Company shall be exercised by the Company or
its assigns by giving the Holder written notice on or before the last day of the Option Shares Repurchase Period or Non-Option Shares Repurchase Period, as applicable, of its intention to exercise such repurchase right. Upon such notification, the
Holder shall promptly surrender to the Company, free and clear of any liens or encumbrances, any certificates representing the Shares being purchased, together with a duly executed stock power for the transfer of such Shares to the Company or the
Company’s assignee or assignees. Upon the Company’s or its assignee’s receipt of the certificates from the Holder, the Company or its assignee or assignees shall deliver to him, her or them a check for the Option Shares Repurchase
Price or the Non-Option Shares Repurchase Price, as applicable; provided, however, that the Company may pay the Option Shares Repurchase Price or Non-Option Shares Repurchase Price, as applicable, by offsetting and canceling any indebtedness
then owed by the Holder to the Company. 
 (d) Escrow Arrangement. 

(i) Escrow. In order to carry out the provisions of Sections 9(b) and 9(c), of this Agreement more effectively, the Company shall hold
any Issued Shares in escrow together with separate stock powers executed by the Holder in blank for transfer, and any Permitted Transferee shall, as an additional condition to any transfer of Issued Shares, execute a like stock power as to such
Issued Shares. The Company shall not dispose of the Issued Shares except as otherwise provided in this Agreement. In the event of any repurchase by the Company (or any of its assigns), the Company is hereby authorized by the Holder and any Permitted
Transferee, as the Holder’s and each such Permitted Transferee’s attorney-in-fact, to date and complete the stock powers necessary for the transfer of the Issued Shares being purchased and to transfer such Issued Shares in accordance with
the terms hereof. At such time as any Issued Shares are no longer subject to the Company’s repurchase, first refusal and drag along rights, the Company shall, at the written request of the Holder, deliver to the Holder (or the relevant
Permitted Transferee) a certificate representing such Issued Shares with the balance of the Issued Shares to be held in escrow pursuant to this Section 9(d). 

(ii) Remedy. Without limitation of any other provision of this Agreement or other rights, in the event that a Holder, any Permitted
Transferees or any other Person is required to sell a Holder’s Issued Shares pursuant to the provisions of Sections 9(b) or 9(c) and in the further event that he or she refuses or for any reason fails to deliver to the Company or its designated
purchaser of such Issued Shares the certificate or certificates evidencing such Issued Shares together with a related stock power, the Company or such designated purchaser may deposit the applicable purchase price for such Issued Shares with a bank
designated by the Company, or with the Company’s independent public accounting firm, as agent or trustee, or in escrow, for such Holder, any Permitted Transferees or other Person, to be held by such bank or accounting firm for the benefit of
and for delivery to him, her, them or it, and/or, in its discretion, pay such purchase price by offsetting any indebtedness then owed by such Holder as provided above. Upon any such deposit and/or offset by the Company or its designated purchaser of
such 

 
amount and upon notice to the Person who was required to sell the Issued Shares to be sold pursuant to the provisions of Sections 9(b) or 9(c), such Issued Shares shall at such time be deemed to
have been sold, assigned, transferred and conveyed to such purchaser, such Holder shall have no further rights thereto (other than the right to withdraw the payment thereof held in escrow, if applicable), and the Company shall record such transfer
in its stock transfer book or in any appropriate manner. 
 (e) Lockup Provision. A Holder agrees, if requested by the Company
and any underwriter engaged by the Company, not to sell or otherwise transfer or dispose of any Issued Shares (including pursuant to Rule 144 under the Securities Act) held by him or her for such period following the effective date of any
registration statement of the Company filed under the Securities Act as the Company or such underwriter shall specify reasonably and in good faith, not to exceed one hundred eighty (180) days in the case of the Company’s initial public
offering (or, if required by such underwriter, such longer period of time as is necessary to enable such underwriter to issue a research report or make a public appearance that relates to an earnings release or announcement by the Company within
eighteen (18) days prior to or after the date that is one hundred eighty (180) days after the effective date of the registration statement relating to such offering, but in any event not to exceed two hundred ten (210) days following
the effective date of the registration statement relating to such offering) or ninety (90) days in the case of any other public offering. The provisions of this Section 9(e) shall be in addition to and not in lieu of any other lockup
provisions applicable to Holder. 
 (f) Adjustments for Changes in Capital Structure. If, as a result of any reorganization,
recapitalization, reclassification, stock dividend, stock split, reverse stock split or other similar change in the Common Stock, the outstanding shares of Common Stock are increased or decreased or are exchanged for a different number or kind of
shares of the Company’s stock, the restrictions contained in this Section 9 shall apply with equal force to additional and/or substitute securities, if any, received by Holder in exchange for, or by virtue of his or her ownership of,
Issued Shares. 
 (g) Termination. The terms and provisions of Sections 9(b) and 9(c) shall terminate upon the closing of the
Company’s initial public offering or upon consummation of any Sale Event, in either case as a result of which shares of the Company (or a successor entity) of the same class as the Issued Shares are registered under Section 12 of the
Exchange Act and publicly traded on any national securities exchange. 
  

	SECTION 10.	TAX WITHHOLDING 

 (a) Payment by Grantee. Each grantee shall, no later than the
date as of which the value of an Award or of any Stock or other amounts received thereunder first becomes includable in the gross income of the grantee for Federal income tax purposes, pay to the Company, or make arrangements satisfactory to the
Committee regarding payment of, any Federal, state, or local taxes of any kind required by law to be withheld with respect to such income. The Company and its Subsidiaries shall, to the extent permitted by law, have the right to deduct any such
taxes from any payment of any kind otherwise due to the grantee. The Company’s obligation to deliver stock certificates to any grantee is subject to and conditioned on any such tax obligations being satisfied by the grantee. 

 (b) Payment in Stock. Subject to approval by the Committee, a grantee may elect to have
the minimum required tax withholding obligation satisfied, in whole or in part, by (i) authorizing the Company to withhold from shares of Stock to be issued pursuant to any Award a number of shares with an aggregate Fair Market Value (as of the
date the withholding is effected) that would satisfy the withholding amount due, or (ii) transferring to the Company shares of Stock owned by the grantee with an aggregate Fair Market Value (as of the date the withholding is effected) that
would satisfy the minimum withholding amount due. 
  

	SECTION 11.	AMENDMENTS AND TERMINATION 

 The Board may, at any time, amend or discontinue the Plan
and the Committee may, at any time, amend or cancel any outstanding Award (or provide substitute Awards at the same or a reduced exercise or purchase price or with no exercise or purchase price) in a manner not inconsistent with the terms of the
Plan, provided that such price, if any, must satisfy the requirements which would apply to the substitute or amended Award if it were then initially granted under this Plan for the purpose of satisfying changes in law or for any other lawful
purpose, but no such action shall adversely affect rights under any outstanding Award without the holder’s consent. In addition, to the extent determined by the Committee to be required by the Code to ensure that Incentive Stock Options granted
under the Plan are qualified under Section 422 of the Code, Plan amendments shall be subject to approval by the Company’s stockholders who are entitled to vote at a meeting of stockholders. Nothing in this Section 11 shall limit the
Committee’s authority to take any action permitted pursuant to Section 3(c). 
  

	SECTION 12.	STATUS OF PLAN 

 With respect to the portion of any Award that has not been exercised and
any payments in cash, Stock or other consideration not received by a grantee, a grantee shall have no rights greater than those of a general creditor of the Company unless the Committee shall otherwise expressly determine in connection with any
Award or Awards. In its sole discretion, the Committee may authorize the creation of trusts or other arrangements to meet the Company’s obligations to deliver Stock or make payments with respect to Awards hereunder, provided that the existence
of such trusts or other arrangements is consistent with the foregoing sentence. 
  

	SECTION 13.	GENERAL PROVISIONS 

 (a) No Distribution; Compliance with Legal Requirements. The
Committee may require each person acquiring Stock pursuant to an Award to represent to and agree with the Company in writing that such person is acquiring the shares without a view to distribution thereof. No shares of Stock shall be issued pursuant
to an Award until all applicable securities law and other legal requirements have been satisfied. The Committee may require the placing of restrictive legends on certificates for Stock and Awards as it deems appropriate. 

(b) Delivery of Stock Certificates. Stock certificates to grantees under this Plan shall be deemed delivered for all purposes when the
Company or a stock transfer agent of the Company shall have mailed such certificates in the United States mail, addressed to the grantee, at the grantee’s last known address on file with the Company. 

 (c) Right of First Refusal, Co-Sale and Drag-Along Rights. At any time that a Holder, as a
result of an issuance of an Award hereunder or as a result of a transfer of Issued Shares pursuant to Section 9, would own one percent (1%) or more of the Common Stock then outstanding (calculated on an as converted-basis, and assuming the
exercise of all rights, options and warrants and conversion of all convertible securities), then, as a condition to such issuance or transfer, such Holder shall execute (i) a counterpart signature page to that certain Amended and Restated Right
of First Refusal and Co-Sale Agreement by and among the Company and the parties thereto dated as of October 25, 2007 (as the same may be amended, restated, or otherwise modified from time-to-time, the “ROFR Agreement”), such
Holder to become bound by the provisions of the ROFR Agreement as a “Key Holder”; (ii) an “Adoption Agreement” agreeing to be bound by and subject to the terms of that certain Amended and Restated Voting Agreement by and
among the Company and the parties thereto dated as of October 25, 2007 (as the same may be amended, restated or otherwise modified from time to time, the “Voting Agreement”), such Holder to become bound by the provisions of the
Voting Agreement as a “Stockholder.” Copies of the ROFR Agreement and the Voting Agreement may be obtained by any Holder at no cost by written request to the Company. 

(d) Other Compensation Arrangements; No Employment Rights. Nothing contained in this Plan shall prevent the Board from adopting other or
additional compensation arrangements, including trusts, and such arrangements may be either generally applicable or applicable only in specific cases. The adoption of this Plan and the grant of Awards do not confer upon any employee any right to
continued employment with the Company or any Subsidiary. 
 (e) Loans to Award Recipients. The Company shall have the authority to
make loans to recipients of Awards hereunder (including to facilitate the purchase of shares) and shall further have the authority to issue shares for promissory notes hereunder. 

(f) Designation of Beneficiary. Each grantee to whom an Award has been made under the Plan may designate a beneficiary or beneficiaries
to exercise any Award or receive any payment under any Award payable on or after the grantee’s death. Any such designation shall be on a form provided for that purpose by the Committee and shall not be effective until received by the Committee.
If no beneficiary has been designated by a deceased grantee, or if the designated beneficiaries have predeceased the grantee, the beneficiary shall be the grantee’s estate. 

(g) Headings and Certain Defined Terms. Headings and captions are for convenience only and are not to be used in the interpretation of
this Plan. The words “include”, “includes” and “including” will be deemed to be followed by the phrase “without limitation”. The words “herein”, “hereof” and “hereunder”, and
words of similar import, will be construed to refer to this Plan in its entirety and not to any particular provision hereof. All references herein to Sections, unless otherwise specifically provided, will be construed to refer to Sections this Plan.

 (h) Legend. Any certificate(s) representing the Issued Shares shall carry substantially the following legend: 

 THE TRANSFERABILITY OF THIS CERTIFICATE AND THE SHARES OF STOCK REPRESENTED HEREBY ARE SUBJECT TO
THE RESTRICTIONS, TERMS AND CONDITIONS (INCLUDING REPURCHASE AND RESTRICTIONS AGAINST TRANSFERS) CONTAINED IN THE ZAFGEN, INC. AMENDED AND RESTATED 2006 STOCK OPTION PLAN AND ANY AGREEMENT ENTERED INTO THEREUNDER BY AND BETWEEN THE COMPANY AND THE
HOLDER OF THIS CERTIFICATE (A COPY OF WHICH IS AVAILABLE AT THE OFFICES OF THE COMPANY FOR EXAMINATION). 
  

	SECTION 14.	EFFECTIVE DATE OF PLAN 

 This Plan shall become effective upon approval by the
stockholders in accordance with applicable law. Subject to such approval by the stockholders and to the requirement that no Stock may be issued hereunder prior to such approval, Stock Options and other Awards may be granted hereunder on and after
adoption of this Plan by the Board. 
  

	SECTION 15.	GOVERNING LAW 

 This Plan and all Awards and actions taken thereunder shall be governed
by, and construed in accordance with, the laws of the State of Delaware, applied without regard to conflict of law principles. 
  

	SECTION 16.	DISPUTE RESOLUTION 

 (a) Except as provided below, any dispute arising out of or relating
to this Plan or any Award made hereunder, or any agreement executed in connection herewith, or the breach, termination or validity of this Plan, any such Award or any such agreement, shall be finally settled by binding arbitration conducted
expeditiously in accordance with the J.A.M.S./Endispute Comprehensive Arbitration Rules and Procedures (the “J.A.M.S. Rules”). The arbitration shall be governed by the United States Arbitration Act, 9 U.S.C. Sections 1-16, and judgment
upon the award rendered by the arbitrators may be entered by any court having jurisdiction thereof. The place of arbitration shall be Boston, Massachusetts. 

(b) The arbitration shall commence within sixty (60) days of the date on which a written demand for arbitration is filed by any party
hereto. In connection with the arbitration proceeding, the arbitrator shall have the power to order the production of documents by each party and any third-party witnesses. In addition, each party may take up to three (3) depositions as of
right, and the arbitrator may in his or her discretion allow additional depositions upon good cause shown by the moving party. However, the arbitrator shall not have the power to order the answering of interrogatories or the response to requests for
admission. In connection with any arbitration, each party to the arbitration shall provide to the other, no later than seven (7) business days before the date of the arbitration, the identity of all persons that may testify at the arbitration
and a copy of all documents that may be introduced at the arbitration or considered or used by a party’s witness or expert. The arbitrator’s decision and award shall be made and 

 
delivered within six (6) months of the selection of the arbitrator. The arbitrator’s decision shall set forth a reasoned basis for any award of damages or finding of liability. The
arbitrator shall not have power to award damages in excess of actual compensatory damages and shall not multiply actual damages or award punitive damages, and each party hereby irrevocably waives any claim to such damages. 

(c) The Company, each recipient of an Award hereunder, each party to an agreement governed hereby and any other holder of Stock issued under
this Plan (each, a “Party”) covenants and agrees that such party will participate in the arbitration in good faith. This Section 14 applies equally to requests for temporary, preliminary or permanent injunctive relief, except that in
the case of temporary or preliminary injunctive relief any party may proceed in court without prior arbitration for the limited purpose of avoiding immediate and irreparable harm. 

(d) Each Party (i) hereby irrevocably submits to the jurisdiction of any United States District Court of competent jurisdiction for the
purpose of enforcing the award or decision in any such proceeding, (ii) hereby waives, and agrees not to assert, by way of motion, as a defense, or otherwise, in any such suit, action or proceeding, any claim that it is not subject personally
to the jurisdiction of the above-named courts, that its property is exempt or immune from attachment or execution (except as protected by applicable law), that the suit, action or proceeding is brought in an inconvenient forum, that the venue of the
suit, action or proceeding is improper or that this Plan or any Award or agreement therefor or the subject matter hereof may not be enforced in or by such court, and (iii) hereby waives and agrees not to seek any review by any court of any
other jurisdiction which may be called upon to grant an enforcement of the judgment of any such court. Each Party hereby consents to service of process by registered mail at the address to which notices are to be given. Each Party agrees that its,
his or her submission to jurisdiction and its, his or her consent to service of process by mail is made for the express benefit of each other Party. Final judgment against any Party in any such action, suit or proceeding may be enforced in other
jurisdictions by suit, action or proceeding on the judgment, or in any other manner provided by or pursuant to the laws of such other jurisdiction. 
 DATE
APPROVED BY BOARD OF DIRECTORS: February 1, 2006; amended and restated and share increase October 14, 2008 
 DATE APPROVED BY
STOCKHOLDERS: February 1, 2006, share increase November 3, 2008 

 AMENDMENT NO. 1 

TO 
 ZAFGEN, INC. 

AMENDED AND RESTATED 2006 STOCK OPTION PLAN 

The Zafgen, Inc. Amended and Restated 2006 Stock Option Plan (the “Plan”) is hereby amended by the Board of Directors and
stockholders of Zafgen, Inc., a Delaware corporation (the “Company”), as follows: 
 Section 3(a) of the Plan is
amended and restated to read in its entirety as follows: 
 “(a) Stock Issuable. The maximum number of Shares reserved and
available for issuance under the Plan shall be 4,363,864 Shares, subject to adjustment as provided in Section 3(b). For purposes of this limitation, the Shares underlying any Awards which are forfeited, canceled, reacquired by the Company,
satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added back to the Shares available for issuance under the Plan. Subject to such overall limitation, Shares may be issued up to such maximum number
pursuant to any type or types of Award. The Shares available for issuance under the Plan may be authorized but unissued Shares or Shares reacquired by the Company and held in its treasury.” 

ADOPTED BY BOARD OF DIRECTORS: February 16, 2010 
 ADOPTED
BY STOCKHOLDERS: February 16, 2010 

 AMENDMENT NO. 2 

TO 
 ZAFGEN, INC. 

AMENDED AND RESTATED 2006 STOCK OPTION PLAN 

The Zafgen, Inc. Amended and Restated 2006 Stock Option Plan (the “Plan”) is hereby amended by the Board of Directors and
stockholders of Zafgen, Inc., a Delaware corporation (the “Company”), as follows: 
 Section 3(a) of the Plan is
amended and restated to read in its entirety as follows: 
 “(a) Stock Issuable. The maximum number of Shares reserved and
available for issuance under the Plan shall be 9,863,864 Shares, subject to adjustment as provided in Section 3(b). For purposes of this limitation, the Shares underlying any Awards which are forfeited, canceled, reacquired by the Company,
satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added back to the Shares available for issuance under the Plan. Subject to such overall limitation, Shares may be issued up to such maximum number
pursuant to any type or types of Award. The Shares available for issuance under the Plan may be authorized but unissued Shares or Shares reacquired by the Company and held in its treasury.” 

ADOPTED BY BOARD OF DIRECTORS: June 30, 2011 
 ADOPTED BY
STOCKHOLDERS: June 30, 2011 

 AMENDMENT NO. 3 

TO 
 ZAFGEN, INC. 

AMENDED AND RESTATED 2006 STOCK OPTION PLAN 

The Zafgen, Inc. Amended and Restated 2006 Stock Option Plan, as amended (the “Plan”) is hereby amended by the Board of
Directors and stockholders of Zafgen, Inc., a Delaware corporation, as follows: 
 Section 3(a) of the Plan is amended and restated to
read in its entirety as follows: 
 “(a) Stock Issuable. The maximum number of Shares reserved and available for issuance under
the Plan shall be increased from 9,863,864 Shares to 10,863,864 Shares, subject to adjustment as provided in Section 3(b). For purposes of this limitation, the Shares underlying any Awards which are forfeited, canceled, reacquired by the
Company, satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added back to the Shares available for issuance under the Plan. Subject to such overall limitation, Shares may be issued up to such maximum
number pursuant to any type or types of Award. The Shares available for issuance under the Plan may be authorized but unissued Shares or Shares reacquired by the Company and held in its treasury.” 

ADOPTED BY BOARD OF DIRECTORS: March 7, 2013 
 ADOPTED BY
STOCKHOLDERS: April 26, 2013 

 AMENDMENT NO. 4 

TO 
 ZAFGEN, INC. 

AMENDED AND RESTATED 2006 STOCK OPTION PLAN 

The Zafgen, Inc. Amended and Restated 2006 Stock Option Plan, as amended (the “Plan”) is hereby amended by the Board of
Directors and stockholders of Zafgen, Inc., a Delaware corporation, as follows: 
 Section 3(a) of the Plan is amended and restated to
read in its entirety as follows: 
 “(a) Stock Issuable. The maximum number of Shares reserved and available for issuance under the Plan
shall be increased from 10,863,864 Shares to 11,863,864 Shares, subject to adjustment as provided in Section 3(b). For purposes of this limitation, the Shares underlying any Awards which are forfeited, canceled, reacquired by the Company,
satisfied without the issuance of Stock or otherwise terminated (other than by exercise) shall be added back to the Shares available for issuance under the Plan. Subject to such overall limitation, Shares may be issued up to such maximum number
pursuant to any type or types of Award. The Shares available for issuance under the Plan may be authorized but unissued Shares or Shares reacquired by the Company and held in its treasury.” 

ADOPTED BY BOARD OF DIRECTORS: November 22, 2013 
 ADOPTED
BY STOCKHOLDERS: November 22, 2013 

 Incentive Stock Option Agreement 

under Zafgen, Inc. 

Amended and Restated 2006 Stock Option Plan 
  

			
	Name of Optionee:	  	 __________________ (the “Optionee”)

		
	No. of Underlying Shares:	  	 __________ Shares of Common Stock

		
	Grant Date:	  	 __________________ (the “Grant Date”)

		
	Expiration Date:	  	 __________________ (the “Expiration Date”)

		
	Vesting Start Date:	  	 __________________ (the “Vesting Start Date”)

		
	Option Exercise Price/Share:	  	 $_________________ (the “Option Exercise Price”)

 Pursuant to the Zafgen, Inc. Amended and Restated 2006 Stock Option Plan (the “Plan”), Zafgen, Inc., a Delaware
corporation (together with all successors thereto, the “Company”), hereby grants to the Optionee, who is an employee of the Company or any of its Subsidiaries, an Option to purchase, on or prior to the Expiration Date (or such earlier date
as provided in Section 3 below), all or any part of the number of shares of Common Stock of the Company indicated above (the “Underlying Shares,” with such shares once issued being referred to herein and in the Plan as “Option
Shares”) at the Option Exercise Price per share indicated above. 
 Notwithstanding anything in this Incentive Stock Option Agreement (the
“Agreement”) to the contrary, this Stock Option and any Option Shares shall be subject to, and governed by, all the terms and conditions of the Plan, including, without limitation, Section 9 thereof concerning certain restrictions on
transfer of Option Shares and related matters. To the extent there is any inconsistency between the terms of the Plan and of this Agreement, the terms of the Plan shall control. 

All capitalized terms used in this Agreement and not otherwise defined shall have the respective meanings given such terms in the Plan. 

1. Vesting and Exercisability. 

(a) No portion of this Stock Option may be exercised until such portion shall have vested and become exercisable. Except as set forth in
Section 1(b) below, and subject to the determination of the Committee in its sole discretion to accelerate the vesting schedule hereunder, this Stock Option shall be vested and exercisable with respect to the Underlying Shares in accordance
with the following schedule: 
  

			
	 One Year Anniversary of the Vesting Start Date (25%)

(the “Initial Vesting Date”)
	  	[# of options]
		
	Month 131 - Month 47 [Date]	  	[# of options]
		
	Month 48 - [Date]	  	[# of options]

  

	1 	The remainder of the Options to vest over 3 years, in equal monthly installments, rounded down to the nearest share, at the end of each successive month following the Initial Vesting Date, until the fourth anniversary
of the Vesting Start Date, on which date all remaining unvested Options shall vest. 

  
 1 

 (b) In the case of a Sale Event, this Stock Option shall be treated as provided in
Section 4(a) of the Plan. 
 2. Exercise of Stock Option. Prior to the Expiration Date (or such earlier date provided in
Section 3 below), the Optionee may exercise this Stock Option by delivering a Stock Option exercise notice (an “Exercise Notice”) in the form of Appendix A hereto indicating his or her election to purchase some or all of
the Underlying Shares with respect to which this Stock Option is exercisable at the time of such notice. 
 3. Termination of
Employment. Except as the Committee may otherwise expressly provide, or as may otherwise be expressly provided in any employment agreement between the Company and the Optionee, if the Optionee’s employment with the Company or a
Subsidiary terminates, the period within which the Optionee may exercise this Stock Option may be subject to earlier termination as set forth below: 

(a) Termination of Employment Due to Death or Disability. If the Optionee’s employment terminates by reason of such Optionee’s
death or disability (as defined in Section 422(c) of the Code), this Stock Option may be exercised, to the extent exercisable on the date of such termination, by the Optionee or by the Optionee’s legal representative or legatee for a
period of twelve (12) months from the date of such termination or until the Expiration Date, if earlier. 
 (b) Termination for
Cause. If the Optionee’s employment is terminated by the Company for Cause, all Options (unvested and vested) shall terminate immediately. “Cause” means any of the following: (i) dishonesty, embezzlement, misappropriation of
assets or property of the Company; (ii) gross negligence, misconduct, neglect of duties, theft, fraud, or breach of fiduciary duty to the Company; (iii) violation of federal or state securities laws; (iv) breach of an employment,
consulting or other agreement with the Company; or (v) the conviction of a felony, or any crime involving moral turpitude, including a plea of guilty or nolo contendre. 

(c) Other Termination. If the Optionee’s employment terminates for any reason other than death or disability or Cause, this Stock
Option may be exercised, to the extent exercisable on the date of such termination, by the Optionee for a period of three (3) months from the date of termination or until the Expiration Date, if earlier. 

(d) Treatment of Unvested Options on Termination of Employment. Any portion of this Stock Option that is not exercisable on the date of
termination of the Optionee’s employment with the Company, for any reason, shall terminate immediately and be null and void and of no further force and effect. 

4. Incorporation of Plan. Notwithstanding anything herein to the contrary, this Stock Option shall be subject to and governed by
all the terms and conditions of the Plan. In the event of a conflict between this Agreement and the Plan, the terms of the Plan shall govern. 

5. Transferability. This Agreement is personal to the Optionee and is not transferable by the Optionee in any manner other than
by will or by the laws of descent and distribution. All transfers of Options are governed by the terms of the Plan. 
 6. Status of
Stock Option. The Optionee understands that, while this Stock Option is intended to qualify as an “incentive stock option” as defined in Section 422 of the Code to the extent permitted under applicable law, the Company makes
no representation or warranty that this Stock Option 

  
 2 

 
will, in fact, so qualify. In order to obtain the benefits of an incentive stock option under Section 422 of the Code, the Optionee understands that this Stock Option must be exercised
within three (3) months after termination of employment or within twelve (12) months after termination of employment if such termination is due to death or disability; provided, that in no event may this Stock Option be exercised
after the Expiration Date. The Optionee further understands that, to obtain such benefits, no sale or other disposition may be made of Option Shares for which incentive stock option treatment is desired within the
one-year period beginning on the day after the day of the transfer of such Option Shares to him or her, nor within the two-year period beginning on the day after the
Grant Date of this Stock Option. If the Optionee disposes (whether by sale, gift, transfer or otherwise) of any such Option Shares within either of these periods (a “disqualifying disposition”), he or she will notify the Company within
thirty (30) days after such disposition. The Optionee also agrees to provide the Company with any information concerning any such dispositions required by the Company for tax purposes. Further, to the extent Underlying Shares and any other
incentive stock options of the Optionee having an aggregate Fair Market Value in excess of $100,000 (determined as of the Grant Date) vest in any year, such options will not qualify as incentive stock options. To the extent that any portion of the
Stock Option does not qualify as an incentive stock option, whether due to a disqualifying disposition or otherwise, it shall be deemed a non-qualified stock option. 

7. Miscellaneous Provisions. 

(a) Change and Modifications. This Agreement may not be orally changed, modified or terminated, nor shall any oral waiver of any of its
terms be effective. This Agreement may be changed, modified or terminated only by an agreement in writing signed by the Company and the Optionee. 

(b) Governing Law. This Agreement shall be governed by and construed in accordance with the laws of Delaware without regard to conflict
of law principles. 
 (c) Equitable Relief. The parties hereto agree and declare that legal remedies may be inadequate to enforce the
provisions of this Agreement and that equitable relief, including specific performance and injunctive relief, may be used to enforce the provisions of this Agreement. 

(d) Headings. The headings are intended only for convenience in finding the subject matter and do not constitute part of the text of
this Agreement and shall not be considered in the interpretation of this Agreement. 
 (e) Saving Clause. If any provision(s) of this
Agreement shall be determined to be illegal or unenforceable, such determination shall in no manner affect the legality or enforceability of any other provision hereof. 

(f) Notices. All notices, requests, consents and other communications shall be in writing and be deemed given when delivered personally,
by telex or facsimile transmission or when received if mailed by first class registered or certified mail, postage prepaid. Notices to the Company or the Optionee shall be addressed as set forth underneath their signatures below, or to such other
address or addresses as may have been furnished by such party in writing to the other. 
 (g) Benefit and Binding Effect. This
Agreement shall be binding upon and shall inure to the benefit of the parties hereto, their respective successors, permitted assigns, and legal representatives. The Company has the right to assign this Agreement, and such assignee shall become
entitled to all the rights of the Company hereunder to the extent of such assignment. 

  
 3 

 (h) Counterparts. For the convenience of the parties and to facilitate execution, this
Agreement may be executed in two or more counterparts, each of which shall be deemed an original, but all of which shall constitute one and the same document. 

[SIGNATURE PAGE FOLLOWS] 

  
 4 

 The foregoing Agreement is hereby accepted and the terms and conditions thereof hereby agreed to
by the undersigned as of the date first above written. 
  

			
	ZAFGEN, INC.
		
	By:	 	 
		 	Name:
		 	Title:
		
	Address:	 	148 Sidney Street
		 	Cambridge, MA 02139

 The undersigned hereby acknowledges receiving and reviewing a copy of the Plan, including, without limitation,
Section 9 thereof, and understands that the Stock Option granted hereby is subject to the terms of the Plan and of this Agreement. This Agreement is hereby accepted, and the terms and conditions thereof and of the Plan hereby agreed to, by the
undersigned as of the date first above written. 
  

	
	OPTIONEE:
	
	 
	 Name:

	
	 Address:

DESIGNATION OF BENEFICIARY:                   
                                         
                                         
                                         
                                         
  
 Beneficiary’s Address: 

  
 5 

 SPOUSE’S CONSENT2 

The undersigned hereby acknowledges receiving and reviewing a copy of the Plan, including, without limitation, Section 9 thereof, and understands that the
Stock Option granted hereby is subject to the terms of the Plan and of this Agreement. This Agreement is hereby accepted, and the terms and conditions hereof and of the Plan are hereby agreed to, by the undersigned as of the date first above
written. 
  

	
	SPOUSE:
	
	 
	 Name:

	
	 Address:

  

	2 	Required only if Optionee’s state of residence is a community property state such as Arizona, California, Idaho, Louisiana, New Mexico, Nevada, Texas, Washington or Wisconsin. 

  
 6 

 Appendix A 

STOCK OPTION EXERCISE NOTICE 
 Zafgen,
Inc. 
 Attention: Treasurer 
  

 
  

Pursuant to the terms of the stock option agreement between myself and Zafgen, Inc. (the “Company”) dated
            (the “Agreement”), under the Company’s Amended and Restated 2006 Stock Option Plan, I, [Insert Name]
            , hereby [Circle One] partially/fully exercise such Stock Option by including herein payment in the amount of
$            representing the purchase price for [Fill in number of Underlying Shares]             Option Shares. I have chosen
the following form(s) of payment: 
  

					
	[   ]	    	1.	    	Cash
	[   ]	    	2.	    	Certified or bank check payable to Zafgen, Inc.
	[   ]	    	3.	    	Other (as described in the Plan (please describe))
		    		    	                                     
                                         
                                         
                                         
                             .

 In connection with my exercise of the Stock Option as set forth above, I hereby represent and warrant to
the Company as follows: 
 (i) I am purchasing the Option Shares for my own account for investment only, and not for resale
or with a view to the distribution thereof. 
 (ii) I have had such an opportunity as I have deemed adequate to obtain from
the Company such information as is necessary to permit me to evaluate the merits and risks of my investment in the Company and have consulted with my own advisers with respect to my investment in the Company. 

(iii) I have sufficient experience in business, financial and investment matters to be able to evaluate the risks involved in
the purchase of the Option Shares and to make an informed investment decision with respect to such purchase. 
 (iv) I can
afford a complete loss of the value of the Option Shares and am able to bear the economic risk of holding such Option Shares for an indefinite period of time. 

(v) I understand that the Option Shares may not be registered under the Securities Act of 1933 (it being understood that the
Option Shares are being issued and sold in reliance on the exemption provided in Rule 701 thereunder) or any applicable state securities or “blue sky” laws and may not be sold or otherwise transferred or disposed of in the absence of an
effective registration statement under the Securities Act of 1933 and under any applicable state securities or “blue sky” laws (or exemptions from the registration requirements thereof). I further acknowledge that certificates representing
Option Shares will bear restrictive legends reflecting the foregoing. 

  
 7 

 (vi) I understand and agree that the Option Shares when issued will continue to
be subject to the Plan, including Section 9 thereof. 
  

	
	Sincerely yours,
	
	 
	Name:
	
	Address:
	
	 
	 
	 

  
 8 

 Non-Qualified Stock Option Agreement 

under the Zafgen, Inc. 

Amended and Restated 2006 Stock Option Plan 
  

			
	Name of Optionee:	  	 __________________ (the “Optionee”)

		
	No. of Underlying Shares:	  	 __________ Shares of Common Stock

		
	Grant Date:	  	 __________________ (the “Grant Date”)

		
	Expiration Date:	  	 __________________ (the “Expiration Date”)

		
	Vesting Start Date:	  	 __________________ (the “Vesting Start Date”)

		
	Option Exercise Price/Share:	  	 $_________________ (the “Option Exercise Price”)

 Pursuant to the Zafgen, Inc. Amended and Restated 2006 Stock Option Plan (the “Plan”), Zafgen, Inc., a Delaware
corporation (together with all successors thereto, the “Company”), hereby grants to the Optionee, who is an officer, employee, director, consultant or other key person of the Company or any of its Subsidiaries, an Option to purchase, on or
prior to the Expiration Date (or such earlier date as provided in Section 3 below), all or any part of the number of shares of Common Stock of the Company indicated above (the “Underlying Shares,” with such shares once issued being
referred to herein and in the Plan as “Option Shares”) at the Option Exercise Price per share indicated above. 
 Notwithstanding anything in this
Non-Qualified Stock Option Agreement (the “Agreement”) to the contrary, this Stock Option and any Option Shares shall be subject to, and governed by, all the terms and conditions of the Plan, including, without limitation, Section 9
thereof concerning certain restrictions on transfer of Option Shares and related matters. To the extent there is any inconsistency between the terms of the Plan and of this Agreement, the terms of the Plan shall control. 

All capitalized terms used in this Agreement and not otherwise defined shall have the respective meanings given such terms in the Plan. 

1. Vesting and Exercisability.  

(a) No portion of this Stock Option may be exercised until such portion shall have vested and become exercisable. Except as set forth in
Section 1(b) below, and subject to the determination of the Committee in its sole discretion to accelerate the vesting schedule hereunder, this Stock Option shall be vested and exercisable with respect to the Underlying Shares in accordance
with the following schedule: 
  

			
	 One Year Anniversary of the Vesting Start Date (25%)

(the “Initial Vesting Date”)
	  	[# of options]
		
	Month 131 - Month 47 [Date]	  	[# of options]
		
	Month 48 - [Date]	  	[# of options]

  

	1 	The remainder of the Options to vest over 3 years, in equal monthly installments, rounded down to the nearest share, at the end of each successive month following the Initial Vesting Date, until the fourth anniversary
of the Vesting Start Date, on which date all remaining unvested Options shall vest. 

 (b) In the case of a Sale Event, this Stock Option shall be treated as provided in
Section 4(a) of the Plan. 
 2. Exercise of Stock Option. Prior to the Expiration Date (or such earlier date provided in
Section 3 below), the Optionee may exercise this Stock Option by delivering a Stock Option exercise notice (an “Exercise Notice”) in the form of Appendix A hereto indicating his or her election to purchase some or all of
the Underlying Shares with respect to which this Stock Option is exercisable at the time of such notice.  
 3. Termination of
Service Relationship. Except as the Committee may otherwise expressly provide, or as may otherwise be expressly provided in any agreement between the Company and the Optionee, if the Optionee’s service relationship with the Company or a
Subsidiary terminates, the period within which the Optionee may exercise this Stock Option may be subject to earlier termination as set forth below: 

(a) Termination of Service Relationship Due to Death or Disability. If the Optionee’s service relationship terminates by reason of
such Optionee’s death or disability (as defined in Section 422(c) of the Code), this Stock Option may be exercised, to the extent exercisable on the date of such termination, by the Optionee or by the Optionee’s legal representative
or legatee for a period of twelve (12) months from the date of such termination or until the Expiration Date, if earlier. 
 (b)
Termination for Cause. If the Optionee’s service relationship is terminated by the Company for Cause, all Options (unvested and vested) shall terminate immediately. “Cause” means any of the following: (i) dishonesty,
embezzlement, misappropriation of assets or property of the Company; (ii) gross negligence, misconduct, neglect of duties, theft, fraud, or breach of fiduciary duty to the Company; (iii) violation of federal or state securities laws;
(iv) breach of an employment, consulting or other agreement with the Company; or (v) the conviction of a felony, or any crime involving moral turpitude, including a plea of guilty or nolo contendre. 

(c) Other Termination. If the Optionee’s service relationship terminates for any reason other than death or disability or Cause,
this Stock Option may be exercised, to the extent exercisable on the date of such termination, by the Optionee for a period of three (3) months from the date of termination or until the Expiration Date, if earlier. 

(d) Treatment of Unvested Options on Termination of Service Relationship. Any portion of this Stock Option that is not exercisable on
the date of termination of the Optionee’s service relationship with the Company, for any reason, shall terminate immediately and be null and void and of no further force and effect. 

4. Incorporation of Plan. Notwithstanding anything herein to the contrary, this Stock Option shall be subject to and governed by
all the terms and conditions of the Plan. In the event of a conflict between this Agreement and the Plan, the terms of the Plan shall govern. 

5. Transferability. This Agreement is personal to the Optionee and is not transferable by the Optionee in any manner other than
by will or by the laws of descent and distribution. All transfers of Options are governed by the terms of the Plan. 
 6. Status of
Stock Option. This Stock Option is not intended to qualify as an “incentive stock option” as defined in Section 422(b) of the Code. 

  
 2 

 7. Miscellaneous Provisions. 

(a) Change and Modifications. This Agreement may not be orally changed, modified or terminated, nor shall any oral waiver of any of its
terms be effective. This Agreement may be changed, modified or terminated only by an agreement in writing signed by the Company and the Optionee. 

(b) Governing Law. This Agreement shall be governed by and construed in accordance with the laws of Delaware without regard to conflict
of law principles. 
 (c) Equitable Relief. The parties hereto agree and declare that legal remedies may be inadequate to enforce the
provisions of this Agreement and that equitable relief, including specific performance and injunctive relief, may be used to enforce the provisions of this Agreement. 

(d) Headings. The headings are intended only for convenience in finding the subject matter and do not constitute part of the text of
this Agreement and shall not be considered in the interpretation of this Agreement. 
 (e) Saving Clause. If any provision(s) of this
Agreement shall be determined to be illegal or unenforceable, such determination shall in no manner affect the legality or enforceability of any other provision hereof. 

(f) Notices. All notices, requests, consents and other communications shall be in writing and be deemed given when delivered personally,
by telex or facsimile transmission or when received if mailed by first class registered or certified mail, postage prepaid. Notices to the Company or the Optionee shall be addressed as set forth underneath their signatures below, or to such other
address or addresses as may have been furnished by such party in writing to the other. 
 (g) Benefit and Binding Effect. This
Agreement shall be binding upon and shall inure to the benefit of the parties hereto, their respective successors, permitted assigns, and legal representatives. The Company has the right to assign this Agreement, and such assignee shall become
entitled to all the rights of the Company hereunder to the extent of such assignment. 
 (h) Counterparts. For the convenience of the
parties and to facilitate execution, this Agreement may be executed in two or more counterparts, each of which shall be deemed an original, but all of which shall constitute one and the same document. 

[SIGNATURE PAGE FOLLOWS] 

  
 3 

 The foregoing Agreement is hereby accepted and the terms and conditions thereof hereby agreed to
by the undersigned as of the date first above written. 
  

			
	ZAFGEN, INC.
		
	By:	 	 
		 	Name:
		 	Title:
		
	Address:	 	148 Sidney Street
		 	Cambridge, MA 02139

 The undersigned hereby acknowledges receiving and reviewing a copy of the Plan, including, without limitation,
Section 9 thereof, and understands that the Stock Option granted hereby is subject to the terms of the Plan and of this Agreement. This Agreement is hereby accepted, and the terms and conditions thereof and of the Plan hereby agreed to, by the
undersigned as of the date first above written. 
  

	
	OPTIONEE:
	
	 
	 Name:

	
	 Address:

 DESIGNATION OF BENEFICIARY: 

Beneficiary’s Address: 

  
 4 

 SPOUSE’S CONSENT2 

The undersigned hereby acknowledges receiving and reviewing a copy of the Plan, including, without limitation, Section 9 thereof, and understands that the
Stock Option granted hereby is subject to the terms of the Plan and of this Agreement. This Agreement is hereby accepted, and the terms and conditions hereof and of the Plan are hereby agreed to, by the undersigned as of the date first above
written. 
  

	
	SPOUSE:
	
	 
	 Name:

	
	 Address:

  

	2 	Required only if Optionee’s state of residence is a community property state such as Arizona, California, Idaho, Louisiana, New Mexico, Nevada, Texas, Washington or Wisconsin. 

  
 5 

 Appendix A 

STOCK OPTION EXERCISE NOTICE 
 Zafgen,
Inc. 
 Attention: Treasurer 
  

 
  

Pursuant to the terms of the stock option agreement between myself and Zafgen, Inc. (the “Company”) dated
            (the “Agreement”), under the Company’s Amended and Restated 2006 Stock Option Plan, I, [Insert Name]
            , hereby [Circle One] partially/fully exercise such Stock Option by including herein payment in the amount of
$            representing the purchase price for [Fill in number of Underlying Shares]             Option Shares. I have chosen
the following form(s) of payment: 
  

					
	[   ]	    	1.	    	Cash
	[   ]	    	2.	    	Certified or bank check payable to Zafgen, Inc.
	[   ]	    	3.	    	Other (as described in the Plan (please describe))
		    		    	                                     
                                         
                                         
                                         
                                .

 In connection with my exercise of the Stock Option as set forth above, I hereby represent and warrant to
the Company as follows: 
 (i) I am purchasing the Option Shares for my own account for investment only, and not for resale
or with a view to the distribution thereof. 
 (ii) I have had such an opportunity as I have deemed adequate to obtain from
the Company such information as is necessary to permit me to evaluate the merits and risks of my investment in the Company and have consulted with my own advisers with respect to my investment in the Company. 

(iii) I have sufficient experience in business, financial and investment matters to be able to evaluate the risks involved in
the purchase of the Option Shares and to make an informed investment decision with respect to such purchase. 
 (iv) I can
afford a complete loss of the value of the Option Shares and am able to bear the economic risk of holding such Option Shares for an indefinite period of time. 

(v) I understand that the Option Shares may not be registered under the Securities Act of 1933 (it being understood that the
Option Shares are being issued and sold in reliance on the exemption provided in Rule 701 thereunder) or any applicable state securities or “blue sky” laws and may not be sold or otherwise transferred or disposed of in the absence of an
effective registration statement under the Securities Act of 1933 and under any applicable state securities or “blue sky” laws (or exemptions from the registration requirements thereof). I further acknowledge that certificates representing
Option Shares will bear restrictive legends reflecting the foregoing. 
 (vi) I understand and agree that the Option Shares
when issued will continue to be subject to the Plan, including Section 9 thereof. 

  
 6 

 
	
	Sincerely yours,
	
	 
	Name:
	
	Address:
	
	 
	 
	 

  
 7EX-10.3

 Exhibit 10.3 

***Text Omitted and Filed Separately with the Securities and Exchange Commission 

Confidential Treatment Requested Under 17 C.F.R. Sections 200.80(b)(4) and 230.406 

EXCLUSIVE LICENSE AGREEMENT 

This Exclusive License Agreement (this “Agreement”), dated as of July 6, 2009 (the “Effective Date”),
is made by and between Zafgen, Inc., a Delaware corporation (“Zafgen”), and Chong Kun Dang Pharmaceutical Corporation, a corporation organized under the laws of the Republic of Korea (“CKD”). CKD and Zafgen are
sometimes hereinafter referred to each as a “Party” and collectively as the “Parties.” 
 WHEREAS, CKD has
been engaged in the development of CKD-732 and a variety of other molecules, which target methionine aminopeptidase 2, and owns and otherwise controls certain patent rights and know-how with respect thereto; 

WHEREAS, Zafgen desires to acquire exclusive rights under the CKD Patent Rights (as defined below) and CKD Know-How (as defined below) in
order to continue the development thereof and products based thereupon; and 
 WHEREAS, the Parties desire to enter into an agreement
pursuant to which CKD will grant an exclusive license to Zafgen under the CKD Patent Rights and CKD Know-How for Zafgen to develop and commercialize Licensed Compounds and Licensed Products (as defined below). 

NOW, THEREFORE, the Parties hereby agree as follows: 

Section 1. Definitions. 
 For the
purpose of this Agreement, the following words and phrases shall have the meanings set forth below: 
 1.1 “Affiliate” of
an entity means any other entity which (directly or indirectly) is controlled by, controls or is under common control with such entity. For the purposes of this definition, the term “control” (including, with correlative meanings, the
terms “controlled by” and “under common control with”) as used with respect to an entity means (i) in the case of a corporate entity, direct or indirect ownership of voting securities entitled to cast at least fifty percent
(50%) of the votes in the election of directors or (ii) in the case of a non-corporate entity, direct or indirect ownership of at least fifty percent (50%) of the equity interests with the power to direct the management and policies
of such entity, provided that if local law restricts foreign ownership, control shall be established by direct or indirect ownership of the maximum ownership percentage that may, under such local law, be owned by foreign interests. 

1.2 “CKD Know-How” means all Technology, now existing or hereafter arising during the time the license grant set forth in
Section 2.1 is in effect, owned or otherwise Controlled by CKD or any of its Affiliates, that is related to the CKD Patent Rights or that is reasonably necessary or useful for the manufacture, use, sale, offer for sale, importation,
research, development or commercialization of any Licensed Compounds or Licensed Products or Improvements. Exhibit A attached hereto lists certain CKD Know-How. 

***Confidential Treatment Requested*** 

 1.3 “CKD Patent Rights” means the patents and patent applications listed in
Exhibit B attached hereto, plus (a) all divisionals, continuations, continuations-in-part thereof or any other patent application claiming priority directly or indirectly to (i) any of the patents or patent applications
identified on Exhibit B or (ii) any patent or patent application from which the patents or patent applications identified on Exhibit B claim direct or indirect priority, (b) all patents issuing on any of the
foregoing, owned or otherwise Controlled by CKD or any of its Affiliates during the time the license grant set forth in Section 2.1 is in effect that are reasonably necessary for the manufacture, use, sale, offer for sale, importation,
research, development or commercialization or other exploitation of any Licensed Compounds or Licensed Products, and (c) with all registrations, reissues, reexaminations, renewals, supplemental protection certificates and extensions of any of
the foregoing, and all foreign counterparts thereof. 
 1.4 “Combination Product” means a Licensed Product that includes at
least one additional active ingredient other than Licensed Compound. Drug delivery vehicles, adjuvants, and excipients shall not be deemed to be “active ingredients”, except in the case where such delivery vehicle, adjuvant, or excipient
is recognized as an active ingredient in accordance with 21 C.F.R. 210.3(b)(7). 
 1.5 “Commercially Reasonable
Efforts” means, with respect to Licensed Products, the carrying out of development and commercialization activities using the efforts that a company within the pharmaceutical industry and similarly situated to Zafgen would reasonably devote
to a product of similar market potential or profit potential resulting from its own research efforts, based on conditions then prevailing and taking into account, without limitation, issues of safety and efficacy, product profile, the proprietary
position, the then current competitive environment for such product and the likely timing of such product’s entry into the market, the regulatory environment and status of such product, and other relevant scientific, technical and commercial
factors, 
 1.6 “Confidential Information” means all Technology, chemical or biological materials, marketing plans,
strategies and customer lists, and other information that are disclosed or provided by such Party or its Affiliates to the other Party or its Affiliates, regardless of whether any of the foregoing are marked “confidential” or
“proprietary” or communicated to the other by the disclosing Party or its Affiliates in oral, written, graphic, or electronic form. 

1.7 “Confidentiality Agreement” means those certain confidentiality agreements, dated March 19, 2007 and
November 11, 2008, by and between the Parties. 
 1.8 “Controlled” or “Controls”, when used in
reference to patent or other intellectual property rights or Technology, means the legal authority or right of a person or entity to grant a license or sublicense of intellectual property rights to another person or entity, or to otherwise disclose
or provide Technology to such other person or entity, without breaching the terms of any agreement with a Third Party. 

  
 ***Confidential Treatment
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 2 

 1.9 “FDA” means the United States Food and Drug Administration or any successor
agency thereto. 
 1.10 “Field” means the treatment and diagnosis of any disease or condition in humans and animals. 

1.11 “First Commercial Sale” means, with respect to any Licensed Product on a country-by-country basis, the first sale for
use by the general public of such Licensed Product in such country after marketing approval of such Licensed Product has been granted, or marketing and sale of such Licensed Product is otherwise permitted, by the applicable regulatory authority of
such country. 
 1.12 “Generic Product” means any pharmaceutical product containing as an active ingredient a Licensed
Compound (or any salt, solvate, crystalline or noncrystalline form of such Licensed Compound) that is also contained in a Licensed Product, and which pharmaceutical product is sold in the same country as such Licensed Product by any Third Party that
is not a Sublicensee or Affiliate. 
 1.13 “Improvements” means all Technology that amount to improvements to any of the
inventions claimed by the CKD Patent Rights or to the CKD Know-How made, developed, conceived, owned or otherwise Controlled by CKD or any of its Affiliates after the date hereof, whether or not patentable or patented. 

1.14 “IND” means Investigational New Drug Application filed with the FDA required for initiation of clinical trials in humans
for the applicable Licensed Product in the United States. 
 1.15 “Licensed Compound” means (a) the compound known as
CKD-732, (b) any metabolic precursors, prodrugs, isomers (chiral and otherwise), metabolites, hydrates, anhydrides, solvates, salt forms, free acids or bases, esters, amides, ethers, complexes, conjugates or polymorphs of any compounds covered
by the foregoing clause (a) or this clause (b), (c) all other back-up molecules in CKD’s development program mat target methionine aminopeptidase 2 and (d) any metabolic precursors, prodrugs, isomers (chiral and
otherwise), metabolites, hydrates, anhydrides, solvates, salt forms, free acids or bases, esters, amides, ethers, complexes, conjugates or polymorphs of any compounds covered by the foregoing clause (c) or this clause (d). 

1.16 “Licensed Product” means any pharmaceutical product containing a Licensed Compound (alone or with other active
ingredients), in all forms, presentations, formulations and dosage forms. For clarification, Licensed Product shall include any Combination Product. 

1.17 “Limited Territory” means the Republic of Korea. 

1.18 “NDA” means a New Drug Application filed with the FDA required for marketing approval for the applicable Licensed
Product in the United States. 

  
 ***Confidential Treatment
Requested*** 
  
 3 

 1.19 “Net Sales” means, with respect to any Licensed Product, the amount
received by Zafgen and its Affiliates and Sublicensees for bona fide sales of such Licensed Product to a Third Party (other than Sublicensees and Zafgen’s Affiliates but including distributors for resale), less: 

(a) discounts (including cash, quantity and patient program discounts), retroactive price reductions, charge-back payments and rebates granted
to managed health care organizations or to federal, state and local governments, their agencies, and purchasers and reimbursers or to trade customers; 

(b) credits or allowances actually granted upon claims, damaged goods, rejections or returns of such Licensed Product, including such Licensed
Product returned in connection with recalls or withdrawals and expired inventory; 
 (c) freight out, postage, shipping and insurance
charges for delivery of such Licensed Product; and 
 (d) taxes or duties levied on, absorbed or otherwise imposed on the sale of such
Licensed Product, including value-added taxes, or other governmental charges otherwise imposed upon the billed amount, as adjusted for rebates and refunds, to the extent not paid by the Third Party. 

Net Sales shall not include any payments among Zafgen, its Affiliates and Sublicensees. Net Sales shall be determined in accordance with
generally accepted accounting principles, consistently applied in the United States. 
 Net Sales for any Combination Product shall be
calculated on a country-by-country basis by multiplying actual Net Sales of such Combination Product by the fraction A/B, where A is the weighted average price paid for the Licensed Product contained in such Combination Product if such Licensed
Product is sold separately in finished form in such country, and B is the weighted average invoice price paid for such Combination Product in such country. If such Licensed Product is not sold separately in finished form in such country, the parties
shall determine Net Sales for such Licensed Product by mutual agreement based on the relative contribution of such Licensed Product and each such other active ingredients in such Combination Product in accordance with the above formula, and shall
take into account in good faith any applicable allocations and calculations that may have been made for the same period in other countries. 

1.20 “Phase II Trial” means a human clinical trial of a Licensed Product with a sufficient number of subjects that is
designed to establish that a pharmaceutical product is safe and efficacious for its intended uses, which trial is intended to support regulatory approval of a Licensed Product, all as described in 21 C.F.R. 312.21(b). For purposes of this Agreement,
“Initiation of Phase II Trial” for a Licensed Product means the first dosing of such Licensed Product in a human patient in a Phase II Trial. 

1.21 “Phase III Trial” means a human clinical trial of a Licensed Product on a sufficient number of subjects that is designed
to establish that a pharmaceutical product is safe and efficacious for its intended use, and to determine warnings, precautions and adverse reactions that are associated with such pharmaceutical product in the dosage range to be

  
 ***Confidential Treatment
Requested*** 
  
 4 

 
prescribed, which trial is intended to support regulatory approval of a Licensed Product, all as described in 21 C.F.R. 312.21(c). For purposes of this Agreement, “Initiation of
Phase III Trial” for a Licensed Product means the first dosing of such Licensed Product in a human patient in a Phase III Trial. 

1.22 “Phase IV Trial” means a human clinical trial for a Licensed Product commenced after receipt of marketing approval in
the country for which such trial is being conducted and that is conducted within the parameters of the marketing approval for the Licensed Product. Phase IV Trials may include, without limitation, epidemiological studies, modeling and
pharmacoeconomic studies, investigator sponsored clinical trials of Licensed Product and post-marketing surveillance studies. 
 1.23
“Proof of Concept Trial” means a human clinical trial of a Licensed Product designed to evaluate weight loss for anti-obesity effects, “Initiation of Proof of Concept Trial” for a Licensed Product means the first
dosing of such Licensed Product in a human patient in a Proof of Concept Trial. 
 1.24 “Technology” means know-how, trade
secrets, chemical and biological materials, formulations, information, documents, studies, results, data and regulatory approvals, data, filings and correspondence (including DMFs), including biological, chemical, pharmacological, toxicological,
preclinical, clinical and assay data, manufacturing processes and data, specifications, sourcing information, assays, method and process validations, quality control and testing procedures, whether or not patented or patentable and patent filings
and office actions and/or other correspondences. 
 1.25 “Territory” means worldwide with the exception of the Republic of
Korea. 
 1.26 “Third Party” means any person or entity other than Zafgen or CKD or any of their Affiliates. 

1.27 “Valid Claim” means a claim of an issued and unexpired patent contained within the CKD Patent Rights, which claim has
not been revoked or held invalid or unenforceable by a court or other government agency of competent jurisdiction from which no appeal can be or has been taken and has not been held or admitted to be invalid or unenforceable through re-examination,
disclaimer, reissue, opposition procedure, nullity suit or otherwise, and which claim covers a Licensed Product or its use. 
 Section 2. License
Grant by CKD. 
 2.1 Exclusive License. CKD, for itself and on behalf of its Affiliates, hereby grants to Zafgen and its
Affiliates a non-transferable (except in accordance with Section 10.1). exclusive (even as to CKD and its Affiliates), license in the Field in the Territory with the right to sublicense in accordance with Section 2.2, under
the CKD Patent Rights and CKD Know-How, to make, have made, use, sell, offer to sell, import, research, develop, commercialize and otherwise exploit Licensed Compounds and Licensed Products and Improvements. The foregoing license grant includes the
right to make reference to all regulatory approvals, data, filings and correspondence (including DMFs) contained within the CKD Know-How. 

  
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 5 

 2.2 Sublicenses. 

(a) The exclusive license contained in Section 2.1 includes the right to grant sublicenses (through multiple tiers) to Third
Parties (each such Third Party sublicensee, a “Sublicensee”), provided that Zafgen shall provide CKD thirty (30) days prior written notice before entering into any sublicense agreement and Zafgen shall remain responsible for
the performance of its Sublicensees hereunder. Zafgen shall provide CKD with a copy of the sublicense agreement for its Sublicensees within ninety (90) days of execution, which copy may be redacted to exclude financial and other sensitive terms
and shall be treated as Confidential Information of Zafgen hereunder. 
 (b) Each sublicense granted by Zafgen to any rights licensed to it
hereunder shall terminate immediately upon the termination of the license from CKD to Zafgen with respect to such rights, provided that such sublicensed rights shall not terminate if, as of the effective date of such termination by CKD pursuant to
Section 9.2, a Sublicensee is not in material default of its obligations to Zafgen under its sublicense agreement, and within thirty (30) days of such termination the Sublicensee agrees in writing to be bound directly to CKD under a
license agreement substantially similar to this Agreement with respect to the rights sublicensed hereunder and the financial obligations of the licensee, substituting such Sublicensee for Zafgen. For the sake of clarity, CKD shall be allowed to
renegotiate any provisions of such sublicense that would have a material adverse effect on CKD’s business and that arise solely out of the substitution of Sublicensee for Zafgen. 

2.3 Restrictions on CKD. CKD and its Affiliates shall not grant or provide to any Third Party any Technology, patent or other
intellectual property rights or Confidential Information inconsistent with the terms of this Agreement. For as long as the license grant set forth in Section 2.1 is in effect, (i) CKD Know-How shall be treated as Confidential
Information of both Zafgen and CKD, and CKD and its Affiliates shall not disclose CKD Know-How except as permitted by Section 7.1(b) or 7.1(c), and (ii) CKD and its Affiliates shall not provide to any person or entity (other
than Zafgen) any Licensed Compounds whose use or sale infringes a Valid Claim. 
 2.4 CKD Development Efforts. CKD, on behalf of
itself and its Affiliates and any sublicensees, shall provide Zafgen with any report that analyzes the data from any study involving any use of the Licensed Compound in the Limited Territory (each an “Interpretable Result,”
explaining the earliest interpretable results) within thirty (30) days after receipt of such Interpretable Result. Zafgen shall have the opportunity to provide input and feedback regarding CKD’s development of the Licensed Compound in the
Limited Territory to the extent that a review of an Interpretable Result suggests that CKD’s development efforts could effect Zafgen’s development of Licensed Products, and CKD shall consider in good faith such input and feedback. In
addition, CKD will periodically provide any other data or information regarding its development efforts of the Licensed Compound in the Limited Territory that could effect Zafgen’s development efforts of Licensed Products. Any information,
including any Interpretable Results, disclosed by CKD pursuant to this Section 2.4, shall be deemed CKD’s Confidential Information and shall only be used as specified in this Agreement. 

  
 ***Confidential Treatment
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 6 

 Section 3. Transfer of CKD Know-How. 

3.1 Documentation. During the thirty (30) day period following the Effective Date, CKD shall promptly provide to Zafgen copies of
all documents, data or other information, including without limitation, regulatory, intellectual property and manufacturing and supply matters, that maybe reasonably useful or necessary to develop and commercialize the Licensed Compounds and the
Licensed Products, and that has not already been provided to Zafgen during the diligence process. 
 3.2 Technical Assistance. During
the six (6) month period following the Effective Date, CKD shall cooperate with Zafgen to transfer to Zafgen any additional CKD Know-How licensed under Section 2.1, to facilitate the transfer of development efforts related to
Licensed Compounds and Licensed Products. Such cooperation shall include, without limitation, providing Zafgen with reasonable access by teleconference or in-person at CKD’s facilities to CKD personnel involved in the research and development
of Licensed Compounds and Licensed Products to provide Zafgen with a reasonable level of technical assistance and consultation in connection with the transfer of CKD Know-How. 

Section 4. Development and Commercialization. 

4.1 Commercially Reasonable Efforts. 

(a) Zafgen, or one of its Affiliates or Sublicensees, as applicable, shall use Commercially Reasonable Efforts to develop and commercialize at
least one Licensed Product in accordance with the development schedule attached hereto as Exhibit C (the “Development Schedule”), which may be amended from time to time in accordance with the terms of that certain
Manufacturing and Supply Agreement, by and between Zafgen and CKD, dated as of even date herewith (the “Manufacturing Agreement”), to adjust the schedule to account for delays in delivery of Product (as defined in the Manufacturing
Agreement). If the development efforts are delayed by more than [...***...] from that which is set forth in the Development Schedule, the Parties shall take reasonable measures to remedy such delay. If development efforts are delayed by more
than [...***...] from that which is set forth on the Development Schedule, and the Parties agree that there is no reasonable method to moving the development efforts ahead without further undue delay, this Agreement shall be terminated within
thirty (30) days of such agreement. 
 (b) Zafgen shall provide CKD with informal development reports on a bi-annual basis, the form
and content of which shall be mutually agreed upon by the Parties. The contents of such development reports shall be deemed Zafgen’s Confidential Information and shall only be used as specified in this Agreement. 

4.2 Responsibilities and Costs. Zafgen shall have sole responsibility for, and shall bear all its costs of conducting, all development
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and Licensed Products (including manufacturing all required materials, filing for and obtaining all required regulatory approvals and submitting any adverse event reports to the applicable
regulatory authority). Zafgen shall own the results of all such activities, and as between the Parties, all such regulatory approvals shall be obtained by and in the name of Zafgen (or its Affiliates or Sublicensees). 

Section 5. Zafgen Payments. The payments set forth in this Section 5 only relate to Licensed Products for human uses. If Zafgen
develops a Licensed Product for the treatment and/or diagnosis of any disease or condition in animals, the Parties shall enter into a written amendment to this Agreement, documenting the payments to be made to CKD with respect to Licensed Products
for such uses. 
 5.1 Initial License Fee. Zafgen shall pay to CKD a non-refundable, one-time fee of [...***...] U.S. dollars
(US$[...***...]), which shall be paid to CKD as follows: 
 (a) [...***...] U.S. dollars (US$[...***...]) shall be paid to
CKD within [...***...] days of the Effective Date; and 
 (b) The remaining [...***...] U.S. dollars (US$[...***...])
shall be paid to CKD within [...***...] days after the date on which each of the following conditions has been satisfied: 
  

	 	(i)	[...***...]; 

  

	 	(ii)	[...***...]; and 

  

	 	(iii)	[...***...]. 

 5.2 One Time Fee. Zafgen shall pay to CKD a one-time non-refundable
payment of [...***...] U.S. dollars (US$[...***...]) within [...***...] days after [...***...]. 
 5.3 Milestone
Payments. As set forth in the following table, Zafgen shall make non-refundable Milestone Payments to CKD upon achievement of each of the Milestones Events. Each Milestone Payment shall be payable by Zafgen to CKD within [...***...] days
after the achievement of the corresponding Milestone Event with respect to the first Licensed Product. Only one set of Milestone Payments are payable hereunder no matter how many times any of the Milestone Events are achieved. 

 

			
	 “Milestone Event”
	  	“Milestone Payment”
	 1. [...***...]
	  	US$[...***...]
	 2. [...***...]
	  	US$[...***...]
	 3. [...***...]
	  	US$[...***...]
	 4. [...***...]
	  	US$[...***...]
	 5. [...***...]
	  	US$[...***...]
	 6. [...***...]
	  	US$[...***...]

  
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 5.4 Royalties. 

(a) Royalties. Subject to the terms and conditions of this Agreement (including the remainder of this Section 5). Zafgen
shall pay to CKD royalties, on a country-by-country and product-by-product basis for the period of time specified in Section 5.4(b), at the graduated royalty rates specified in the following table with respect to the aggregate annual
worldwide Net Sales of all Licensed Products in a calendar year: 
  

			
	 Aggregate Annual Worldwide Net Sales of All

Licensed Products in a Calendar Year
	  	 Royalty Rate

	 On such Net Sales up to [...***...] U.S. dollars (US$[...***...])
	  	 [...***...] percent

([...***...]%)

	 On such Net Sales above [...***...] U.S. dollars (US$[...***...]) and less than [...***...] U.S. dollars
(US$[...***...])
	  	 [...***...] percent

([...***...]%)

	 On such Net Sales above [...***...] U.S. dollars (US$[...***...])
	  	 [...***...] percent

([...***...]%)

 The applicable royalty rate shall be determined by reference to all Net Sales on which royalties are paid in a
given calendar year. By way of example, in a given calendar year, if the aggregate annual Net Sales in the Territory for all Licensed Products for which royalties are due under this Section were USD$[...***...], the following royalty
payment would be payable (subject to all reductions set forth in this Agreement): [...***...]. 
 (b) Royalty Term. The
royalties due under Section 5.4(a) shall be payable on Net Sales from the First Commercial Sale of a particular Licensed Product, on a country-by-country basis, until the later of (i) the expiration of the last to expire patent in
such country within the CKD Patent Rights containing a Valid Claim covering such Licensed Product or its use for which regulatory approval has been obtained in such country or (ii) ten (10) years from such First Commercial Sale in such
country (the “Royalty Period”). For clarity, for the purpose of determining the ten (10)-year period under Section 5.4(b)(ii) above, with respect to all Licensed Products containing the same Licensed Compound, the date
on which the First Commercial Sale of the first such Licensed Product is made shall be deemed as the First Commercial Sale of all such Licensed Products. In addition, for the purposes of this Section 5.4(h), the variations of any
Licensed Compound identified in clauses (b) and (d) of the definition of the term “Licensed Compound” shall be deemed as the same type of “Licensed Compound.” 

(c) Generic Competition. If during the Royalty Period, a Generic Product is launched for commercial sale in a country where royalties
are payable, the royalty rates specified in Section 5.4(a) shall be reduced by [...***...] percent ([...***...]%) in such country. Such reduction shall be first applied with respect to such country starting with sales in the
calendar quarter following the first commercial sale of such Generic Product. 
 (d) Only One Royalty. Only one royalty shall be due
with respect to the sale of the same unit of Licensed Product. Only one royalty shall be due hereunder on the sale of a Licensed Product even if the manufacture, use, sale, offer for sale or importation of such Licensed Product infringes more than
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 (e) Exceptions. No royalties shall accrue on the disposition of Licensed Products in
reasonable quantities by Zafgen, its Affiliates or Sublicensees as part of an expanded access program, a Phase IV Trial, or as donations to non-profit institutes, government agencies for non-commercial purposes, provided, in each case that
either Zafgen, its Affiliates or Sublicensees supply such Licensed Product at or below cost. 
 5.5 Sublicensing Payments. Zafgen
shall pay CKD [...***...] percent ([...***...]%) of any upfront licensing fees that Zafgen receives as a result of sublicensing any of its rights under this Agreement to a Sublicensee, provided that Zafgen’s total obligation under
this Section 5.5 shall not exceed $US[...***...] in any calendar year. Any payment due to CKD pursuant to this Section 5.5, shall be made within [...***...] days after Zafgen’s receipt of such upfront payment
from the Sublicensee. 
 5.6 Credits and Reductions. [...***...] percent ([...***...]%) of Third Party running royalties
of actual costs paid or payable by Zafgen, its Affiliates or Sublicensees for licenses and acquisitions by Zafgen, its Affiliates or Sublicensees for patent or other intellectual property rights reasonably necessary for the manufacture, use, sale,
offer for sale or importation of any Licensed Product in a particular country shall be creditable against payments owed CKD under Section 5.4. Notwithstanding the foregoing provisions of this Section, in no event shall CKD receive less
than [...***...] percent ([...***...]%) of the aggregate original payments due under Section 5.4 for any given calendar quarter (with any unused credits to accumulate and be applied against future payments due to CKD). 

5.7 Payment Terms. 
 (a)
Manner of Payment. All payments to be made by Zafgen hereunder shall be made in U.S. dollars by wire transfer to such bank account as CKD may designate. 

(b) Reports and Royalty Payments. For as long as royalties are due under Section 5.4. Zafgen shall furnish to CKD a written
report, within [...***...] days after the end of each calendar quarter (with the first such written report being provided at the end of the calendar quarter during which the First Commercial Sale took place), showing the amount of Net Sales of
Licensed Products and royalty due for such calendar quarter. Royalty payments for each calendar quarter shall be due at the same time as such written report for the calendar quarter. The report shall include, at a minimum, the following information
for the applicable calendar quarter, each listed by product and by country of sale: (i) the number of units of Licensed Products sold by Zafgen and its Affiliates and Sublicensees on which royalties are owed CKD hereunder; (ii) the gross
amount received for such sales; (iii) deductions taken from such gross amount as specified in the definition of “Net Sales”; (iv) Net Sales; (v) the amounts of any credits or reductions permitted by Section 5.6
or elsewhere hereunder; (vi) the royalties and Milestone Payments owed to CKD, listed by category; and (vii) the computations for any applicable currency conversions pursuant to Section 5.7(d). Zafgen shall use commercially
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information listed in the foregoing clauses (other than clause (iv)) as it relates to Net Sales made by such Sublicensee, and to the extent successful, will include such Sublicensee
information in such report. All such reports shall be treated as Confidential Information of Zafgen. 
 (c) Records and Audits.
Zafgen shall keep, and shall cause each of its Affiliates and Sublicensees, as applicable, to keep adequate books and records of accounting for the purpose of calculating all royalties payable to CKD hereunder. For the two (2) years next
following the end of the calendar year to which each shall pertain, such books and records of accounting (including those of Zafgen’s Affiliates and Sublicensees, as applicable) shall be kept at each of their principal places of business and
shall be open for inspection at reasonable times and upon reasonable notice by an independent certified accountant selected by CKD, which is reasonably acceptable to Zafgen, for the sole purpose of inspecting the royalties due to CKD under this
Agreement. In no event shall such inspections be conducted hereunder more frequently than once every twelve (12) months. Such accountant must have executed and delivered to Zafgen and its Affiliates and Sublicensees, as applicable, a
confidentiality agreement as reasonably requested by Zafgen, which shall include provisions limiting such accountant’s disclosure to CKD to only the results and basis for such results of such inspection. The results of such inspection, if any,
shall be binding on both Parties. Any underpayments shall be paid by Zafgen within thirty (30) days of notification of the results of such inspection. Any overpayments shall be fully creditable against amounts payable in subsequent payment
periods. CKD shall pay for such inspections, except that in the event there is any upward adjustment in aggregate royalties payable for any calendar year shown by such inspection of more than ten percent (10%) of the amount paid, Zafgen shall
reimburse CKD for any reasonable out-of-pocket costs of such accountant. Any underpayments or overpayments under this Section 5.7(c) shall be subject to the currency exchange provisions set forth in Section 5.7(d) as applied
to the calendar quarter during which the royalty obligations giving rise to such underpayment or overpayment were incurred by Zafgen. 
 (d)
Currency Exchange. With respect to Net Sales invoiced in U.S. dollars, the Net Sales and the amounts due to CKD hereunder shall be expressed in U.S. dollars. With respect to Net Sales invoiced in a currency other than U.S. dollars, the Net
Sales shall be expressed in the domestic currency of the entity making the sale, together with the U.S. dollar equivalent, calculated using the official rate of exchange of such domestic currency as quoted by The Wall Street Journal,
New York edition, for the last business day of the calendar quarter for which the payment is made. 
 (e) Tax Withholding;
Value-Added Tax. Zafgen shall have the right to withhold from payments due hereunder any tax which CKD is liable to under the appropriate tax laws and for the payments of which Zafgen is responsible. CKD shall be sent tax receipts by Zafgen
certifying the payments of the tax, so that CKD may use it for claiming a credit on the tax payable by CKD in The Republic of Korea on such payments. No deduction shall be made or a reduced amount shall be deducted if CKD furnishes a document from
all required tax authorities to Zafgen sufficiently before the due date of the payments, certifying that the payments are exempt from tax or subject to a reduced tax rate according to the applicable convention for the avoidance of double taxation.
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due to CKD hereunder shall be borne by Zafgen. Besides the above said, both Parties will undertake commercially reasonable efforts to minimize the allover tax burden for each of the Parties.
Value-added tax shall apply as legally required. 
 (f) Interest Due. Zafgen shall pay CKD interest on any payments that are not paid
on or before the date such payments are due under this Agreement at a rate of one-half percent (0.5%) per month or the maximum applicable legal rate, if less, calculated on the total number of days payment is delinquent. 

Section 6. Patent Prosecution, Infringement and Extensions. 

6.1 Appointment and Cooperation. With respect to all of the rights and activities of Zafgen set forth in this Section 6. CKD
hereby appoints Zafgen as its agent for such purposes with the authority to act on CKD’s behalf with respect to the CKD Patent Rights. CKD shall cooperate with Zafgen in the exercise of Zafgen’s authority granted herein, and shall execute
such documents and take such additional action as Zafgen may request in connection therewith. The Parties shall update Exhibit B upon either Party’s reasonable request. 

6.2 Additional Patents. Each Party shall give prompt notice to the other Party if such Party applies for or obtains any patent with
respect to the Licensed Products and/or the Licensed Technology in the Territory and the Limited Territory. Any additional patent obtained for CKD’s improvement of the Licensed Products shall be the sole property of CKD, but any additional
patent obtained for Zafgen’s improvement shall be the sole property of Zafgen. Each Party shall grant an exclusive license with regards to any additional patents in the Territory and the Limited Territory without any royalty or other
consideration. 
 6.3 Prosecution and Maintenance. 

(a) By Zafgen. On the Effective Date, CKD shall provide Zafgen with copies of the complete prosecution files for all patents and patent
applications listed on Exhibit B. Zafgen shall be solely responsible for the preparation, prosecution (including any interferences, oppositions, reissue proceedings and reexaminations) and maintenance of the CKD Patent Rights, and all
filing, prosecution, and maintenance decisions with respect to the CKD Patent Rights shall be made by Zafgen, provided CKD shall retain the right to give comments to Zafgen on material aspects of those activities. Zafgen shall be responsible for all
its costs incurred for such preparation, prosecution and maintenance. Each Party shall provide to the other Party copies of any papers relating to the filing, prosecution or maintenance of CKD Patent Rights promptly upon receipt. CKD shall not take
any action with respect to the prosecution or maintenance of any CKD Patent Rights without the prior written consent of Zafgen, except as contemplated by Section 6.2(b). 

(b) By CKD. Zafgen shall not knowingly permit any of the CKD Patent Rights to be abandoned in any country without CKD first being given
an opportunity to assume full responsibility for the continued prosecution and maintenance of same. In the event that Zafgen decides not to continue the prosecution or maintenance of a patent application or patent within CKD Patent Rights in any
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at least thirty (30) days prior to any pending lapse or abandonment thereof. In the event that CKD elects to assume responsibility for such prosecution and maintenance within thirty
(30) days of Zafgen’s notice, Section 6.2(a) shall thereafter apply to such patent application(s) and patent(s) except that the role of Zafgen and CKD shall be reversed thereunder (including that CKD shall be solely responsible
for all costs arising from those activities). Such patent application(s) and patent(s) shall otherwise continue to be subject to all of the terms and conditions of the Agreement in the same way as the other CKD Patent Rights. 

6.4 Enforcement and Defense. 

(a) By Zafgen. In the event that CKD or Zafgen becomes aware of a suspected infringement of any CKD Patent Right, or any such CKD Patent
Right is challenged in any action or proceeding (other than any interferences, oppositions, reissue proceedings or reexaminations, which are addressed above), such Party shall notify the other Party promptly, and following such notification, the
Parties shall confer. Zafgen shall have the right, but shall not be obligated, to defend any such action or proceeding or bring an infringement action with respect to such infringement at its own expense, in its own name and entirely under its own
direction and control, or settle any such action or proceeding by sublicense. CKD shall reasonably assist Zafgen in any action or proceeding being defended or prosecuted if so requested, and shall join such action or proceeding if reasonably
requested by Zafgen or required by applicable law. CKD shall have the right to participate in any such action or proceeding with its own counsel at its own expense and without reimbursement. 

(b) By CKD. If Zafgen elects not to settle, defend or bring any action for infringement described in Section 6.3(a) and so
notifies CKD, then, if and only if such infringement would give rise to royalties payable to CKD hereunder had Zafgen conducted the alleged infringing activities, CKD may defend or bring such action at its own expense, in its own name and entirely
under its own direction and control, subject to the following: Zafgen shall reasonably assist CKD in any action or proceeding being defended or prosecuted if so requested, and shall join such action or proceeding if requested by CKD or required by
applicable law. Zafgen shall have the right to participate in any such action or proceeding with its own counsel at its own expense and without reimbursement. No settlement of any such action or proceeding which restricts the scope, or adversely
affects the enforceability, of a CKD Patent Right may be entered into by CKD without the prior written consent of Zafgen. 
 (c)
Withdrawal. If either Party brings an action or proceeding under this Section 6.3 and subsequently ceases to pursue or withdraws from such action or proceeding after full discussion with the other party, it shall promptly notify
the other Party and the other Party may substitute itself for the withdrawing Party under the terms of this Section 6.3. 
 (d)
Damages. In the event that either Party exercises the rights conferred in this Section 6.3 and recovers any damages or other sums in such action or proceeding or in settlement thereof, such damages or other sums recovered shall
first be applied to all out-of-pocket costs and expenses incurred by the Parties in connection therewith (including reasonable attorneys’ fees), unless not reimbursable hereunder. If such recovery is insufficient to cover all such costs and
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before any of the other Party’s costs. If after such reimbursement any funds shall remain from such damages or other sums recovered, such funds shall be retained by the Party that controlled
the action or proceeding under this Section 6.3; provided, however, that (i) if Zafgen is the Party that controlled such action or proceeding, CKD shall receive out of any such remaining recovery received by Zafgen an amount equal
to royalties payable hereunder by treating such remaining recovery as “Net Sales” hereunder and (ii) if CKD is the Party that controlled such action or proceeding, the remaining recovery received by CKD shall be shared equally between
Zafgen and CKD. 
 6.5 Third Party IP Claims. In the event of (i) a holding in any action or proceeding enjoining Zafgen or any
of its Affiliates or Sublicensees from manufacturing, using, selling, offering for sale, importing, developing or commercializing any Licensed Compounds or Licensed Products, or holding Zafgen or any such other entities liable for damages for any
such activities, in each case such holding unappealable or unappealed within the time allowed for appeal, or (ii) a settlement of any action or proceeding requiring payment of damages by Zafgen or any such party, CKD shall refund to Zafgen
royalties paid with respect to all Licensed Products affected by such action or proceeding, sufficient to reimburse Zafgen and all such entities for all damages and costs and expenses paid or incurred by any of them with respect to such action or
proceeding attributable to infringement or misappropriation of any Third Party’s patent or other intellectual property rights, provided that, in the event that such refund is not sufficient to compensate for all such damages and expenses,
Zafgen shall be entitled to reduce royalties payable to CKD under Section 5.4(a) in each subsequent calendar quarter until such time as Zafgen recovers in full all such damages and expenses. 

6.6 Patent Extensions: Orange Book Listings; Patent Certifications. 

(a) Patent Term Extension. If elections with respect to obtaining patent term extension or supplemental protection certificates or
their equivalents in any country with respect to CKD Patent Rights or other patent rights covering Licensed Products or their manufacture or use are available, Zafgen shall have the sole right to make any such elections. 

(b) Data Exclusivity and Orange Book Listings. With respect to data exclusivity periods (such as those periods listed in the FDA’s
Orange Book (including any available pediatric extensions) or periods under national implementations of Article 10.1(a)(iii) of Directive 2001/EC/83, and all equivalents in any country), Zafgen shall have the sole right to seek and
maintain all such data exclusivity periods available for the Licensed Products. 
 (c) Notification of Patent Certification. CKD
shall notify and provide Zafgen with copies of any allegations of alleged patent invalidity, unenforceability or non-infringement of a CKD Patent Right pursuant to a Paragraph IV Patent Certification by a Third Party filing an Abbreviated New Drug
Application, an application under § 505(b)(2) of the United States Federal Food, Drug, and Cosmetic Act, as amended, or any other similar patent certification by a Third Party, and any foreign equivalent thereof. Such notification and
copies shall be provided to Zafgen within two (2) days after CKD receives such certification, and shall be sent to the address set forth in Section 10.5. 

  
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 Section 7. Confidential Information and Publicity. 

7.1 Confidentiality. 
 (a)
Confidential Information. Except as expressly provided herein, each of the Parties agrees that, for itself and its Affiliates, and for as long as this Agreement is in effect and for a period of ten (10) years thereafter, a Party and its
Affiliates (the “Receiving Party”) receiving Confidential Information of the other Party or its Affiliates (the “Disclosing Party”) shall (i) not disclose such Confidential Information to any Third Party
without the prior written consent of the Disclosing Party, except for disclosures expressly permitted below, and (ii) not use such Confidential Information for any purpose except those licensed or otherwise authorized or permitted by this
Agreement. For clarity, all Confidential Information of Zafgen received by or disclosed to CKD hereunder shall be used by CKD only for ensuring that Zafgen complies with its obligations hereunder and for no other purposes. 

(b) Exceptions. The obligations in Section 7.1(a) shall not apply with respect to any portion of the Confidential
Information that the Receiving Party can show by competent proof: 
 (i) is publicly disclosed by the Disclosing Party,
either before or after it is disclosed to the Receiving Party hereunder; 
 (ii) was known to the Receiving Party or any of
its Affiliates, without any obligation to keep it confidential or any restriction on its use, prior to disclosure by the Disclosing Party; 

(iii) is subsequently disclosed to the Receiving Party or any of its Affiliates by a Third Party lawfully in possession thereof
and without any obligation to keep it confidential or any restriction on its use; 
 (iv) is published by a Third Party or
otherwise becomes publicly available or enters the public domain, either before or after it is disclosed to the Receiving Party; or 

(v) has been independently developed by employees or contractors of the Receiving Party or any of its Affiliates without the
aid, application or use of Confidential Information of the Disclosing Party. 
 (c) Authorized Disclosures. The Receiving Party may
disclose Confidential Information belonging to the Disclosing Party to the extent (and only to the extent) such disclosure is reasonably necessary in the following instances: 

(i) subject to Section 7.2, by either Party in order to comply with applicable non-patent law (including any
securities law or regulation or the rules of a securities exchange) and with judicial process, if in the reasonable opinion of the Receiving Party’s counsel, such disclosure is necessary for such compliance; 

  
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 (ii) by either Party, in connection with prosecuting or defending litigation,
making regulatory filings, and filing, prosecuting and enforcing patent applications and patents (including CKD Patent Rights in accordance with Section 6): 

(iii) by Zafgen, on a “need to know basis” to its Affiliates, potential and future collaborators (including
Sublicensees), permitted acquirers or assignees under Section 10.1, research collaborators, subcontractors, investment bankers, investors, lenders, and their and each of Zafgen and its Affiliates’ respective directors, employees,
contractors and agents; and 
 (iv) by CKD, “on a need to know basis” to its Affiliates, permitted acquirers or
assignees under Section 10.1 investment bankers, investors, lenders, and their and CKD and its Affiliates’ respective directors, employees, contractors and agents, 

provided that (1) with respect to Sections 7.1(c)(i) or 7.1(c)(ii), where reasonably possible, the Receiving Party shall notify the
Disclosing Party of the Receiving Party’s intent to make any disclosure pursuant thereto sufficiently prior to making such disclosure so as to allow the Disclosing Party adequate time to take whatever action it may deem appropriate to protect
the confidentiality of the information to be disclosed, and (2) with respect to Sections 7.1(c)(iii) and 7.1(c)(iv), each of those named people and entities must be bound prior to disclosure by confidentiality and non-use
restrictions at least as restrictive as those contained in this Section 7 (other than investment bankers, investors and lenders, who must be bound prior to disclosure by commercially reasonable obligations of confidentiality). In
addition to the foregoing, Zafgen and its Affiliates and Sublicensees may make such disclosures of CKD Know-How specifically concerning the Licensed Compound and its use as any of them may deem reasonably necessary for their business. If and when
any Confidential Information is disclosed in accordance with this Section 7.1, such disclosure shall not cause any such information to cease to be Confidential Information except to the extent that such disclosure results in a public
disclosure of such information (other than through breach of this Agreement). 
 7.2 Terms of this Agreement; Publicity; Use of Name.
The Parties agree that the terms of this Agreement shall be treated as Confidential Information of both Parties, and thus may be disclosed only as permitted by Section 7.1(c). Each Party agrees not to issue any press release or public
statement disclosing information relating to this Agreement or the transactions contemplated hereby or the terms hereof without the prior written consent of the other Party, which consent shall not be unreasonably withheld, or as permitted by
Section 7.1(c). Under no circumstances may either Party use the name of the other Party or any of its personnel in any publication or any form of advertising without such other Party’s prior written consent. 

7.3 Relationship to the Confidentiality Agreement. This Agreement supersedes the Confidentiality Agreement, provided that all
“Confidential Information” disclosed or received by the Parties thereunder shall be deemed “Confidential Information” hereunder and shall be subject to the terms and conditions of this Agreement. 

  
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 Section 8. Warranties; Limitations of Liability; Indemnification. 

8.1 CKD Representations and Warranties. CKD covenants, represents and warrants to Zafgen that as of the Effective Date: 

(a) CKD is a corporation duly organized, validly existing and in good standing under the laws of the Republic of Korea, and it has full right
and authority to enter into this Agreement and to grant the licenses and other rights to Zafgen as herein described. 
 (b) This Agreement
has been duly authorized by all requisite corporate action, and when executed and delivered will become a valid and binding contract of CKD enforceable against CKD in accordance with its terms, subject to applicable bankruptcy, insolvency,
reorganization, moratorium and other law affecting creditors’ rights generally from time to time in effect, and to general principles of equity. 

(c) The execution, delivery and performance of this Agreement does not conflict with any other agreement, contract, instrument or
understanding, oral or written, to which CKD is a party, or by which it is bound, nor will it violate any law applicable to CKD. 
 (d) All
necessary consents, approvals and authorizations of all regulatory and governmental authorities and other persons or entities required to be obtained by CKD in connection with the execution and delivery of this Agreement and the performance of its
obligations hereunder have been obtained. 
 (e) Exhibit A contains a list of all CKD Know-How in CKD’s possession as of
the Effective Date that CKD has reasonably concluded Zafgen will find reasonably necessary or useful for the manufacture, use, sale, offer for sale, importation, research, development or commercialization or other exploitation of any Licensed
Compounds or Licensed Products or Improvements. Attached hereto as Exhibit B is a complete and accurate list of all patents and patent applications owned (in whole or in part) or otherwise Controlled by CKD or any of its Affiliates that
the manufacture, use, sale, offer for sale or importation of any Licensed Compounds (alone or as part of any Combination Product) would infringe. To the knowledge of CKD, the issued claims included in the CKD Patent Rights are valid and enforceable,
and no written claim has been made (except by a patent examiner during prosecution of the patent application(s) that resulted in any such issued patent claims), and no action or proceeding has been commenced or threatened, alleging to the contrary.
CKD is the sole and exclusive owner of all right, title and interest in and to the CKD Patent Rights. None of the CKD Patent Rights or CKD Know-How is subject to any Hen, security interest or other encumbrance. To CKD’s knowledge, the
conception and reduction to practice of the CKD Patent Rights have not constituted or involved the misappropriation of trade secrets or other rights or property of any Third Party. There are no claims, judgments or settlements against or amounts
with respect thereto owed by CKD or any of its Affiliates relating to the CKD Patent Rights. To CKD’s knowledge, there has been no infringement by any Third Party of any CKD Patent Rights. The use or practice of the license grant contained in
Section 2.1 shall not trigger any payment obligation by CKD or any of its Affiliates or Former Licensees (as defined below) to any Third Party. 

  
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 (f) There is no pending action or proceeding alleging, or, to CKD’s knowledge, any written
communication alleging, that the manufacture, use, sale, offer for sale or importation of any Licensed Compounds (alone or as part of any Combination Product), the activities of CKD or any of its Affiliates or any of their licensees with respect to
any such Licensed Compounds, or the practice or use of the CKD Patent Rights or CKD Know-How, has or will infringe or misappropriate any patent or other intellectual property rights of any Third Party. 

(g) CKD has never granted any license to a Third Party under any CKD Patent Rights or CKD Know-How with respect to any Licensed Compound, nor
has CKD been granted any license from a Third Party under any CKD Patent Rights or CKD Know-How with respect to any Licensed Compound. 

(h) As of the Effective Date, CKD does not have any knowledge of any scientific or clinical, regulatory or other facts or circumstances that
would materially and adversely affect the safety, efficacy or market performance of any Licensed Compounds (alone or as part of any Combination Product) that have not been communicated to Zafgen. 

8.2 Zafgen Representations and Warranties. Zafgen covenants, represents and warrants to CKD that as of the Effective Date: 

(a) Zafgen is a corporation duly organized, validly existing and in good standing under the laws of state in which it is incorporated, and it
has full right and authority to enter into this Agreement and to accept the rights and licenses granted as herein described. 
 (b) This
Agreement has been duly authorized by all requisite corporate action, and when executed and delivered will become a valid and binding contract of Zafgen enforceable against Zafgen in accordance with its terms, subject to applicable bankruptcy,
insolvency, reorganization, moratorium and other laws affecting creditors’ rights generally from time to time in effect, and to general principles of equity. 

(c) The execution, delivery and performance of this Agreement does not conflict with any other agreement, contract, instrument or
understanding, oral or written, to which Zafgen is a party, or by which it is bound, nor will it violate any law applicable to Zafgen. 

(d) All necessary consents, approvals and authorizations of all regulatory and governmental authorities and other persons or entities required
to be obtained by Zafgen in connection with the execution and delivery of this Agreement. 
 8.3 Disclaimer. EXCEPT AS EXPRESSLY SET
FORTH HEREIN, NEITHER CKD NOR ZAFGEN MAKES ANY REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. 

8.4 Limitation of Liability. NOTWITHSTANDING ANYTHING IN THIS AGREEMENT OR OTHERWISE, NEITHER PARTY SHALL BE LIABLE TO THE OTHER OR ANY
THIRD PARTY WITH RESPECT TO ANY SUBJECT MATTER OF THIS 

  
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AGREEMENT FOR ANY INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES; PROVIDED, HOWEVER, THAT THIS SECTION 8.4 SHALL NOT APPLY TO THE PARTIES’ INDEMNIFICATION RIGHTS AND OBLIGATIONS
UNDER SECTIONS 8.6(a) AND 8.6(b). 
 8.5 Performance by Affiliates. The Parties recognize that each Party may
perform some or all of its obligations under this Agreement through Affiliates and Third Party contractors; provided, however, that each Party shall remain responsible and liable for the performance by its Affiliates and Third Party contractors and
shall cause its Affiliates and Third Party contractors to comply with the provisions of this Agreement in connection therewith. 
 8.6
Indemnification. 
 (a) Zafgen Indemnity. Zafgen hereby agrees to indemnify and hold CKD and its Affiliates, and their
respective employees, directors, agents and contractors, and their respective successors, heirs and assigns and representatives (“CKD Indemnitees”) harmless from and against all claims, liability, threatened claims, damages,
expenses (including reasonable attorneys’ fees), suits, proceedings, losses or judgments, whether for money or equitable relief, of any kind, including death, personal injury, illness, product liability or property damage or the failure to
comply with applicable law (but not infringement or misappropriation of CKD Patent Rights) (collectively, “Losses”), arising from any Third Party claim due to the use, manufacture, sale, development or commercialization of any
Licensed Compounds or Licensed Products by or for Zafgen or any of its Affiliates, Sublicensees, agents and contractors, except to the extent that such Losses arise from (a) the negligence, recklessness or willful misconduct of any CKD
Indemnitees or (b) any breach of this Agreement by CKD. 
 (b) CKD Indemnity. CKD hereby agrees to indemnify and hold Zafgen,
its Affiliates and Sublicensees, and their respective employees, directors, agents and contractors, and their respective successors, heirs and assigns and representatives (“Zafgen Indemnitees”) harmless from and against all Losses
arising from any Third Party claim due to the use, manufacture, sale, development or commercialization of any Licensed Compounds or Licensed Products by or for CKD or any of its Affiliates, licensees (other than Zafgen and its Affiliates and
Sublicensees), agents and contractors, except to the extent that such Losses arise from (a) the negligence, recklessness or willful misconduct of any Zafgen Indemnitees or (b) any breach of this Agreement by Zafgen. 

(c) Indemnification Procedure. A claim to which indemnification applies under Section 8.6(a) or 8.6(b) shall be
referred to herein as a “Claim”. If any person or entity (each, an “Indemnitee”) intends to claim indemnification under this Section 8.6, the Indemnitee shall notify the other Party (the
“Indemnitor”) in writing promptly upon becoming aware of any claim that may be a Claim (it being understood and agreed, however, that the failure by an Indemnitee to give such notice shall not relieve the Indemnitor of its
indemnification obligation under this Agreement except and only to the extent that the Indemnitor is actually prejudiced as a result of such failure to give notice). The Indemnitor shall have the right to assume and control the defense of such Claim
at its own expense with counsel selected by the Indemnitor and reasonably acceptable to the Indemnitee; provided, however, that an Indemnitee shall have the 

  
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right to retain its own counsel, with the fees and expenses to be paid by the Indemnitee, if representation of such Indemnitee by the counsel retained by the Indemnitor would be inappropriate due
to actual or potential differing interests between such Indemnitee and any other party represented by such counsel in such proceedings. If the Indemnitor does not assume the defense of such Claim as aforesaid, the Indemnitee may defend such Claim
but shall have no obligation to do so. The Indemnitee shall not settle or compromise any Claim without the prior written consent of the Indemnitor, and the Indemnitor shall not settle or compromise any Claim in any manner which would have an adverse
effect on the Indemnitee’s interests, without the prior written consent of the Indemnitee, which consent, in each case, shall not be unreasonably withheld. The Indemnitee shall reasonably cooperate with the Indemnitor at the Indemnitor’s
expense and shall make available to the Indemnitor all pertinent information under the control of the Indemnitee, which information shall be subject to Section 7.1. 

8.7 Insurance. Zafgen shall procure and maintain insurance policies for the following coverages with respect to personal injury, bodily
injury and property damage arising out of Zafgen’s performance under this Agreement: (a) during the term of this Agreement, comprehensive general liability, including broad form and contractual liability, in a minimum amount of
$[...***...] combined single limit per occurrence and in the aggregate; (b) prior to the commencement of clinical trials involving any Licensed Products, clinical trials coverage in a minimum amount of $[...***...] combined single
limit per occurrence and in the aggregate; and (c) prior to the First Commercial Sale of the first Licensed Product, product liability coverage, in a minimum amount of $[...***...] combined single limit per occurrence and in the
aggregate, with the coverage provided for in clauses (b) and (c) to remain in force during the term of this Agreement and for at least [...***...] years thereafter. Zafgen shall provide CKD with insurance certificates evidencing the
required coverage upon CKD’s request for such certificates. CKD shall have no liability hereunder with respect to insurance costs, including, but not limited to insurance fees and compensation not covered by insurance. 

Section 9. Term, Termination and Survival. 

9.1 Term. This Agreement shall commence as of the Effective Date and, unless sooner terminated in accordance with the terms hereof or by
mutual written consent, shall continue on a country-by-country and product-by-product basis until the end of the period during which royalties are due hereunder on Net Sales of such Licensed Product in such country. Upon the end of such period for
such Licensed Product in such country, the license grant contained in Section 2.1 shall become perpetual, irrevocable and fully paid up with respect to such Licensed Product in such country. 

9.2 Termination for Material Default. Either Party shall have the right to terminate this Agreement upon delivery of written notice to
the other Party in the event of any default in the performance by such other Party of any of such other Party’s material obligations under this Agreement, provided that such default has not been cured within ninety (90) days after written
notice thereof is given by the non-defaulting Party to the defaulting Party specifying the nature of the alleged default, provided the Parties shall take all reasonable steps to resolve the matter pursuant to the process set forth in
Section 10.6(a) during the applicable cure period and before any such termination becomes effective. Termination of this Agreement by CKD under this 

  
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Section 9.2 shall be on a country-by-country and product-by-product basis (and not for the Agreement as a whole) if the default giving rise to termination is reasonably specific to
one or more countries or one or more products (e.g., a royalty dispute for one product in one or more countries). 
 9.3
Termination for Convenience. Zafgen may terminate this Agreement in full for any reason effective upon sixty (60) days prior notice to CKD. 

9.4 Termination for Insolvency. To the extent permitted by law, upon the filing or institution of bankruptcy, reorganization,
liquidation or receivership proceedings, or upon an assignment of a substantial portion of the assets for the benefit of creditors (a “Bankruptcy Event”) by either Party, CKD, in the case of a Bankruptcy Event by Zafgen, or Zafgen,
in the case of a Bankruptcy Event by CKD, may terminate this Agreement; provided, however, that, in the case of any involuntary bankruptcy proceeding, such right to terminate shall only become effective if the subject Party consents to the
involuntary bankruptcy or such proceeding is not dismissed within ninety (90) days after the filing thereof Each Party shall retain and may fully exercise all of its rights and elections under the U.S. Bankruptcy Code and foreign equivalents,
including that upon commencement of a bankruptcy proceeding by or against such Party undergoing a bankruptcy proceeding (the “Affected Party”) under the U.S. Bankruptcy Code or foreign equivalents, the non-Affected Party shall be
entitled to complete duplicates of or complete access to, as such non-Affected Party deems appropriate, any Technology and patent and other intellectual property rights and all embodiments hereof licensed or to be transferred to such non-Affected
Party hereunder by the Affected Party. Such Technology, rights and embodiments shall be promptly delivered to the non-Affected Party (i) upon any such commencement of a bankruptcy proceeding and upon written request therefore by the
non-Affected Party, unless the Affected Party elects to continue to perform all of its obligations under this Agreement, or (ii) if not delivered under the foregoing clause (i), upon the rejection of this Agreement by or on behalf of the
Affected Party and upon written request therefore by the non-Affected Party. This Section 9.4 is without prejudice to any rights the non-Affected Party may have arising under the U.S. Bankruptcy Code, foreign equivalents or other law.

 9.5 Effect of Certain Terminations. Upon termination of this Agreement by CKD pursuant to Section 9.2 or 9A or
by Zafgen pursuant to Section 9.3, or with respect to each applicable product and country as to which termination occurs pursuant to Section 9.2 (the rights and obligations of the Parties as to the remaining products and
countries in which termination under Section 9.2 has not occurred, being unaffected by such termination), all rights and licenses granted to Zafgen in Section 2 shall terminate with respect to each such terminated product and
country, with all rights of Zafgen under CKD Patent Rights for each such terminated product and country reverting to CKD, and Section 2.2(b) shall apply to all Sublicensees in each such terminated country for each such terminated
product. Further, upon any such termination and at CKD’s reasonable request, on a country-by-country and product-by-product basis, Zafgen shall grant to CKD a license to use, and shall provide to CKD a copy of, all regulatory approvals, data,
filings and correspondence (including DMFs) then in Zafgen’s Control relating to such product and applicable to such country, but only for the continued development and commercialization of such product in such country, and provided that
(i) all such information shall be treated as Confidential Information of Zafgen hereunder, (ii) such license and use shall be subject to any 

  
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rights of any Sublicensees that survive any such termination as contemplated by Section 2.2(b) and this Section 9 (including, if such Sublicensee is an exclusive
sublicensee for such product in such country, then there shall not be any such license nor any provision of such information by Zafgen but such Sublicensee shall agree to be bound to CKD in place of Zafgen for purposes of this sentence), and
(iii) if such termination occurs after Zafgen or any of its Affiliates or Sublicensees has filed for an NDA or its foreign equivalent or has obtained regulatory approval or has made a First Commercial Sale for such product in such country, then
CKD shall pay to Zafgen commercially reasonable royalties in an amount to be agreed to by the Parties on sales of such product in such country to reflect the investment in and value contributed by Zafgen and its Affiliates and Sublicensees to the
development and commercialization of such product. 
 9.6 Right to Sell-Off Inventory. Upon termination of this Agreement for any
reason, should Zafgen or any of its Affiliates or Sublicensees have any inventory of any Licensed Product, each of them shall have six (6) months thereafter in which to dispose of such inventory (subject to the payment to CKD of any royalties
due hereunder thereon). 
 9.7 Survival. In addition to the termination consequences set forth in Section 9.5, the
following provisions shall survive expiration or termination of this Agreement for any reason, as well as any other provision which by its terms or by the context thereof, is intended to survive such termination: Sections 1,
2.2(b), 2.3, 5.4-5.6, 6.3 (but only with respect to any action or proceeding initiated before such expiration or termination), 6A, 7, 8.3, 8.4, 8.5, 8.6, 9 and
10. Expiration or termination of this Agreement for any reason shall not relieve the Parties of any liability or obligation which accrued hereunder prior to the effective date of such termination or expiration, nor preclude either Party from
pursuing all rights and remedies it may have hereunder or at law or in equity, subject to Section 10.6, with respect to any breach of this Agreement nor prejudice either Party’s right to obtain performance of any obligation. 

Section 10. General Provisions. 

10.1 Trademarks. CKD can use any trademark that is owned by Zafgen and associated with a Licensed Product, in the Limited Territory,
provided that such use is restricted to and consistent with Zafgen’s use of such trademark within the Territory. Zafgen shall have the right, in its sole discretion, to determine if CKD’s use of a trademark in the Limited Territory meets
the requirements of this Section 10.1. 
 10.2 Assignment. Except as expressly provided by Section 2.1,
2.2 or 8.5, neither Party may assign this Agreement, delegate its obligations or otherwise transfer licenses or other rights created by this Agreement, without the prior written consent of the other Party, which consent shall not be
unreasonably withheld; provided that each Party may assign this Agreement as a whole without such consent to an Affiliate or in connection with the acquisition (whether by merger, consolidation, sale of assets, chance in control (by operation of law
or otherwise) or otherwise) of such Party or of that part of such Party’s business to which this Agreement relates, provided that such Party provides written notice to the other Party of such assignment and the assignee thereof agrees in
writing to be bound as such Party hereunder. Any assignment or transfer in violation of this Section 10.2 shall be void. This Agreement shall inure to the benefit of, and be binding upon, the legal representatives, successors and
permitted assigns of the Parties. 

  
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 10.3 Force Majeure. Neither Party shall be held liable or responsible to the other Party
nor be deemed to have defaulted under or breached this Agreement for failure or delay in fulfilling or performing any term of this Agreement if, but only to the extent that, such failure or delay results from causes beyond the reasonable control of
the affected Party, potentially including fire, floods, embargoes, terrorism, war, acts of war (whether war be declared or not), insurrections, riots, civil commotions, strikes, lockouts or other labor disturbances, acts of God or acts, omissions or
delays in acting by any governmental authority; provided that the Party affected shall promptly notify the other of the force majeure condition and shall exert reasonable efforts to eliminate, cure or overcome any such causes and to resume
performance of its obligations as soon as possible. 
 10.4 Severability. If any one or more of the provisions contained in this
Agreement is held invalid, illegal or unenforceable in any respect, the validity, legality and enforceability of the remaining provisions contained herein shall not in any way be affected or impaired thereby, unless the absence of the invalidated
provision(s) adversely affects the substantive rights of the Parties. The Parties shall in such an instance use their reasonable best efforts to replace the invalid, illegal or unenforceable provision(s) with valid, legal and enforceable
provision(s) which, insofar as practical, implement the purposes of this Agreement. 
 10.5 Amendment; Waiver. Except as set forth in
Section 4.1(a) or elsewhere in this Agreement, this Agreement may not be modified or amended, in whole or part, except by a written instrument signed by the Parties; provided that any unilateral undertaking or waiver made by one Party in
favor of the other shall be enforceable if undertaken in a writing signed by the Party to be charged with the undertaking or waiver. No delay or omission by either Party hereto in exercising any right or power occurring upon any noncompliance or
default by the other Party with respect to any of the terms of this Agreement shall impair any such right or power or be construed to be a waiver thereof. A waiver by either of the Parties of any of the covenants, conditions or agreements to be
performed by the other shall not be construed to be a waiver of any succeeding breach thereof or of any other covenant, condition or agreement herein contained. 

10.6 Notices. Except as otherwise provided herein, all notices under this Agreement shall be sent by certified mail or by recognized
international express, postage prepaid, to the following addresses of the respective Parties: 
  

			
	If to Zafgen, to:	  	 Zafgen, Inc.
 5 Cambridge Center, Floor 2

Cambridge, MA 02142
 Attention: President

  
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	With a required copy to:	  	 Goodwin Procter LLP
 53 State Street

Boston, MA 02109
 Attention: Mitchell S. Bloom, Esq.

		
	If to CKD, to:	  	 Chong Kun Dang Pharmaceuticals
 368, 3-ga,
Chungjeong-ro, Seodaemun-gu,
 Seoul 120-756, Korea
 Attention:
President

 or to such address as each Party may hereafter designate by notice to the other Party. A notice shall be deemed to have been
given on the date it is received by all required recipients for the noticed Party. 
 10.7 Dispute Resolution. Disputes arising under
or in connection with this Agreement shall be resolved pursuant to this Section 10.7. 
 (a) In the event of a dispute between
the Parties, the Parties shall first attempt in good faith to resolve such dispute by negotiation and consultation between themselves. In the event that such dispute is not resolved on an informal basis within [...***...] days, any Party may,
by written notice to the other, have such dispute referred to each of the Parties’ respective CEOs or his or her designee (who shall be a senior executive), who shall attempt in good faith to resolve such dispute by negotiation and consultation
for a [...***...] day period following receipt of such written notice. 
 (b) In the event the Parties’ CEOs (or designees) are
not able to resolve such dispute, either Party may at any time after such [...***...]-day period submit such dispute to be finally settled by arbitration administered in accordance with the Commercial Arbitration Rules of the American
Arbitration Association (“AAA”) in effect at the time of submission. The arbitration shall be heard and determined by three (3) arbitrators. Zafgen and CKD shall each appoint one arbitrator and the third arbitrator shall be
selected by the two Party-appointed arbitrators, or, failing agreement within [...***...] days following the date of receipt by the respondent of the claim, by the AAA. Such arbitration shall take place in San Francisco, California. The
arbitration award so given shall be a final and binding determination of the dispute, shall be fully enforceable in any court of competent jurisdiction, and shall not include any damages expressly prohibited by Section 8.4. 

(c) Costs of arbitration are to be divided by the Parties in the following manner: Zafgen shall pay for the arbitrator it chooses, CKD shall
pay for the arbitrator it chooses, and the costs of the third arbitrator shall be divided equally between the Parties. Except in a proceeding to enforce the results of the arbitration or as otherwise required by law, neither Party nor any arbitrator
may disclose the existence, content or results of any arbitration hereunder without the prior written consent of both Parties. 

  
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 (d) Notwithstanding anything in this Section 10 to the contrary, each Party shall
have the right to seek injunctive or other equitable relief that may be necessary to avoid irreparable harm, maintain the status quo or preserve the subject matter of the arbitration. The Party seeking such equitable relief shall have the right to
decide the appropriate jurisdiction and forum for such action. Each Party further agrees that service of any process, summons, notice or document by personal delivery, by registered mail, or by a recognized international express delivery service
provider to such Party’s respective address set forth above shall be effective service of process for any action, suit or proceeding in the applicable court with respect to matters to which it has submitted to jurisdiction in this
Section 10. Each Party irrevocably and unconditionally waives any objection to the laying of venue of any action, suit or proceeding arising out of this Agreement or transactions contemplated hereby in the applicable court, and hereby
and thereby further irrevocably and unconditionally waives and agrees not to plead or claim in any such court that any such action, suit or proceeding brought in any such court had been brought in an inconvenient forum. 

10.8 Applicable Law. This Agreement shall be governed by and construed in accordance with the laws of the Republic of Korea, without
regard to its conflicts of law provisions. 
 10.9 Further Assurances. Each Party agrees to do and perform all such further acts and
things and shall execute and deliver such other agreements, certificates, instruments and documents necessary or that the other Party may deem advisable in order to carry out the intent and accomplish the purposes of this Agreement and to evidence,
perfect or otherwise confirm its rights hereunder. 
 10.10 Relationship of the Parties. Each Party is an independent contractor
under this Agreement. Nothing contained herein is intended or is to be construed so as to constitute CKD and Zafgen as partners, agents or joint venturers. Neither Party shall have any express or implied right or authority to assume or create any
obligations on behalf of or in the name of the other Party or to bind the other Party to any contract, agreement or undertaking with any Third Party. There are no express or implied third party beneficiaries hereunder (except for Zafgen Indemnitees
other than Zafgen and CKD Indemnitees other than CKD for purposes of Section 8.6). 
 10.11 Entire Agreement. This
Agreement (along with the Exhibits) contains the entire understanding of the Parties with respect to the subject matter hereof and supersedes and replaces any and all previous arrangements and understandings, including the Confidentiality Agreement,
whether oral or written, between the Parties with respect to the subject matter hereof. 
 10.12 Headings. The captions to the
several Sections hereof are not a part of this Agreement, but are merely guides or labels to assist in locating and reading the several Sections hereof. 

10.13 Waiver of Rule of Construction. Each Party has had the opportunity to consult with counsel in connection with the review,
drafting and negotiation of this Agreement. Accordingly, the rule of construction that any ambiguity in this Agreement shall be construed against the drafting party shall not apply. 

  
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 10.14 Interpretation. Whenever any provision of this Agreement uses the term
“including” (or “includes”), such term shall be deemed to mean “including without limitation” (or “includes without limitations”). “Herein,” “hereby,” “hereunder,” “hereof
and other equivalent words refer to this Agreement as an entirety and not solely to the particular portion of this Agreement in which any such word is used. All definitions set forth herein shall be deemed applicable whether the words defined are
used herein in the singular or the plural. Unless otherwise provided, all references to Sections and Exhibits in this Agreement are to Sections and Exhibits of this Agreement. References to any Sections include Sections and subsections that are part
of the related Section (e.g., a Section numbered “Section 2.2” would be part of “Section 2”, and references to “Section 2.2” would also refer to material contained in the subsection
described as “Section 2.2(a)”). 
 10.15 Counterparts: Facsimiles. This Agreement may be executed in two or more
counterparts, each of which shall be deemed an original and all of which together shall constitute one and the same instrument. Facsimile execution and delivery of this Agreement by either Party shall constitute a legal, valid and binding execution
and delivery of this Agreement by such Party. 
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 IN WITNESS WHEREOF, the Parties have caused this Exclusive License Agreement to be executed by
their respective duly authorized officers as of the Effective Date. 
  

			
	CHONG KUN DANG PHARMACEUTICAL CORPORATION
		
	By:	 	 /s/ Jung Woo Kim

		 	Jung Woo Kim
		 	President
		
	Date:	 	 6 July, 2009

	
	ZAFGEN, INC.
		
	By:	 	 /s/ Thomas Hughes

		 	Thomas Hughes
		 	President & Chief Executive Officer
		
	Date:	 	 29 June 2009

  
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 EXHIBIT A 

CKD KNOW-HOW TO BE TRANSFERRED TO ZAFGEN 

None. 

  
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 EXHIBIT B 

CKD PATENT RIGHTS 
  

													
	 No.
	  	 Status
	  	 Title
	  	 Licensor
	  	 Country
	  	 Application No.
(Date)
	  	 Registration

No. (Date)

	1	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	2	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	3	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	4	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	5	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	6	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	7	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	8	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	9	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]

  
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 EXHIBIT C 

Development Schedule of Zafgen* 
  

			
	 Activity
	  	 Time

	 [...***...]
	  	[...***...]
	 [...***...]
	  	[...***...]
	 [...***...]
	  	[...***...]
	 [...***...]
	  	[...***...]

  

	*	Subject to amendment as set forth in the Agreement. 

  
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 Amendment No. 1 to Exclusive License Agreement 

This Amendment No. 1 to Exclusive License Agreement (the “Amendment”), dated September 30, 2009, is by and between
Zafgen, Inc., a Delaware corporation (“Zafgen”), and Chong Kun Dang Pharmaceutical Corporation, a corporation organized under the laws of the Republic of Korea (“CKD”), and amends that certain Exclusive License
Agreement, dated as of July 6, 2009, by and between Zafgen and CKD (the “Agreement”). Defined terms used but not otherwise defined herein, shall have the meanings ascribed to such terms in the Agreement. 

The Parties hereby agree as follows: 
  

	 	1.	The following shall be added as a new Section 2.5 to the Agreement: 

 “2.5
Pharmacovigilance Agreement. The Parties shall enter into a Pharmacovigilance Agreement, in the form attached hereto as Exhibit D, to clarify their responsibilities with respect to notification and reporting of adverse events
related to use of the Licensed Compound and Licensed Products.” 
  

	 	2.	The following shall be amended to the list of CKD Patent Rights contained on Exhibit B of the Agreement: 

  

													
	 No.
	  	 Status
	  	 Title
	  	 Licensor
	  	 Country
	  	 Application No.
(Date)
	  	 Registration

No. (Date)

	1	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	2	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	3	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	4	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	5	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	6	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	7	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	8	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	9	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]

  

	 	3.	The Pharmacovigilance Agreement attached hereto as Exhibit A, shall be added to the Agreement as Exhibit D. 

  

	 	4.	This Amendment shall be governed and construed in accordance with the laws of the Republic of Korea, without regard to its conflicts of law provisions. 

  
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	 	5.	This Amendment may be executed in multiple counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. 

 

	 	6.	Except to the extent amended hereby, the terms and provisions of the Agreement shall remain in full force and effect. 

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 IN WITNESS WHEREOF, the Parties have caused this Amendment No. 1 to Exclusive License
Agreement to be executed by their respective duly authorized officers as of the date first set forth above. 
  

			
	CHONG KUN DANG PHARMACEUTICAL CORPORATION
		
	By:	 	 /s/ Jung Woo Kim

		 	Jung Woo Kim
		 	President
	
	ZAFGEN, INC.
		
	By:	 	 /s/ Matthias Jaffe

		 	Matthias Jaffe
		 	Chief Financial Officer

  
 ***Confidential Treatment
Requested*** 
  

 EXHIBIT A 

Pharmacovigilance Agreement 

  
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 Pharmacovigilance Agreement 

This Pharmacovigilance Agreement (this “Agreement”) is made as of September 30, 2009 (the “Effective
Date”) by and between Chong Kun Dang Pharmaceutical Corporation, a corporation organized under the laws of the Republic of Korea (“CKD”) and Zafgen, Inc., a Delaware corporation (“Zafgen”). Zafgen and CKD
each may be referred to herein as a “Party” and collectively as the “Parties.” 
 WHEREAS, on
July 6, 2009, Zafgen and CKD entered into that certain Exclusive License Agreement, as amended by Amendment No. 1 to the License Agreement, dated as of even date herewith (as the same may be amended from time to time, the “License
Agreement”), pursuant to which CKD granted exclusive rights to the CKD Patent Rights to Zafgen, worldwide, with the exception of the Republic of Korea; and 

WHEREAS, in accordance with Section 2.5 of the License Agreement, the parties have agreed to enter into this Agreement to clarify
their responsibilities with respect to notification and reporting of adverse events. 
 NOW THEREFORE, the Parties hereby
agree as follows: 
  

	1.	Definitions. Unless otherwise defined herein or in the License Agreement, all capitalized terms used in this Agreement shall be consistent with the terms used in the finalized International Conference for
Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (“ICH”) guidelines relating to the collection, maintenance, analysis and reporting of adverse drug experiences, adverse events
(“AE”) and serious adverse events (“SAE”). 

  

	 	1.1	“Awareness Date” means the first date (according to the receiving Party’s time zone) that either Party first receives reportable information on an AE, including an SAE, that is associated with the
use of the Compound. For clarity, the Awareness Date shall be counted as day zero for safety data exchange purposes. 

  

	 	1.2	“Compound” means the Licensed Compound or a Licensed Product, as applicable. 

  

	 	1.3	“Non-Sponsor Party” means the other Party to this Agreement who is not acting as the Sponsor Party with respect to the safety reporting obligations hereunder. 

 

	 	1.4	“Regulatory Authority” shall mean the applicable supra national, federal, national, regional, state, provincial or local regulatory agencies, departments, bureaus, commissions, councils or other
government entities regulating or otherwise exercising authority with respect to the Compound. 

  

	 	1.5	“Sponsor Party” shall mean a Party that is conducting a sponsored clinical trial with the Compound. 

  

	 	1.6	“SUSAR” shall mean Suspected Unexpected Serious Adverse Reaction. 

  
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	2.	Reporting Obligations of the Parties to Each Other. In order to allow the Parties to fulfill their safety reporting obligations to the applicable Regulatory Authorities, the Parties shall exchange information on
SAEs, AEs and other adverse drug experiences, in accordance with the following schedule: 

  

	 	2.1	Reporting of SAEs and Deaths. A Sponsor Party shall report any SAEs or AEs that have resulted in death, have been life-threatening and that have occurred during the course of such Sponsor Party’s clinical
trial to the Non-Sponsor Party within twenty-four (24) hours of the Awareness Date. The report should include: (i) identifiable patients, (ii) suspect medication products, (iii) identifiable reporting source and (iv) events
or outcomes identified as SUSAR if applicable. The Sponsor Party shall assess and process the SAE information and will forward completed SAE reports to the Non-Sponsor Party within seven (7) calendar days after the Awareness Date. SAE reports
shall be in English. CKD shall report to Zafgen in accordance with a Council for International Organizations of Medical Sciences (“CIOMS”) I report format, as set forth in Exhibit A attached hereto. Zafgen shall report
to CKD in accordance with CKD’s format, as set forth in Exhibit B attached hereto. The reports covered by this Section shall be delivered by e-mail or facsimile. 

 

	 	2.2	Reporting of AEs. Sponsor Party shall report any AEs, that do not qualify as SAEs, that have occurred during the course of Sponsor Party’s clinical trial to the Non-Sponsor Party after completion of Sponsor
Party’s clinical trial. The AE reports shall be in English and shall be include at least: (i) adverse event term, (ii) CTC grade (if available), (iii) starting date, (iv)end date, (v) seriousness and (vi) causality
between a medicinal product and event. The reports covered by this Section shall be delivered by a method agreed upon by the Parties. 

  

	 	2.3	Reporting of Other Safety Information. A Party shall report to the other Party (a) any spontaneous reports of AEs related to the use of the Compound that are not from a Sponsor Party’s clinical trial
with the Compound, including reports from literature sources and (b) any other clinical or pre-clinical safety related information, including without limitation, pre-clinical findings that suggest a significant risk for human subjects,
identification of a significant hazard to the patient population receiving the Compound, or signals for potential new adverse drug reactions, every six (6) months during the Term of this Agreement, or at such earlier time period as is
reasonably requested by the other Party. Reports shall be in English. 

  

	 	2.4	Follow-up Investigations. AE information identified from follow-up investigations shall be exchanged in accordance with the timelines and formats set forth in Sections 2.1 through 2.3 above. The Party who
receives the initial report shall be responsible for conducting follow-up investigations with the reporter of the AE. Each party should report the follow-up investigation results to the other party periodically until the clinical responses are
completed (disappearance of the AE or impossibility of follow-up investigation). 

  
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	3.	Reporting Obligations to Regulatory Authorities. 

  

	 	3.1	Zafgen shall fulfill the expedited and periodic safety reporting obligations of the applicable Regulatory Authorities for the Compound in the countries in the Territory where Zafgen holds a marketing authorization or a
clinical trial application for the Compound. 

  

	 	3.2	CKD shall fulfill the expedited and periodic safety reporting obligations of the applicable Regulatory Authorities for the Compound in the countries in the Limited Territory where CKD holds a marketing authorization or
a clinical trial application for the Compound. 

  

	 	3.3	Each Party shall, upon the other Party’s reasonable request, provide information to help the other Party compile periodic reports and respond to the safety inquiries of the applicable Regulatory Authorities, within
the applicable regulatory time frames. Furthermore, each Party will provide the other Party with copies of safety reports submitted to the applicable Regulatory Authorities within five (5) business days after such reports have been submitted.

  

	4.	Additional Reporting Requirements. Any other safety reporting obligations of the Parties, including clinical investigator notifications, shall be prepared by the Parties according to their respective standard
operating procedures and exchange copies for information/distribution according to their respective standard operating procedures, as appropriate. 

  

	5.	Term. This Agreement shall commence on the Effective Date and shall continue to be in effect until the Parties execute a writing that states that neither Party has a legitimate interest in continuing to receive
the information, reports, and notifications provided for herein in order to comply with applicable regulatory requirements related to the use of the Compound. 

  

	6.	Confidentiality. All information exchanged by the Parties in accordance with this Agreement shall be considered Confidential Information and is subject to the obligations and restrictions regarding Confidential
Information set forth in Section 7 of the License Agreement. 

  

	7.	Dispute resolution. Any disputes that arise under this Agreement shall be resolved in accordance with Section 10.7 of the License Agreement. 

 

	8.	License Agreement. Unless otherwise stated herein, in the event of a conflict between this Agreement and the License Agreement, the License Agreement shall control. 

 

	9.	Miscellaneous. 

  

	 	9.1	 Amendment; Waiver. This Agreement may not be modified or amended, in whole or part, except by a written instrument signed by the Parties;
provided that any unilateral undertaking or waiver made by one Party in favor of the other shall be enforceable if undertaken in a writing signed by the Party to be charged with 

  
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the undertaking or waiver. No delay or omission by either Party hereto in exercising any right or power occurring upon any noncompliance or default by the other Party with respect to any of the
terms of this Agreement shall impair any such right or power or be construed to be a waiver thereof. A waiver by either of the Parties of any of the covenants, conditions or agreements to be performed by the other shall not be construed to be a
waiver of any succeeding breach thereof or of any other covenant, condition or agreement herein contained. 

  

	 	9.2	Applicable Law. This Agreement shall be governed by and construed in accordance with the laws of the Republic of Korea, without regard to its conflicts of law provisions. 

 

	 	9.3	Further Assurances. Each Party agrees to do and perform all such further acts and things and shall execute and deliver such other agreements, certificates, instruments and documents necessary or that the other
Party may deem advisable in order to carry out the intent and accomplish the purposes of this Agreement and to evidence, perfect or otherwise confirm its rights hereunder. 

 

	 	9.4	Entire Agreement. This Agreement contains the entire understanding of the Parties with respect to the subject matter hereof and supersedes and replaces any and all previous arrangements and understandings,
whether oral or written, between the Parties with respect to the subject matter hereof. 

  

	 	9.5	Counterparts; Facsimiles. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original and all of which together shall constitute one and the same instrument. Facsimile
execution and delivery of this Agreement by either Party shall constitute a legal, valid and binding execution and delivery of this Agreement by such Party. 

[Remainder of Page Intentionally Left Blank] 

  
 ***Confidential Treatment
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 IN WITNESS WHEREOF, the Parties have caused this Pharmacovigilance Agreement to be executed by
their respective duly authorized officers as of the Effective Date. 
  

			
	CHONG KUN DANG PHARMACEUTICAL CORPORATION
		
	By:	 	 /s/ Jung Woo Kim

		 	Jung Woo Kim
		 	President
	
	ZAFGEN, INC.
		
	By:	 	 /s/ Matthias Jaffe

		 	Matthias Jaffe
		 	Chief Financial Officer

  
 ***Confidential Treatment
Requested*** 
  

 EXHIBIT A 

CIOMS I Form 
 

 
 EXHIBIT A CIOMS I Form CIOMS FORM SUSPECT ADVERSE REACTION REPORT REACTION INFORMATION 1. PATIENT INITIALS (first. Last) 1a. COUNTRY 2.
DATE OF BIRTH Day Month Year 2a. AGE years 3. SEX 4-6 REACTION ONSET Day Month Year 7 + 13 DESCRIBE REACTIONS(S) (including relevant tests/lab data) 8-12 CHECK ALL APPROPRIATE TO ADVERSE REACTION PATIENT DIED INVOLVED OR PROLONGED INPATIENT
HOSPIALISATION INVOLVED PERSISTENCE OR SIGNIFICANT DISABILITY OR INCAPACITY LIFE THREATENING SUSPECT DRUG(S) INFORMATION 14. SUSPECT DRUG(S) (include generic name) 15. DAILY DOSE(S) 16. ROUTE(S) OF ADMINISTRATION 17. INDICATION(S) FOR USE 18.
THERAPY DATES (form/to) 19. THERAPY DURATION 20 DID REACTION ABATE AFTER STOPPING DRUG YES NO NA 21. DID REACTION REAPPEAR AFTER REINTRO-DUCTION YES NO NA III. CONCOMITANT DRUG(S) AND HISTORY 22. CONCOMITANT DRUG(S) AND DATES OF ADMINISTRATION
(exclude those used to treat reaction) 23. OTHER RELEVANT HISTORY (e.g. diagnostics, allergics, pregnancy with last month of period, etc.) IV. MANUFACTURER INFORMATION 24a. NAME AND ADDRESS OF MANUFACTURER 24b. MFR CONTROL NO. 24c. DATE RECEIVED BY
MANUFACTURER 24d. REPORT SOURCE STUDY LITERATURE HEALTH PROFESSIONAL DATE OF THIS REPORT 25a. REPORT TYPE INITIAL FOLLOWUP ***Confidential Treatment Requested*** 

  
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 EXHIBIT B 
  

 
 SAE Report Report type Initial Follow-up( times) Investigational Product Protocol No. Study Title Country, Site Name Principal
Investigator Patient Allocation Number* Initials Sex Date of birth (YY.MM.DD) Age Height Body Weight Medical treatment M W . . cm kg Inpatient Outpatient Others Pregnancy(Period: weeks) Last menstruation date ( / / ) Not applicable
*Allocation Number means Randomization Number SAE Name of SAE Date 1 Relationship to suspected drug 2 Action taken with suspected drug Final outcome 4 Seriousness criteria 5 Start End 1 If necessary, please write down the duration and time from
administration of suspected drug to reaction 2 1. Definitely related 2. Probably related 3. Possibly related 4. Probably not related 5. Definitely not related 6. Unknown 3 1. Drug withdrawn 2. Dose reduced 3. Dose increased 4. Dose not changed 5.
Unknown 6. Not Applicable 4 1. Recovered/Resolved 2. Under recovering/Under resolving 3. Not recovered/Not resolved 4. Recovered with sequelae / Resolved with sequelae 5. Death 6. Unknown 5 1. Death 2. Life-threatening 3. Requiring inpatient
hospitalization or prolongation of existing hospitalization 4. Persistent or significant disability/incapacity 5. Congenital abnormality /birth defect 6. Other medically important condition Death Yes No Date of death . . Reported Cause of death
Autopsy Yes No Unknown Drug information Suspect drug (Brand/INN/Batch No.) Formul-ation/ Unit Daily dose/ Usage Route of administ-ration Administration duration Indication Result of withdrawal / dose reduction 1 Result of re-administration 2 From To
Other concomitant medication 1 1 : AE disappeared /improved 2 : Not disappeared/Not improved 3 : Not stop/Not reduce dose 2 1 : AE recurrence/worsened 2 : Not recurrence/Not worsened 3 : Not re-administration 

  
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 Medical history and disease Yes No Unknown Disease/Surgery /Others Start date Continuation (Yes/No/Unknown) End date Note Medical
history related with SAE Yes No Unknown Name of drug (as reported) Start date of administration End date of administration Indication SAE Follow-up test to find out causes Operated Not operated Date Test (name) Unit Lower limit of normal Upper limit
of normal Result Additional information (Yes/No) SAE detail description Name of SAE Duration Persisted Description in detail : Additional information : Reporter’s opinion : Reporter information Name Position Profession (specialty) Name of
institute Tel Fax Address e-mail 

  
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 Amendment No. 2 to Exclusive License Agreement 

This Amendment No. 1 to Exclusive License Agreement (the “Amendment”), dated October 7, 2010, is by and between
Zafgen, Inc., a Delaware corporation (“Zafgen”), and Chong Kun Dang Pharmaceutical Corporation, a corporation organized under the laws of the Republic of Korea (“CKD”), and amends that certain Exclusive License
Agreement, dated as of July 6, 2009, by and between Zafgen and CKD (the “Agreement”). Defined terms used but not otherwise defined herein, shall have the meanings ascribed to such terms in the Agreement. 

The Parties hereby agree as follows: 
  

	 	1.	The following shall be amended to the list of CKD Patent Rights contained on Exhibit B of the Agreement: 

  

													
	 No.
	  	 Status
	  	 Title
	  	 Licensor
	  	 Country
	  	 Application No.
(Date)
	  	 Registration

No. (Date)

	1	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	2	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	3	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	4	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	5	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	6	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	7	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	8	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	9	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	10	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]
	11	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]	  	[...***...]

  

	 	2.	This Amendment shall be governed and construed in accordance with the laws of the Republic of Korea, without regard to its conflicts of law provisions. 

 

	 	3.	This Amendment may be executed in multiple counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. 

 

	 	4.	Except to the extent amended hereby, the terms and provisions of the Agreement shall remain in full force and effect. 

[Remainder of Page Intentionally Left Blank] 

  
 ***Confidential Treatment
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 IN WITNESS WHEREOF, the Parties have caused this Amendment No. 2 to Exclusive License
Agreement to be executed by their respective duly authorized officers as of the date first set forth above. 
  

			
	CHONG KUN DANG PHARMACEUTICAL CORPORATION
		
	By:	 	 /s/ Jung Woo Kim

		 	Jung Woo Kim
		 	President
	
	ZAFGEN, INC.
		
	By:	 	 /s/ Matthias Jaffe

		 	Matthias Jaffe
		 	Chief Financial Officer

  
 ***Confidential Treatment
Requested*** 
  

 Amendment No. 3 to Exclusive License Agreement 

This Amendment No. 3 to Exclusive License Agreement (the “Amendment”), dated February 28, 2011, is by and between
Zafgen, Inc., a Delaware corporation; (“Zafgen”) and Chong Kun Dang Pharmaceutical Corporation, a corporation organized under the laws of the Republic of Korea (“CKD”), and amends that certain Exclusive License
Agreement, dated as of July 6, 2009, by and between Zafgen and CKD (the “Agreement”). Defined terms used but not otherwise defined herein, shall have the meanings ascribed to such terms in the Agreement. 

The Parties hereby agree as follows: 
  

	 	1.	The following shall be added as a new Section 5.3 of the Agreement and restated to read in its entirety as follows: 

“Each Milestone Payment shall be payable by Zafgen to CKD within [...***...] days after the achievement of the corresponding
Milestone Event with respect to the first Licensed Product; provided, however, that the Milestone Payment associated with the first Milestone Event, ‘[...***...]’ shall be paid upon the sooner to occur of (i) [...***...]
after [...***...] and (ii) [...***...], as opposed to [...***...] days after achievement of such Milestone Event.” 
  

	 	2.	This Amendment shall be governed and construed in accordance with the laws of the Republic of Korea, without regard to its conflicts of law provisions. 

 

	 	3.	This Amendment may be executed in multiple counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. 

 

	 	4.	Except to the extent amended hereby, the terms and provisions of the Agreement shall remain in full force and effect 

[Remainder of Page Intentionally Left Blank] 

  
 ***Confidential Treatment
Requested*** 
  

 IN WITNESS WHEREOF, the Parties have caused this Amendment No. 3 to Exclusive License
Agreement to be executed by their respective duly authorized officers as of the date first set forth above. 
  

			
	CHONG KUN DANG PHARMACEUTICAL CORPORATION
		
	By:	 	 /s/ Jung Woo Kim

		 	Jung Woo Kim
		 	President
	
	ZAFGEN, INC.
		
	By:	 	 /s/ Matthias Jaffe

		 	Matthias Jaffe
		 	Chief Financial Officer

  
 ***Confidential Treatment
Requested***

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