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:
	
	 
	 
	 



  
 7