Document:

Form of Nonstatutory Stock Option Agreement under the 1998 Stock Option Plan

 Exhibit 10.21 
  
 ACHILLION PHARMACEUTICALS, INC 
  
 Nonstatutory Stock Option Agreement 
 Granted
Under 1998 Stock Option Plan 
  
 1. Grant
of Option. 
  
 This agreement evidences the grant by
Achillion Pharmaceuticals, Inc., a Delaware corporation (the “Company”), on                     , (the “Grant Date”) to
                    , a consultant to the Company (the “Participant”), of an option to purchase, in whole or in part, on the terms
provided herein and in the Company’s 1998 Stock Option Plan (the “Plan”), a total of X             shares (the “Shares”) of common stock, $.001 par
value per share, of the Company (“Common Stock”) at $            per Share. Unless earlier terminated, this option shall expire on
                    (the “Final Exercise Date”). For purposes of this Agreement, the “Vesting Commencement Date” shall be
                    . 
  
 It is intended that the option evidenced by this agreement shall not be an incentive stock option as defined in Section 422 of the Internal Revenue
Code of 1986, as amended and any regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term “Participant”, as used in this option, shall be deemed to include any person who acquires
the right to exercise this option validly under its terms. 
  
 2. Vesting Schedule. 
  
 (a) Option Exercise Schedule. This option will become exercisable (“vest”) as to 25% of the original number of Shares on the first anniversary of the Grant Date and as to an additional 6.25% of the original number of Shares
at the end of each successive three-month period following the first vesting date until the fourth anniversary of the Grant Date. 
  
 The right of exercise shall be cumulative so that to the extent the option is not exercised in any period to the maximum extent permissible it shall
continue to be exercisable, in whole or in part, with respect to all shares for which it is vested until the earlier of the Final Exercise Date or the termination of this option under Section 3 hereof or the Plan. 
  
 (b) Early Exercise Alternative. Notwithstanding the exercisability
schedule set forth in paragraph 2(a), the Participant may elect to exercise this option as to the unvested Shares (in addition to the vested Shares) if simultaneously with such exercise the Participant enters into a Stock Restriction Agreement with
the Company (the “Stock Restriction Agreement”). The Stock Restriction Agreement provides that the unvested Shares shall be subject to a right of repurchase in favor of the Company in the event that the Participant ceases to be employed by
the Company. 
  
 3. Exercise of Option.

  
 (a) Form of Exercise. Each election to exercise this
option shall be in writing, signed by the Participant, and received by the Company at its principal office, accompanied by this agreement, and payment in full in the manner provided in the Plan. The Participant may purchase less than the number of
shares covered hereby, provided that no partial exercise of this option may be for any fractional share or for fewer than ten whole shares. 

 (b) Continuous Relationship with the Company Required. Except as otherwise provided in this
Section 3, this option may not be exercised unless the Participant, at the time he or she exercises this option, is, and has been at all times since the Grant Date, an employee, officer or director of, or consultant or advisor to, the Company
or any parent or subsidiary of the Company as defined in Section 424(e) or (f) of the Code (an “Eligible Participant”). 
  
 (c) Termination of Relationship with the Company. If the Participant ceases to be an Eligible Participant for any reason, then, except as provided
in paragraphs (d) and (e) below, the right to exercise this option shall terminate three months after such cessation (but in no event after the Final Exercise Date), provided that this option shall be exercisable only to the
extent that the Participant was entitled to exercise this option on the date of such cessation. Notwithstanding the foregoing, if the Participant, prior to the Final Exercise Date, violates the non-competition or confidentiality provisions of any
employment contract, confidentiality and nondisclosure agreement or other agreement between the Participant and the Company, the right to exercise this option shall terminate immediately upon written notice to the Participant from the Company
describing such violation. 
  
 (d) Exercise Period Upon Death
or Disability. If the Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while he or she is an Eligible Participant and the Company has not terminated such relationship
for “cause” as specified in paragraph (e) below, this option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant, provided that this option shall
be exercisable only to the extent that this option was exercisable by the Participant on the date of his or her death or disability, and further provided that this option shall not be exercisable after the Final Exercise Date. 
  
 (e) Discharge for Cause. If the Participant, prior to the Final
Exercise Date, is discharged by the Company for “Cause,” as determined by the Board of Directors, or is otherwise attributable to a breach, as determined by the Board, by the Participant of an employment agreement with the Company (as
defined below), the right to exercise this option shall terminate immediately upon the effective date of such discharge. For purposes of this Agreement “Cause” shall include willful misconduct by the Participant or willful failure by the
Participant to perform his or her responsibilities to the Company (including, without limitation, breach by the Participant of any provision of any employment, consulting, advisory, nondisclosure, non-competition or other similar agreement between
the Participant and the Company), as determined by the Company, which determination shall be conclusive. The Participant shall be considered to have been discharged for “Cause” if the Company determines, within 30 days after the
Participant’s resignation, that discharge for cause was warranted. 
  
 4. Right of First Refusal. 
  
 (a) If the Participant proposes to sell, assign, transfer, pledge, hypothecate or otherwise dispose of, by operation of law or otherwise (collectively, “transfer”) any Shares acquired upon exercise of this option, then the
Participant shall first give written notice of the 
  

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 proposed transfer (the “Transfer Notice”) to the Company. The Transfer Notice shall name the proposed
transferee and state the number of such Shares the Participant proposes to transfer (the “Offered Shares”), the price per share and all other material terms and conditions of the transfer. 
  
 (b) For 30 days following its receipt of such Transfer Notice, the Company
shall have the option to purchase all (or any portion) of the Offered Shares at the price and upon the terms set forth in the Transfer Notice. In the event the Company elects to purchase all (or any portion) of the Offered Shares, it shall give
written notice of such election to the Participant within such 30-day period. Within 10 days after his receipt of such notice, the Participant shall tender to the Company at its principal offices the certificate or certificates representing the
Offered Shares, duly endorsed in blank by the Participant or with duly endorsed stock powers attached thereto, all in a form suitable for transfer of the Offered Shares to the Company. Promptly following receipt of such certificate or certificates,
the Company shall deliver or mail to the Participant a check in payment of the purchase price for the Offered Shares; provided that if the terms of payment set forth in the Transfer Notice were other than cash against delivery, the
Company may pay for the Offered Shares on the same terms and conditions as were set forth in the Transfer Notice; and provided further that any delay in making such payment shall not invalidate the Company’s exercise of its option
to purchase the Offered Shares. 
  
 (c) If the Company does not
elect to acquire all of the Offered Shares, the Participant may, within the 30-day period following the expiration of the option granted to the Company under subsection (b) above, transfer any remaining Offered Shares to the proposed
transferee, provided that such transfer shall not be on terms and conditions more favorable to the transferee than those contained in the Transfer Notice. Notwithstanding any of the above, all Offered Shares transferred pursuant to
this Section 4 shall remain subject to the right of first refusal set forth in this Section 4 and such transferee shall, as a condition to such transfer, deliver to the Company a written instrument confirming that such transferee shall be
bound by all of the terms and conditions of this Section 4. 
  
 (d) After the time at which the Offered Shares are required to be delivered to the Company for transfer to the Company pursuant to subsection (b) above, the Company shall not pay any dividend to the Participant on account of such
Offered Shares or permit the Participant to exercise any of the privileges or rights of a stockholder with respect to such Offered Shares, but shall, in so far as permitted by law, treat the Company as the owner of such Offered Shares. 

 
 (e) The following transactions shall be exempt from the provisions of this
Section 4: 
  
 (1) any transfer of Shares to or for the
benefit of any spouse, child or grandchild of the Participant, or to a trust for their benefit; 
  
 (2) any transfer pursuant to an effective registration statement filed by the Company under the Securities Act of 1933, as amended (the “Securities
Act”); and 
  
 (3) the sale of all or substantially all of
the shares of capital stock of the Company (including pursuant to a merger or consolidation); 
  
 provided, however, that in the case of a transfer pursuant to clause (1) above, such Shares shall remain subject to the right of first refusal set forth in this Section 4 and such transferee
shall, as a condition to such transfer, deliver to the Company a written instrument confirming that such transferee shall be bound by all of the terms and conditions of this Section 4. 
  

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 (f) The Company may assign its rights to purchase Offered Shares in any particular transaction under this
Section 4 to one or more persons or entities. 
  
 (g) The
provisions of this Section 4 shall terminate upon the earlier of the following events: 
  
 (1) the closing of the sale of shares of Common Stock in an underwritten public offering pursuant to an effective registration statement filed by the Company under the Securities Act; or 
  
 (2) the sale of all or substantially all of the capital stock, assets or
business of the Company, by merger, consolidation, sale of assets or otherwise (other than a merger or consolidation in which all or substantially all of the individuals and entities who were beneficial owners of the Common Stock immediately prior
to such transaction beneficially own, directly or indirectly, more than 75% of the outstanding securities entitled to vote generally in the election of directors of the resulting, surviving or acquiring corporation in such transaction). 

 
 (h) The Company shall not be required (a) to transfer on its books
any of the Shares which shall have been sold or transferred in violation of any of the provisions set forth in this Section 4, or (b) to treat as owner of such Shares or to pay dividends to any transferee to whom any such Shares shall have
been so sold or transferred. 
  
 5. Agreement
in Connection with Public Offering. 
  
 The Participant
agrees, in connection with the initial underwritten public offering of the Company’s securities pursuant to a registration statement under the Securities Act, (i) not to sell, make short sale of, loan, grant any options for the purchase
of, or otherwise dispose of any shares of Common Stock held by the Participant (other than those shares included in the offering) without the prior written consent of the Company or the underwriters managing such initial underwritten public offering
of the Company’s securities for a period of 180 days from the effective date of such registration statement, and (ii) to execute any agreement reflecting clause (i) above as may be requested by the Company or the managing underwriters
at the time of such offering. 
  
 6.
Withholding. 
  
 No Shares will be issued pursuant to the
exercise of this option unless and until the Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding taxes required by law to be withheld in respect of this option.

  
 7. Nontransferability of Option.

  
 This option may not be sold, assigned, transferred, pledged
or otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will or the laws of descent and distribution, and, during the lifetime of the Participant, this option shall be exercisable only by the Participant.

  

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 8. Provisions of the Plan. 
  
 This option is subject to the provisions of the Plan, a copy of which is
furnished to the Participant with this option. 
  

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 IN WITNESS WHEREOF, the Company has caused this option to be executed under its corporate seal by its
duly authorized officer. This option shall take effect as a sealed instrument. 
  

			
	 ACHILLION PHARMACEUTICALS, INC.

		
	 By:
	 	 
	 Name:
	 	Michael D. Kishbauch
	 Title:
	 	President and Chief Executive Officer

  

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 PARTICIPANT’S ACCEPTANCE 
  
 The undersigned hereby accepts the foregoing option and agrees to the terms and conditions thereof. The undersigned hereby
acknowledges receipt of a copy of the Company’s 1998 Stock Option Plan. 
  

			
	 PARTICIPANT:

	
	 
		
	 Address:
	 	 
		
	 	 	 

  

 7Form of Common Stock Warrant

 Exhibit 10.25 
  
 THIS WARRANT AND THE SHARES OF COMMON STOCK ISSUED UPON ITS 
 EXERCISE ARE SUBJECT TO THE RESTRICTIONS ON 
 TRANSFER SET FORTH IN SECTION
5 OF THIS WARRANT
  

	Warrant	No. 

  

	Date	of Issuance: October 28, 2004 

  
 ACHILLION PHARMACEUTICALS, INC. 
  
 Common Stock Purchase Warrant 
  
 (Void after October 28, 2009) 
  
 Achillion
Pharmaceuticals, Inc., a Delaware corporation (the “Company”), for value received, hereby certifies that [name] or its registered assigns (the “Registered Holder”), is entitled, subject to the terms and conditions set forth
below, to purchase from the Company, at any time or from time to time on or after the Initial Exercise Date (as defined below) and on or before 5:00 p.m. (Eastern Standard Time) on October 28, 2009 that number of shares of Common Stock, $.001
par value per share, of the Company (the “Common Stock”) as is determined by application of the formula set forth below. 
  

	 	A.	Qualified Financing. In the event of a closing of a Qualified Financing (as defined below) prior to the closing of a Sale of the Company (as defined below), this Warrant
shall be exercisable from and after the date of the closing of such Qualified Financing (the “Qualified Financing Initial Exercise Date”) for a number of shares of Common Stock equal to the quotient obtained by dividing (A) [$ ] (the
“Base Amount”), by (B) the Qualified Financing Conversion Price (as defined below) and at a purchase price per share equal to the Fair Market Value of the Common Stock on the Qualified Financing Initial Exercise Date, as determined
pursuant to the provisions of Section 1(b)(ii) hereof. 

  

	 	B.	Sale of the Company. If no Qualified Financing has occurred prior to a Sale of the Company, this Warrant shall be exercisable from and after the date immediately proceeding
the date of the closing of such Sale of the Company (the “Sale Initial Exercise Date and, with the Qualified Financing Initial Exercise Date, each an “Initial Exercise Date”) for that number of shares of Common Stock equal to the
quotient obtained by dividing (A) [$ ] (the “Base Amount”), by the Series C Conversion Price (as defined in the Certificate of Incorporation of the Company (as amended and/or restated from time to time, the “Charter”)) and
at a purchase price per share equal to the Fair Market Value of the Common Stock on the Sale Initial Exercise Date, as determined pursuant to the provisions of Section 1(b)(ii) hereof. 

  

	 	C.	Definitions 

  

	 	a.	“Warrant Shares” means the shares purchasable upon exercise of this Warrant, as adjusted from time to time pursuant to the provisions of this Warrant

	 	b.	“Purchase Price” means the purchase price per share, as adjusted from time to time pursuant to the provisions of this Warrant. 

  

	 	c.	“Qualified Financing” means the first closing of the issuance and sale of convertible preferred stock of the Company occurring after October 28, 2004 and prior to the
payment in full of the Notes issued pursuant to the Note and Warrant Purchase Agreement dated as of the date hereof between the Company and the Lenders named therein (the “Note Purchase Agreement”) in which: 

  

	 	i.	the immediately available gross proceeds to the Company, excluding (a) proceeds from any indebtedness of the Maker, including without limitation under any Notes issued pursuant
to the Note Purchase Agreement, that converts into equity in such financing and (b) the amount, if any, invested in such financing by Vertex Pharmaceuticals Incorporated, equal or exceed $10,000,000; and 

  

	 	ii.	unless otherwise agreed by the Lenders holding two-thirds of the principal amount then outstanding under the Notes issued pursuant to the Note Purchase Agreement, the investor
purchasing the largest number of shares in such financing is not a stockholder of the Company as of the date hereof. 

  

	 	d.	“Qualified Financing Conversion Price” means the conversion price of the shares of the Company’s convertible preferred stock issued in the Qualified Financing, as set
forth in the Charter and as from time to time adjusted in accordance with the provisions thereof. 

  

	 	e.	“Sale of the Company” shall mean (i) any merger or consolidation to which the Company is a party (except any merger or consolidation in which the holders of capital
stock of the Company immediately prior to such merger or consolidation continue to hold, immediately following such merger or consolidation and in approximately the same relative proportions as they held voting stock of the Company, at least 51% of
the voting power of the capital stock of (A) the surviving or resulting corporation or (B) if the surviving or resulting corporation is a wholly-owned subsidiary of another corporation immediately following such merger or consolidation, of
the parent corporation of such surviving or resulting corporation), or (ii) the sale of all or substantially all of the assets of the Company. 

  

	 	1.	Exercise. 

  
 (a) Exercise for Cash. On or after the Initial Exercise Date, the Registered Holder may, at its option, elect to exercise this Warrant, in whole or
in part and at any time or from time to time, by surrendering this Warrant, with the purchase form appended hereto as Exhibit I duly executed by or on behalf of the Registered Holder, at the principal office of the Company, or at such
other office or agency as the Company may designate, accompanied by payment in full, in lawful money of the United States, of the Purchase Price payable in respect of the number of Warrant Shares purchased upon such exercise. 
  

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 (b) Cashless Exercise. 
  
 (i) The Registered Holder may, at its option, elect to exercise this Warrant, in whole or in part and at any time or from
time to time, on a cashless basis, by surrendering this Warrant, with the purchase form appended hereto as Exhibit I duly executed by or on behalf of the Registered Holder, at the principal office of the Company, or at such other office or
agency as the Company may designate, by canceling a portion of this Warrant in payment of the Purchase Price payable in respect of the number of Warrant Shares purchased upon such exercise. In the event of an exercise pursuant to this subsection
1(b), the number of Warrant Shares issued to the Registered Holder shall be determined according to the following formula: 
  

			
	 X =
	 	Y(A-B)
	 	 	    A

  

					
	 Where:
	  	X =	  	the number of Warrant Shares that shall be issued to the Registered Holder;
			
	 	  	Y =	  	the number of Warrant Shares for which this Warrant is being exercised (which shall include both the number of Warrant Shares issued to the Registered Holder and the number of Warrant Shares
subject to the portion of the Warrant being cancelled in payment of the Purchase Price);
			
	 	  	A =	  	the Fair Market Value (as defined below) of one share of Common Stock; and
			
	 	  	B =	  	the Purchase Price then in effect.

  
 (ii) The Fair Market
Value per share of Common Stock shall be determined as follows: 
  
 (1) If the Common Stock is listed on a national securities exchange, the Nasdaq National Market or another nationally recognized trading system as of the Actual Exercise Date (as defined below), the Fair Market Value per share of Common
Stock shall be deemed to be the average of the high and low reported sale prices per share of Common Stock thereon on the trading day immediately preceding the Actual Exercise Date (provided that if no such price is reported on such day, the
Fair Market Value per share of Common Stock shall be determined pursuant to clause (2)). 
  
 (2) If the Common Stock is not listed on a national securities exchange, the Nasdaq National Market or another nationally recognized trading system as of the Actual Exercise Date, the Fair Market Value per share of
Common Stock shall be deemed to be the amount most recently determined by the Board of Directors of the Company (the “Board”) to represent the fair market value per share of the Common Stock (including without limitation a determination
for purposes of granting Common Stock options or issuing Common Stock under any plan, agreement or arrangement with employees of the Company); and, upon request of the Registered Holder, the Board (or a representative thereof) shall, as promptly as
reasonably practicable, notify the Registered Holder of the Fair Market Value per share of Common Stock 
  

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 and furnish the Registered Holder with reasonable documentation of the Board’s determination of such Fair Market
Value. Notwithstanding the foregoing, if the Board has not made such a determination within the three-month period prior to the Actual Exercise Date, then (A) the Board shall make, and shall provide or cause to be provided to the Registered
Holder notice of, a determination of the Fair Market Value per share of the Common Stock within 15 days of a request by the Registered Holder that it do so, and (B) the exercise of this Warrant pursuant to this subsection 1(b) shall be delayed
until such determination is made and notice thereof is provided to the Registered Holder. 
  
 (c) Actual Exercise Date. Each exercise of this Warrant shall be deemed to have been effected immediately prior to the close of business on the day on which this Warrant shall have been surrendered to the
Company as provided in subsection 1(a) or 1(b) above (the “Actual Exercise Date”). At such time, the person or persons in whose name or names any certificates for Warrant Shares shall be issuable upon such exercise as provided in
subsection 1(d) below shall be deemed to have become the holder or holders of record of the Warrant Shares represented by such certificates. 
  
 (d) Issuance of Certificates. As soon as practicable after the exercise of this Warrant in whole or in part, the Company, at its expense, will
cause to be issued in the name of, and delivered to, the Registered Holder, or as the Registered Holder (upon payment by the Registered Holder of any applicable transfer taxes) may direct: 
  
 (i) a certificate or certificates for the number of full Warrant Shares to
which the Registered Holder shall be entitled upon such exercise plus, in lieu of any fractional share to which the Registered Holder would otherwise be entitled, cash in an amount determined pursuant to Section 3 hereof; and 
  
 (ii) in case such exercise is in part only, a new warrant or warrants (dated
the date hereof) of like tenor, calling in the aggregate on the face or faces thereof for the number of Warrant Shares equal (without giving effect to any adjustment therein) to the number of such shares called for on the face of this Warrant minus
the number of Warrant Shares for which this Warrant was so exercised (which, in the case of an exercise pursuant to subsection 1(b), shall include both the number of Warrant Shares issued to the Registered Holder pursuant to such partial exercise
and the number of Warrant Shares subject to the portion of the Warrant being cancelled in payment of the Purchase Price). 
  
 2. Adjustments. 
  
 (a) Adjustment for Stock Splits and Combinations. If the Company shall at any time or from time to time after the Initial Exercise Date (or, if
this Warrant was issued upon partial exercise of, or in replacement of, another warrant of like tenor, then the date on which such original warrant was first issued) effect a subdivision of the outstanding Common Stock, the Purchase Price then in
effect immediately before that subdivision shall be proportionately decreased. If the Company shall at any time or from time to time after the Initial Exercise Date combine the outstanding shares of Common Stock, the Purchase Price then in effect
immediately before the combination shall be proportionately increased. Any adjustment under this paragraph shall become effective at the close of business on the date the subdivision or combination becomes effective. 
  

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 (b) Adjustment for Certain Dividends and Distributions. In the event the Company at any time, or
from time to time after the Initial Exercise Date shall make or issue, or fix a record date for the determination of holders of Common Stock entitled to receive, a dividend or other distribution payable in additional shares of Common Stock, then and
in each such event the Purchase Price then in effect immediately before such event shall be decreased as of the time of such issuance or, in the event such a record date shall have been fixed, as of the close of business on such record date, by
multiplying the Purchase Price then in effect by a fraction: 
  
 (1) the numerator of which shall be the total number of shares of Common Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such record date, and 
  
 (2) the denominator of which shall be the total number of shares of Common
Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such record date plus the number of shares of Common Stock issuable in payment of such dividend or distribution; 
  
 provided, however, that if such record date shall have been fixed and such
dividend is not fully paid or if such distribution is not fully made on the date fixed therefor, the Purchase Price shall be recomputed accordingly as of the close of business on such record date and thereafter the Purchase Price shall be adjusted
pursuant to this paragraph as of the time of actual payment of such dividends or distributions. 
  
 (c) Adjustment in Number of Warrant Shares. When any adjustment is required to be made in the Purchase Price pursuant to subsections 2(a) or
2(b), the number of Warrant Shares purchasable upon the exercise of this Warrant shall be changed to the number determined by dividing (i) an amount equal to the number of shares issuable upon the exercise of this Warrant immediately prior to
such adjustment, multiplied by the Purchase Price in effect immediately prior to such adjustment, by (ii) the Purchase Price in effect immediately after such adjustment. 
  
 (d) Adjustments for Other Dividends and Distributions. In the event the Company at any time or from time to time
after the Initial Exercise Date shall make or issue, or fix a record date for the determination of holders of Common Stock entitled to receive, a dividend or other distribution payable in securities of the Company (other than shares of Common Stock)
or in cash or other property (other than regular cash dividends paid out of earnings or earned surplus, determined in accordance with generally accepted accounting principles), then and in each such event provision shall be made so that the
Registered Holder shall receive upon exercise hereof, in addition to the number of shares of Common Stock issuable hereunder, the kind and amount of securities of the Company, cash or other property which the Registered Holder would have been
entitled to receive had this Warrant been exercised on the date of such event and had the Registered Holder thereafter, during the period from the date of such event to and including the Actual Exercise Date, retained any such securities receivable
during such period, giving application to all adjustments called for during such period under this Section 2 with respect to the rights of the Registered Holder. 
  
 (e) Adjustment for Reorganization. If there shall occur any reorganization, recapitalization, reclassification,
consolidation or merger involving the Company in which the 
  

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 Common Stock is converted into or exchanged for securities, cash or other property (other than a transaction covered by
subsections 2(a), 2(b) or 2(d)) (collectively, a “Reorganization”), then, following such Reorganization, the Registered Holder shall receive upon exercise hereof the kind and amount of securities, cash or other property which the
Registered Holder would have been entitled to receive pursuant to such Reorganization if such exercise had taken place immediately prior to such Reorganization. In any such case, appropriate adjustment (as determined in good faith by the Board)
shall be made in the application of the provisions set forth herein with respect to the rights and interests thereafter of the Registered Holder, to the end that the provisions set forth in this Section 2 (including provisions with respect to
changes in and other adjustments of the Purchase Price) shall thereafter be applicable, as nearly as reasonably may be, in relation to any securities, cash or other property thereafter deliverable upon the exercise of this Warrant. 
  
 (f) Certificate as to Adjustments. Upon the occurrence of each
adjustment or readjustment of the Purchase Price pursuant to this Section 2 or the Qualified Financing Conversion Price, the Company at its expense shall, as promptly as reasonably practicable, compute such adjustment or readjustment in
accordance with the terms hereof and furnish to the Registered Holder a certificate setting forth such adjustment or readjustment (including the kind and amount of securities, cash or other property for which this Warrant shall be exercisable and
the Purchase Price, as applicable) and showing in detail the facts upon which such adjustment or readjustment is based. The Company shall, as promptly as reasonably practicable after the written request at any time of the Registered Holder, furnish
or cause to be furnished to the Registered Holder a certificate setting forth (i) the Purchase Price or Qualified Conversion Price, as applicable, then in effect and (ii) the number of shares of Common Stock and the amount, if any, of
other securities, cash or property which then would be received upon the exercise of this Warrant. 
  
 3. Fractional Shares. The Company shall not be required upon the exercise of this Warrant to issue any fractional shares, but shall pay the value
thereof to the Registered Holder in cash on the basis of the Fair Market Value per share of Common Stock, as determined pursuant to subsection 1(b)(ii) above. 
  

4. Investment Representations. The initial Registered Holder represents and warrants to the Company as follows: 
  
 (a) Investment. It is acquiring the Warrant, and (if and when it
exercises this Warrant) it will acquire the Warrant Shares, for its own account for investment and not with a view to, or for sale in connection with, any distribution thereof, nor with any present intention of distributing or selling the same; and
the Registered Holder has no present or contemplated agreement, undertaking, arrangement, obligation, indebtedness or commitment providing for the disposition thereof. 
  
 (b) Accredited Investor. The Registered Holder is an “accredited investor” as defined in Rule 501(a) under
the Securities Act of 1933, as amended (the “Act”). 
  
 (c) Experience. The Registered Holder has made such inquiry concerning the Company and its business and personnel as it has deemed appropriate; and the Registered Holder has sufficient knowledge and experience in finance and business
that it is capable of evaluating the risks and merits of its investment in the Company. 
  

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	 	5.	Transfers, etc. 

  
 (a) This Warrant and the Warrant Shares shall not be sold or transferred unless either (i) they first shall have been registered under the Act, or
(ii) the Company first shall have been furnished with an opinion of legal counsel, reasonably satisfactory to the Company, to the effect that such sale or transfer is exempt from the registration requirements of the Act. Notwithstanding the
foregoing, no registration or opinion of counsel shall be required for (i) a transfer by a Registered Holder which is an entity to a wholly owned subsidiary of such entity, a transfer by a Registered Holder which is a partnership to a partner
of such partnership or a retired partner of such partnership or to the estate of any such partner or retired partner, or a transfer by a Registered Holder which is a limited liability company to a member of such limited liability company or a
retired member or to the estate of any such member or retired member, provided that the transferee in each case agrees in writing to be subject to the terms of this Section 5, or (ii) a transfer made in accordance with Rule 144
under the Act. 
  
 (b) Each certificate representing Warrant
Shares shall bear a legend substantially in the following form: 
  

	
	“The securities represented by this certificate have not been registered under the Securities Act of 1933, as amended, and may not be offered, sold or otherwise transferred, pledged or
hypothecated unless and until such securities are registered under such Act or an opinion of counsel satisfactory to the Company is obtained to the effect that such registration is not required.”

  
 The foregoing legend
shall be removed from the certificates representing any Warrant Shares, at the request of the holder thereof, at such time as they become eligible for resale pursuant to Rule 144(k) under the Act. 
  
 (c) The Company will maintain a register containing the name and address of
the Registered Holder of this Warrant. The Registered Holder may change its address as shown on the warrant register by written notice to the Company requesting such change. 
  
 (d) Subject to the provisions of Section 5 hereof, this Warrant and all rights hereunder are transferable, in whole or
in part, upon surrender of this Warrant with a properly executed assignment (in the form of Exhibit II hereto) at the principal office of the Company (or, if another office or agency has been designated by the Company for such purpose,
then at such other office or agency). 
  
 6. No Impairment.
The Company will not, by amendment of its charter or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance
of any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the Registered Holder
against impairment. 
  

 -7- 

	 	7.	Notices of Record Date, etc. In the event: 

  
 (a) the Company shall take a record of the holders of its Common Stock (or other stock or securities at the time deliverable upon the exercise of this
Warrant) for the purpose of entitling or enabling them to receive any dividend or other distribution, or to receive any right to subscribe for or purchase any shares of stock of any class or any other securities, or to receive any other right; or

  
 (b) of any capital reorganization of the Company, any
reclassification of the Common Stock of the Company, any consolidation or merger of the Company with or into another corporation (other than a consolidation or merger in which the Company is the surviving entity and its Common Stock is not converted
into or exchanged for any other securities or property), or any transfer of all or substantially all of the assets of the Company; or 
  
 (c) of the voluntary or involuntary dissolution, liquidation or winding-up of the Company, 
  
 then, and in each such case, the Company will send or cause to be sent to the Registered Holder a notice specifying, as the case may be,
(i) the record date for such dividend, distribution or right, and the amount and character of such dividend, distribution or right, or (ii) the effective date on which such reorganization, reclassification, consolidation, merger, transfer,
dissolution, liquidation or winding-up is to take place, and the time, if any is to be fixed, as of which the holders of record of Common Stock (or such other stock or securities at the time deliverable upon the exercise of this Warrant) shall be
entitled to exchange their shares of Common Stock (or such other stock or securities) for securities or other property deliverable upon such reorganization, reclassification, consolidation, merger, transfer, dissolution, liquidation or winding-up.
Such notice shall be sent at least 5 days prior to the record date or effective date for the event specified in such notice. 
  
 8. Reservation of Stock. The Company will at all times reserve and keep available, solely for issuance and delivery upon the exercise of this
Warrant, such number of Warrant Shares and other securities, cash and/or property, as from time to time shall be issuable upon the exercise of this Warrant. 
  
 9. Exchange or Replacement of Warrants. 
  
 (a) Upon the surrender by the Registered Holder, properly endorsed, to the Company at the principal office of the Company, the Company will, subject to
the provisions of Section 5 hereof, issue and deliver to or upon the order of the Registered Holder, at the Company’s expense, a new Warrant or Warrants of like tenor, in the name of the Registered Holder or as the Registered Holder (upon
payment by the Registered Holder of any applicable transfer taxes) may direct, calling in the aggregate on the face or faces thereof for the number of shares of Common Stock (or other securities, cash and/or property) then issuable upon exercise of
this Warrant. 
  
 (b) Upon receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and (in the case of loss, theft or destruction) upon delivery of an indemnity agreement (with surety if reasonably required) in an amount reasonably
satisfactory to the Company, or (in the case of mutilation) upon surrender and cancellation of this Warrant, the Company will issue, in lieu thereof, a new Warrant of like tenor. 
  

 -8- 

 10. Agreement in Connection with Public Offering. The Registered Holder agrees, in connection with
the initial underwritten public offering of the Company’s securities pursuant to a registration statement under the Act, (i) not to sell, make short sale of, loan, grant any options for the purchase of, or otherwise dispose of any shares
of Common Stock held by the Registered Holder (other than any shares included in the offering) without the prior written consent of the Company or the underwriters managing such initial underwritten public offering of the Company’s securities
for a period of 180 days from the effective date of such registration statement, and (ii) to execute any agreement reflecting clause (i) above as may be requested by the Company or the managing underwriters at the time of such offering;
provided, however, that all other persons selling shares of Common Stock in such offering, all persons holding in excess of 2% of the capital stock of the Company on a fully diluted basis and all executive officers and directors of the Company shall
also have agreed not to sell publicly their Common Stock under the circumstances and pursuant to the terms set forth in this paragraph. 
  
 11. Notices. All notices and other communications from the Company to the Registered Holder in connection herewith shall be mailed by certified or
registered mail, postage prepaid, or sent via a reputable nationwide overnight courier service guaranteeing next business day delivery, to the address last furnished to the Company in writing by the Registered Holder. All notices and other
communications from the Registered Holder to the Company in connection herewith shall be mailed by certified or registered mail, postage prepaid, or sent via a reputable nationwide overnight courier service guaranteeing next business day delivery,
to the Company at its principal office set forth below. If the Company should at any time change the location of its principal office to a place other than as set forth below, it shall give prompt written notice to the Registered Holder and
thereafter all references in this Warrant to the location of its principal office at the particular time shall be as so specified in such notice. All such notices and communications shall be deemed delivered (i) two business days after being
sent by certified or registered mail, return receipt requested, postage prepaid, or (ii) one business day after being sent via a reputable nationwide overnight courier service guaranteeing next business day delivery. 
  
 12. No Rights as Stockholder. Until the exercise of this Warrant, the
Registered Holder shall not have or exercise any rights by virtue hereof as a stockholder of the Company. Notwithstanding the foregoing, in the event (i) the Company effects a split of the Common Stock by means of a stock dividend and the
Purchase Price of and the number of Warrant Shares are adjusted as of the date of the distribution of the dividend (rather than as of the record date for such dividend), and (ii) the Registered Holder exercises this Warrant between the record
date and the distribution date for such stock dividend, the Registered Holder shall be entitled to receive, on the distribution date, the stock dividend with respect to the shares of Common Stock acquired upon such exercise, notwithstanding the fact
that such shares were not outstanding as of the close of business on the record date for such stock dividend. 
  
 13. Amendment or Waiver. This Warrant is one of a series of Warrants issued by the Company, all with the same Original Issue Date and of like
tenor, except as to the number of Warrant Shares subject thereto issued pursuant to the Note Purchase Agreement (collectively, the “Company Warrants”). Any term of this Warrant may be amended or waived (either generally or in a particular
instance and either retroactively or prospectively) with the written consent of 
  

 -9- 

 the Company and the holders of two-thirds of the aggregate Base Amount covered by all Company Warrants then outstanding.
Notwithstanding the foregoing, (a) this Warrant may be amended and the observance of any term hereunder may be waived without the written consent of the Registered Holder only in a manner which applies to all Company Warrants in the same
fashion and (b) the number of Warrant Shares subject to this Warrant and the Purchase Price of this Warrant may not be amended, and the right to exercise this Warrant may not be waived, without the written consent of the Registered Holder (it
being agreed that an amendment to or waiver under any of the provisions of Section 2 of this Warrant shall not be considered an amendment of the number of Warrant Shares or the Purchase Price). The Company shall give prompt written notice to
the Registered Holder of any amendment hereof or waiver hereunder that was effected without the Registered Holder’s written consent. No waivers of any term, condition or provision of this Warrant, in any one or more instances, shall be deemed
to be, or construed as, a further or continuing waiver of any such term, condition or provision. 
  
 14. Section Headings. The section headings in this Warrant are for the convenience of the parties and in no way alter, modify, amend, limit or
restrict the contractual obligations of the parties. 
  
 15.
Governing Law. This Warrant will be governed by and construed in accordance with the internal laws of the State of Connecticut (without reference to the conflicts of law provisions thereof). 
  
 16. Facsimile Signatures. This Warrant may be executed by facsimile
signature. 
  
 [Remainder of page intentionally left blank]

  

 -10- 

 EXECUTED as of the Date of Issuance indicated above. 
  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	  

	Name:	 	Mary Kay Fenton
	Title:	 	Vice President, Finance

  

	
	 ATTEST:

	  

 

  

 -11- 

 EXHIBIT I 
  
 PURCHASE FORM 
  

			
	 To:                            
	  	Dated:                    

  
 The undersigned,
pursuant to the provisions set forth in the attached Warrant (No.             ), hereby elects to purchase (check applicable box): 
  
  ̈                      shares of the Common Stock of Achillion Pharmaceuticals, Inc. covered by such Warrant;
or 
  
  ̈                      the maximum number of shares of Common Stock covered
by such Warrant pursuant to the cashless exercise procedure set forth in subsection 1(b). 
  
 The undersigned herewith makes payment of the full purchase price for such shares at the price per share provided for in such Warrant. Such payment takes the form of (check applicable box or boxes): 

 

	 	 ̈	$                     in lawful money of the United States; and/or

  

	 	 ̈	the cancellation of such portion of the attached Warrant as is exercisable for a total of              Warrant
Shares (using a Fair Market Value of $             per share for purposes of this calculation); and/or 

  

	 	 ̈	the cancellation of such number of Warrant Shares as is necessary, in accordance with the formula set forth in subsection 1(b), to exercise this Warrant with respect to the
maximum number of Warrant Shares purchasable pursuant to the cashless exercise procedure set forth in subsection 1(b). 

  

			
	 Signature:
	 	  

	 Address:
	 	  

	 	 	  

  

 -12- 

  
 EXHIBIT II 
  
 ASSIGNMENT FORM 
  
 FOR VALUE RECEIVED,
                                        
                 hereby sells, assigns and transfers all of the rights of the undersigned under the attached Warrant (No.
            ) with respect to the number of shares of Common Stock of Achillion Pharmaceuticals, Inc. covered thereby set forth below, unto: 
  

					
	 Name of Assignee

	  	 Address

	  	 No. of Shares

  

			
	 Dated:_____________________
	 	Signature:________________________________

  
 Signature Guaranteed: 
  

			
	 By:
	 	  

  
 The signature should be guaranteed by
an eligible guarantor institution (banks, stockbrokers, savings and loan associations and credit unions with membership in an approved signature guarantee medallion program) pursuant to Rule 17Ad-15 under the Securities Exchange Act of 1934.

  

 -13-

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