Document:

Common Stock Warrants

 Exhibit 10.29 
 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS. THEY MAY NOT BE SOLD OR OFFERED FOR SALE IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES
UNDER SAID ACT AND ANY APPLICABLE STATE SECURITIES LAWS OR THE AVAILABILITY OF AN EXEMPTION FROM REGISTRATION UNDER SAID ACT AND ANY APPLICABLE STATE SECURITIES LAWS. 
 STOCK SUBSCRIPTION WARRANT 
 To Purchase 233,000 Shares of Common Stock of 
 ACHILLION PHARMACEUTICALS, INC (the “Company”) 
 DATE OF INITIAL ISSUANCE: November 7, 2000 
 THIS CERTIFIES THAT for value received,
CONNECTICUT INNOVATIONS, INCORPORATED or its registered assigns (the “Holder”) is entitled to purchase from the Company, at any time during the Term of this Warrant, Two Hundred Thirty Three Thousand (233,000) shares of
common stock, $.001 par value, of the Company (the “Common Stock”), at the Warrant Price, payable in lawful money of the United States of America to be paid upon the exercise hereof. The exercise of this Warrant shall be subject to
the provisions, limitations and, restrictions herein contained, and may be exercised in whole or in part. 
 SECTION 1. Definitions.

 For all purposes of this Warrant, the following terms shall have the meanings indicated: 
 Common Stock - shall mean and include the Company’s authorized Common Stock, $.001 par value, as constituted at the date hereof.

 Current Market Price - shall mean, at any date and with respect to one share of Common Stock, the average of the daily
closing prices for the 30 consecutive business days ending five business days before the day in question (as adjusted for any stock dividend, split, combination or reclassification that took effect during such 30 business day period). The closing
price for each day shall be the last reported sales price or, in case no such reported sales took place on such day, the average of the last reported bid and asked prices, in either case on the principal national securities exchange on which the
Common Stock is listed or admitted to trading or as reported by Nasdaq (or if the Common Stock is not at the time listed or admitted for trading on any such exchange or if prices of the Common Stock are not reported by Nasdaq then such price shall
be equal to the average of the last reported bid and asked prices on such day as reported by The National Quotation Bureau Incorporated or any similar reputable quotation and reporting service, if such quotation is not reported by The National
Quotation Bureau Incorporated); provided, however, that if the Common Stock is not traded in such manner that the quotations referred to herein are available for the period required hereunder, the Current Market Price shall be determined in good
faith by the 

 Board of Directors of the Company or, if such determination cannot be made, by a nationally recognized independent
investment banking firm selected by the Board of Directors of the Company (or if such selection cannot be made, by a nationally recognized independent investment banking firm selected by the American Arbitration Association in accordance with its
rules). 
 Exchange Act - shall mean the Securities Exchange Act of 1934, as amended from time to time. 
 Securities Act - shall mean the Securities Act of 1933, as amended. 
 Term of this Warrant - shall mean the period beginning on the date of initial issuance hereof and ending on October 4, 2010.

 Warrant Price - shall mean $1.50 per share, subject to adjustment in accordance with Section 5 hereof. 

Warrant Shares - shall mean shares of Common Stock purchased or purchasable by the Holder of this Warrant upon the exercise hereof.

 SECTION 2. Exercise of Warrant. 
 2.1. Procedure for Exercise of Warrant. To exercise this Warrant in whole or in part (but not as to any fractional share of Common Stock), the Holder shall deliver to the Company at its office referred to in
Section 14 hereof at any time and from time to time during the Term of this Warrant: (i) the Notice of Exercise in the form attached hereto, (ii) cash, certified or official bank check payable to the order of the Company, wire
transfer of funds to the Company’s account, or evidence of any indebtedness of the Company to the Holder (or any combination of any of the foregoing) in the amount of the Warrant Price for each share being purchased, and (iii) this
Warrant. Notwithstanding any provisions herein to the contrary, if the Current Market Price is greater than the Warrant Price (at the date of calculation, as set forth below), in lieu of exercising this Warrant as hereinabove permitted, the Holder
may elect to receive shares of Common Stock equal to the value (as determined below) of this Warrant (or the portion thereof being canceled) by surrender of this Warrant at the office of the Company referred to in Section 14 hereof, together
with the Notice of Exercise, in which event the Company shall issue to the Holder that number of shares of Common Stock computed using the following formula: 
  

			
	 CS
	 	= WCS x (CMP-WP)
		 	              CMP

  

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 where: 
 CS
equals the number of shares of Common Stock to be issued to the Holder; 
 WCS equals the number of shares of Common Stock purchasable under
the Warrant or, if only a portion of the Warrant is being exercised, the portion of the Warrant being exercised (at the date of such calculation); 
 CMP equals the Current Market Price (at the date of such calculation); and 
 WP equals the Warrant Price (as adjusted to the date
of such calculation). 
 In the event of any exercise of the rights represented by this Warrant, a certificate or certificates for the shares of Common Stock
so purchased, registered in the name of the Holder or such other name or names as may be designated by the Holder, shall be delivered to the Holder hereof within a reasonable time, not exceeding fifteen days, after the rights represented by this
Warrant shall have been so exercised; and, unless this Warrant has expired, a new Warrant representing the number of shares (except a remaining fractional share), if any, with respect to which this Warrant shall not then have been exercised shall
also be issued to the Holder hereof within such time. The person in whose name any certificate for shares of Common Stock is issued upon exercise of this Warrant shall for all purposes be deemed to have become the holder of record of such shares on
the date on which the Warrant was surrendered and payment of the Warrant Price and any applicable taxes was made, irrespective of the date of delivery of such certificate, except that, if the date of such surrender and payment is a date when the
stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock transfer books are open. 
 2.2. Transfer Restriction Legend. Each certificate for Warrant Shares shall bear the following legend (and any additional legend
required by (i) any applicable state securities laws and (ii) any securities exchange upon which such Warrant Shares may, at the time of such exercise, be listed) on the face thereof unless at the time of exercise such Warrant Shares shall
be registered under the Securities Act: 
 THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933. THESE SECURITIES MAY NOT BE SOLD OR TRANSFERRED IN THE ABSENCE OF SUCH REGISTRATION OR AN EXEMPTION THEREFROM UNDER SAID ACT. 
 Any certificate issued at any time in exchange or substitution for any certificate bearing such legend (except a new certificate issued upon completion of a public distribution under a registration statement of the
securities represented thereby) shall also bear such legend unless, in the opinion of counsel for the holder thereof (which counsel shall be reasonably satisfactory to counsel for the Company) the securities represented thereby are not, at such
time, required by law to bear such legend. 
  

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 SECTION 3. Covenants as to Common Stock. The Company covenants and agrees that all shares of Common Stock
that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued, fully paid and nonassessable, and free from all taxes (other than income taxes that may be payable by the Holder), liens and
charges with respect to the issue thereof. Without limiting the generality of the foregoing, the Company covenants that it will from time to time take all such action as may be requisite to assure that the stated or par value per share, if any, of
the Common Stock is at all times equal to or less than the then Warrant Price. The Company further covenants and agrees that it will pay when due and payable any and all federal and state taxes which may be payable in respect of the issue of this
Warrant or any Common Stock or certificates therefor issuable upon the exercise of this Warrant. The Company further covenants and agrees that the Company will at all times have authorized and reserved, free from preemptive rights, a sufficient
number of shares of Common Stock to provide for the exercise of the rights represented by this Warrant. The Company further covenants and agrees that if any shares of capital stock to be reserved for the purpose of the issuance of shares upon the
exercise of this Warrant require registration with or approval of any governmental authority under any federal or state law before such shares may be validly issued or delivered upon exercise, then the Company will in good faith and as expeditiously
as possible endeavor to secure such registration or approval, as the case may be. If and so long as the Common Stock issuable upon the exercise of this Warrant is listed on any national securities exchange, the Company will, if permitted by the
rules of such exchange, list and keep listed on such exchange, upon official notice of issuance, all shares of such Common Stock issuable upon exercise of this Warrant. The Company shall take no action which would cause any changes in the Common
Stock as to which an appropriate adjustment in the number of Warrant Shares and Warrant Price could not be readily made pursuant to the intent of Sections 4 and 5 hereof. 
 SECTION 4. Adjustment of Number of Shares. Upon each adjustment of the Warrant Price as provided in Section 5, the Holder shall thereafter be entitled to purchase, at the Warrant Price resulting
from such adjustment, the number of shares (calculated to the nearest tenth of a share) obtained by multiplying the Warrant Price in effect immediately prior to such adjustment by the number of shares purchasable pursuant hereto immediately prior to
such adjustment and dividing the product thereof by the Warrant Price resulting from such adjustment. 
 SECTION 5. Adjustment of Warrant
Price. The Warrant Price shall be subject to adjustment from time to time as follows: 
 (i) Economic Diluting
Issuances. 
 (i) If the Company shall at any time or from time to time during the Term of this Warrant issue shares of Common Stock
other than Excluded Stock (as hereinafter defined) without consideration or for a consideration per share less than the Warrant Price in effect immediately prior to the issuance of such Common Stock, the Warrant Price in effect immediately prior to
each such issuance or adjustment shall forthwith be adjusted to a price equal to the quotient obtained by dividing: 
  

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 (A) an amount equal to the sum of 
 (x) the total number of shares of Common Stock outstanding (including any shares of Common Stock deemed to have been issued pursuant to subdivision (3) of
this clause (i) and to clause (ii) below) immediately prior to such issuance multiplied by the Warrant Price in effect immediately prior to such issuance, plus 
 (y) the consideration received by the Company upon such issuance, 
 by 
 (B) the total number of shares of Common Stock outstanding (including any shares of Common Stock deemed to have been issued pursuant to subdivision (3)
of this clause (i) and to clause (ii) below) immediately after the issuance of such Common Stock. 
 For the purposes of any adjustment of the Warrant Price
pursuant to this clause (i), the following provisions shall be applicable: 
 1. In the case of the issuance of Common Stock for cash, the
consideration shall be deemed to be the amount of cash paid therefor prior to deducting therefrom any discounts, commissions or other expenses allowed, paid or incurred by the Company for any underwriting or otherwise in connection with the issuance
and sale thereof. 
 2. In the case of the issuance of Common Stock for a consideration in whole or in part other than cash, the consideration
other than cash shall be deemed to be the fair market value thereof as determined by the Board of Directors of the Company, irrespective of any accounting treatment. 
 3. In the case of the issuance of (i) options to purchase or rights to subscribe for Common Stock, (ii) securities by their terms convertible into or exchangeable for Common Stock or (iii) options to purchase or
rights to subscribe for such convertible or exchangeable securities: 
 (A) the aggregate maximum number of shares of Common Stock deliverable
upon exercise of such options to purchase or rights to subscribe for Common Stock shall be deemed to have been issued at the time such options or rights were issued and for a consideration equal to the consideration (determined in the manner
provided in subdivisions (1) and (2) above), if any, received by the Company upon the issuance of such options or rights plus the minimum purchase price provided in such options or rights for the Common Stock covered thereby; 
  

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 (B) the aggregate maximum number of shares of Common Stock deliverable upon conversion of or in exchange
for any such convertible or exchangeable securities or upon the exercise of options to purchase or rights to subscribe for such convertible or exchangeable securities and subsequent conversions or exchanges thereof shall be deemed to have been
issued at the time such securities were issued or such options or rights were issued and for a consideration equal to the consideration received by the Company for any such securities and related options or rights (excluding any cash received on
account of accrued interest or accrued dividends), plus the additional consideration, if any, to be received by the Company upon the conversion or exchange of such securities or the exercise of any related options or rights (the consideration in
each case to be determined in the manner provided in subdivisions (1) and (2) above); 
 (C) on any change in the number of shares
of Common Stock deliverable upon exercise of any such options or rights or conversion of or exchange for such convertible or exchangeable securities, other than a change resulting from the antidilution provisions thereof, the Warrant Price shall
forthwith be readjusted to such Warrant Price as would have obtained had the adjustment made upon the issuance of such options, rights or securities not converted prior to such change or options or rights related to such securities not converted
prior to such change being made upon the basis of such change; and 
 (D) on the expiration of any such options or rights, the termination of
any such rights to convert or exchange or the expiration of any options or rights related to such convertible or exchangeable securities, the Warrant Price shall forthwith be readjusted to such Warrant Price as would have obtained had the adjustment
made upon the issuance of such options, rights, securities or options or rights related to such securities being made upon the basis of the issuance of only the number of shares of Common Stock actually issued upon the conversion or exchange of such
securities or upon the exercise of the options or rights related to such securities. 
 (ii) “Excluded Stock” shall mean
shares of Common Stock described in Section D.5.E. of Article IV of the Amended and Restated Certificate of Incorporation of the Company dated as of January 28, 2000, as such Section D.5.E. may hereafter be amended. 
 (iii) Stock Dividends, Subdivisions, Split-Ups. If, at any time during the Term of this Warrant, the number of shares of Common Stock
outstanding is increased by a stock dividend payable in shares of Common Stock or by a subdivision or split-up of shares of Common Stock, then, following the record date fixed for the determination of holders of Common Stock entitled to receive such
stock dividend, subdivision or split-up, the Warrant Price shall be appropriately decreased so that the number of shares of Common Stock issuable upon the exercise hereof shall be increased in proportion to such increase in outstanding shares.

  

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 (iv) Stock Combinations. If, at any time during the Term of this Warrant, the number
of shares of Common Stock outstanding is decreased by a combination of the outstanding shares of Common Stock, then, following the record date for such combination, the Warrant Price shall appropriately increase so that the number of shares of
Common Stock issuable upon the exercise hereof shall be decreased in proportion to such decrease in outstanding shares. 
 (v) Certain
Dividends. If, at any time during the Term of this Warrant, the Company shall declare a cash dividend upon its Common Stock payable otherwise than out of earnings or earned surplus or shall distribute to holders of its Common Stock
shares of its capital stock (other than Common Stock), stock or other securities of other persons, evidences of indebtedness issued by the Company or other persons, assets (excluding cash dividends and distributions) or options or rights (excluding
options to purchase and rights to subscribe for Common Stock or other securities of the Company convertible into or exchangeable for Common Stock), then, in each such case, immediately following the record date fixed for the determination of the
holders of Common Stock entitled to receive such dividend or distribution, the Warrant Price in effect thereafter shall be determined by multiplying the Warrant Price in effect immediately prior to such record date by a fraction of which the
numerator shall be an amount equal to the difference of (x) the Current Market Price of one share of Common Stock minus (y) the fair market value (as determined by the Board of Directors of the Company, whose determination shall be
conclusive) of the stock, securities, evidences of indebtedness, assets, options or rights so distributed in respect of one share of Common Stock, and of which the denominator shall be such Current Market Price. 
 (vi) All calculations under this Section 5 shall be made to the nearest cent or to the nearest one-tenth (1/10) of a share, as the case may be.

 (vii) Whenever the Warrant Price shall be adjusted as provided in Section 5, the Company shall prepare a statement showing the facts
requiring such adjustment and the Warrant Price that shall be in effect after such adjustment. The Company shall cause a copy of such statement to be sent by mail, first class postage prepaid, to each Holder of this Warrant at its, his or her
address appearing on the Company’s records. Where appropriate, such copy may be given in advance and may be included as part of the notice required to be mailed under the provisions of subsection (ix) of this Section 5. 
 (viii) Adjustments made pursuant to clauses (iii), (iv) and (v) above shall be made on the date such dividend, subdivision, split-up,
combination or distribution, as the case may be, is made, and shall become effective at the opening of business on the business day next following the record date for the determination of stockholders entitled to such dividend, subdivision,
split-up, combination or distribution. 
 (ix) In the event the Company shall propose to take any action of the types described in clauses
(iii), (iv) or (v) of this Section 5, the Company shall forward, at the same time and in the same manner, to the Holder of this Warrant such notice, if any, which the Company shall give to the holders of capital stock of the Company.

  

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 (x) In any case in which the provisions of this Section 5 shall require that an adjustment shall
become effective immediately after a record date for an event, the Company may defer until the occurrence of such event issuing to the Holder of all or any part of this Warrant which is exercised after such record date and before the occurrence of
such event the additional shares of capital stock issuable upon such exercise by reason of the adjustment required by such event over and above the shares of capital stock issuable upon such exercise before giving effect to such adjustment exercise;
provided, however, that the Company shall deliver to such Holder a due bill or other appropriate instrument evidencing such Holder’s right to receive such additional shares upon the occurrence of the event requiring such adjustment. 

(xi) The sale or other disposition of any Common Stock theretofore held in the treasury of the Company shall be deemed to be an issuance thereof.

 SECTION 6. Ownership. 
 6.1. Ownership of This Warrant. The Company may deem and treat the person in whose name this Warrant is registered as the holder and owner hereof (notwithstanding any notations of ownership or
writing hereon made by anyone other than the Company) for all purposes and shall not be affected by any notice to the contrary until presentation of this Warrant for registration of transfer as provided in this Section 6. 
 6.2. Transfer and Replacement. Subject to the restrictions on transferability set forth in the Amended and Restated
Stockholders’ Agreement dated as of February 3, 2000 among the Company, the Holder and certain other parties, this Warrant and all rights hereunder are transferable in whole or in part upon the books of the Company by the Holder hereof in
person or by its duly authorized attorney, and a new Warrant or Warrants, of the same tenor as this Warrant but registered in the name of the transferee or transferees (and in the name of the Holder, if a partial transfer is effected) shall be made
and delivered by the Company upon surrender of this Warrant duly endorsed, at the office of the Company referred to in Section 14 hereof. Upon receipt by the Company of evidence reasonably satisfactory to it of the loss, theft or destruction,
and, in such case, of indemnity or security reasonably satisfactory to it, and upon surrender of this Warrant if mutilated, the Company will make and deliver a new Warrant of like tenor, in lieu of this Warrant; provided that if the Holder hereof is
an instrumentality of a state or local government or an institutional holder or a nominee for such an instrumentality or institutional holder an irrevocable agreement of indemnity by such Holder shall be sufficient for all purposes of this
Section 6, and no evidence of loss or theft or destruction shall be necessary. This Warrant shall be promptly cancelled by the Company upon the surrender hereof in connection with any transfer or replacement. Except as otherwise provided above,
in the case of the loss, theft or destruction of a Warrant, the Company shall pay all expenses, taxes and other charges payable in connection with any transfer or replacement of this Warrant, other than stock transfer taxes (if any) payable in
connection with a transfer of this Warrant, which shall be payable by the Holder. Holder will not transfer this Warrant and the rights hereunder except in compliance with federal and state securities laws. 
 SECTION 7. Mergers, Consolidation, Sales. In the case of any proposed consolidation or merger of the Company with another entity, or the proposed
sale of all or substantially all of its 
  

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 assets to another person or entity, or any proposed reorganization or reclassification of the capital stock of the
Company, then, as a condition of such consolidation, merger, sale, reorganization or reclassification, lawful and adequate provision shall be made whereby the Holder of this Warrant shall thereafter have the right to receive upon the basis and upon
the terms and conditions specified herein, in lieu of the shares of the Common Stock of the Company immediately theretofore purchasable hereunder, such shares of stock, securities or assets as may (by virtue of such consolidation, merger, sale,
reorganization or reclassification) be issued or payable with respect to or in exchange for the number of shares of such Common Stock purchasable hereunder immediately before such consolidation, merger, sale, reorganization or reclassification. In
any such case appropriate provision shall be made with respect to the rights and interests of the Holder of this Warrant to the end that the provisions hereof shall thereafter be applicable as nearly as may be, in relation to any shares of stock,
securities or assets thereafter deliverable upon the exercise of this Warrant. In the case of any proposed consolidation or merger of the Company with another entity, or the proposed sale of all or substantially all of its assets to another person
or entity, or any proposed reorganization or reclassification of the capital stock of the Company in which the holders of the Company’s Common Stock are to receive assets in exchange for shares of Common Stock, then, as a condition of such
consolidation, merger, sale, reorganization or reclassification, lawful and adequate provision shall be made whereby the Holder of this Warrant shall have the opportunity to exercise this Warrant at the time of such consolidation, merger, sale,
reorganization or reclassification and receive upon the basis and upon the terms and conditions specified herein, in lieu of the shares of the Common Stock of the Company immediately theretofore purchasable hereunder, such assets as may (by virtue
of such consolidation, merger, sale, reorganization or reclassification) be issued or payable with respect to or in exchange for the number of shares of such Common Stock purchasable hereunder immediately before such consolidation, merger, sale,
reorganization or reclassification. 
 SECTION 8. Notice of Dissolution or Liquidation. In case of any distribution of the assets of the
Company in dissolution or liquidation (except under circumstances when the foregoing Section 7 shall be applicable), the Company shall give notice thereof to the Holder hereof and shall make no distribution to shareholders until the expiration
of thirty (30) days from the date of mailing of the aforesaid notice and, in any case, the Holder hereof may exercise this Warrant prior to the expiration date hereof within thirty (30) days from the date of the giving of such notice, and
all rights herein granted not so exercised within such thirty-day period shall thereafter become null and void. 
 SECTION 9. Notice of Extraordinary
Dividends. If the Board of Directors of the Company shall declare any dividend or other distribution on its Common Stock except out of earned surplus or by way of a stock dividend payable in shares of its Common Stock, the Company shall mail
notice thereof to the Holder hereof not less than 30 days prior to the record date fixed for determining shareholders entitled to participate in such dividend or other distribution, and the Holder hereof shall not participate in such dividend or
other distribution unless this Warrant is exercised prior to such record date. The provisions of this Section 9 shall not apply to distributions made in connection with transactions covered by Section 7. 
 SECTION 10. Fractional Shares. Fractional shares shall not be issued upon the exercise of this Warrant but in any case where the Holder would, except for
the provisions of this Section 10, be entitled under the terms hereof to receive a fractional share upon the complete exercise of this 
  

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 Warrant, the Company shall, upon the exercise of this Warrant for the largest number of whole shares then called for, pay
a sum in cash equal to the excess of the value of such fractional share (determined in such reasonable manner as may be prescribed in good faith by the Board of Directors of the Company) over the Warrant Price for such fractional share. 

SECTION 11. Special Arrangements of the Company. The Company covenants and agrees that during the Term of this Warrant, unless otherwise approved by the
Holder of this Warrant: 
 11.1. Will Not Amend Certificate. The Company will not amend its Certificate of Incorporation to
eliminate as an authorized class of capital stock that class denominated as “Common Stock” on the date hereof. 
 11.2. Will
Bind Successors. This Warrant shall be binding upon any Company or other person or entity succeeding to the Company by merger, consolidation or acquisition of all or substantially all of the Company’s assets. 
 SECTION 12. Registration Rights. The Company, the Holder and certain other parties have executed and delivered a Registration Rights Agreement dated as of
February 3, 2000 (the “Registration Rights Agreement”), pursuant to which the Company has granted certain registration and other rights to the other parties thereto. The Company hereby agrees that the Warrant Shares shall be
entitled to the same rights as Conversion Shares in the Registration Rights Agreement, as if the Warrant Shares were Conversion Shares, except that (a) the Warrant Shares shall not be included in calculating the number of Conversion Shares for
purposes of voting and exercising demand rights under the Registration Rights Agreement and shall not be entitled to vote or make a demand and (b) the Warrant Shares shall be reduced from an underwritten public offering under the provisions of
Section 5 of the Registration Rights Agreement prior to the reduction of any Conversion Shares. 
 SECTION 13. Put. The Company agrees
that this Warrant and the Warrant Shares are securities covered by and entitled to the rights contained in Section 5.37 of the Series B Convertible Preferred Stock Purchase Agreement dated as of February 3, 2000 among the Company, the
Holder and certain other parties. 
 SECTION 14. Notices. Any notice or other document required or permitted to be given or delivered to the
Holder shall be delivered at, or sent by certified or registered mail to, the Holder at 999 West Street, Rocky Hill, CT 06067 or to such other address as shall have been furnished to the Company in writing by the Holder. Any notice or other document
required or permitted to be given or delivered to the Company shall be delivered at, or sent by certified or registered mail to, the Company at 300 George Street New Haven, CT 06511 or to such other address as shall have been furnished in writing to
the Holder by the Company. Any notice so addressed and mailed by registered or certified mail shall be deemed to be given when so mailed. Any notice so addressed and otherwise delivered shall be deemed to be given when actually received by the
addressee. 
 SECTION 15. No Rights as Stockholder; Limitation of Liability. This Warrant shall not entitle the Holder to any of the rights of
a shareholder of the Company. No provision hereof, in the absence of affirmative action by the Holder to purchase shares of Common Stock, and no mere 
  

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 enumeration herein of the rights or privileges of the Holder, shall give rise to any liability of the Holder for the
Warrant Price hereunder or as a shareholder of the Company, whether such liability is asserted by the Company or by creditors of the Company. 
 SECTION
16. Acknowledgment of Continuing Obligation. The Company will, at the time of any exercise of this Warrant in whole or in part, upon request of the holder hereof, acknowledge in writing its continuing obligation to such holder in respect
of any rights (including without limitation any right to registration of the shares of Common Stock issued upon such exercise) to which such holder shall continue to be entitled after such exercise in accordance with this Warrant; provided,
however, that the failure of such holder to make any such request shall not affect the continuing obligation of the Company to such holder in respect of such rights. 
 SECTION 17. Representations and Warranties. The Company hereby represents and warrants to the holder hereof as follows:

 (a) The Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of Delaware, has the
corporate power and authority to conduct its business as presently conducted, has the corporate power and authority to execute, issue and deliver this Warrant and to perform its obligations under this Warrant, has the corporate power and authority
and legal right to own and lease its properties and is duly qualified and in good standing as a foreign corporation in each jurisdiction in which it owns or leases real property or in which the conduct of its business requires such qualification,
except where failure to be so qualified could not be reasonably expected to have a material adverse effect on the Company and its subsidiaries taken as a whole. 
 (b) The execution, delivery, issuance and performance by the Company of this Warrant and the issuance of the Warrant Shares upon exercise of this Warrant have been duly authorized by all necessary corporate action and
do not and will not violate, or result in a breach of, or constitute a default under, or require any consent under, or result in the creation of any lien, charge or encumbrance upon the assets of the Company pursuant to, any law, statute, ordinance,
rule, regulation, order or decree of any court, governmental body or regulatory authority or administrative agency having jurisdiction over the Company or its subsidiaries or any contract, mortgage, loan agreement, note, lease or other instrument
binding upon the Company or its subsidiaries or by which their properties are bound. 
 (c) This Warrant has been duly executed, issued and
delivered by the Company and constitutes a legal, valid, binding and enforceable obligation of the Company. The Warrant Shares, when issued upon exercise of this Warrant in accordance with the terms hereof, will be duly authorized, validly issued,
fully paid and nonassessable shares of Common Stock, with no personal liability attaching to the ownership thereof. 
 (d) The Company has
authorized capital stock consisting of (x) 27,000,000 shares of Common Stock, $.001 par value, of which 1,769,427 shares are issued and outstanding, and (y) 31,883,332 shares of Preferred Stock, $.01 par value, of which (i) 250,000
shares are designated as Series A Convertible Preferred Stock, of which all shares are issued and outstanding, (ii) 15,816,666 shares are designated as Series B Convertible Preferred Stock, of which all shares are issued and outstanding and
(iii) 15,816,666 shares are designated as Series B-1 Convertible Preferred Stock, of which zero (0) shares are issued and outstanding. 
  

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 SECTION 18. Law Governing. This Warrant shall be governed by, and construed and enforced in accordance
with, the laws of the State of Connecticut, without giving effect to its conflict of laws principles. 
 SECTION 19. Miscellaneous. This
Warrant and any provision hereof may be changed, waived, discharged or terminated only by an instrument in writing signed by the party (or any predecessor in interest thereof) against which enforcement of the same is sought. The headings in this
Warrant are for purposes of reference only and shall not affect the meaning or construction of any of the provisions hereof. 
 Signature page
to follow 
  

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 IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by its duly authorized
officer as of the date first written above. 
  
  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	 /s/ William G. Rice

		 	William G. Rice, Ph. D.
		 	Its President
		 	Duly Authorized

  

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 FORM OF NOTICE OF EXERCISE 
 [To be signed only upon exercise of the Warrant] 
 TO BE EXECUTED BY THE
REGISTERED HOLDER 
 TO EXERCISE THE WITHIN WARRANT 
 The undersigned hereby exercises the right to purchase                      shares of Common Stock which the
undersigned is entitled to purchase by the terms of the within Warrant according to the conditions thereof, and herewith makes payment of the Warrant Price of such shares in full. All shares to be issued pursuant hereto shall be issued in the name
of, and the initial address of such person to be entered on the books of the Company shall be: 
  

					
		 	  
 _________________________________
	 	
		 	  
 _________________________________
	 	
		 	  
 _________________________________
	 	

 The shares are to be issued in certificates of the following denominations: 
  

			
	  

	
	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     

 FORM OF ASSIGNMENT 
 (ENTIRE) 
 [To be signed only upon transfer of entire Warrant] 
 TO BE EXECUTED BY THE REGISTERED HOLDER 
 TO TRANSFER THE WITHIN WARRANT 
 FOR VALUE
RECEIVED                     hereby sells, assigns and transfers unto
                     all rights of the undersigned under and pursuant to the within Warrant, and the undersigned does hereby irrevocably
constitute and appoint                      Attorney to transfer the said Warrant on the books of the Company, with full power of
substitution. 
  

			
	  
 
	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     
 NOTICE 

The signature to the foregoing Assignment must correspond to the name as written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever. 

 FORM OF ASSIGNMENT 
 (PARTIAL) 
 [To be signed only upon partial transfer of Warrant] 
 TO BE EXECUTED BY THE REGISTERED HOLDER 
 TO TRANSFER THE WITHIN WARRANT 
 FOR VALUE RECEIVED
                     hereby sells, assigns and transfers unto
                     (i) the rights of the undersigned to purchase          shares of
Common Stock under and pursuant to the within Warrant, and (ii) on a non-exclusive basis, all other rights of the undersigned under and pursuant to the within Warrant, it being understood that the undersigned shall retain, severally (and not
jointly) with the transferee(s) named herein, all rights assigned on such non-exclusive basis. The undersigned does hereby irrevocably constitute and appoint
                     Attorney to transfer the said Warrant on the books of the Company, with full power of substitution. 
  

			
	  

	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     
 NOTICE 

The signature to the foregoing Assignment must correspond to the name as written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever. 

 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS.
THEY MAY NOT BE SOLD OR OFFERED FOR SALE IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES UNDER SAID ACT AND ANY APPLICABLE STATE SECURITIES LAWS OR THE AVAILABILITY OF AN EXEMPTION FROM REGISTRATION UNDER SAID ACT AND ANY
APPLICABLE STATE SECURITIES LAWS. 
 STOCK SUBSCRIPTION WARRANT 
 To Initially Purchase 108,667 Shares of Common Stock of 
 ACHILLION
PHARMACEUTICALS, INC. (the “Company”) 
 DATE OF INITIAL ISSUANCE: March 30, 2001 
 THIS CERTIFIES THAT for value received, CONNECTICUT INNOVATIONS, INCORPORATED or its registered assigns (the “Holder”) is entitled
to purchase from the Company, at any time during the Term of this Warrant, initially One Hundred Eight Thousand Six Hundred Sixty Seven (108,667) shares (the “Initial Warrant Shares”) of common stock, $.001 par
value, of the Company (the “Common Stock”), and, upon the occurrence of certain events, additional Contingent Warrant Shares (as defined below) at the applicable Warrant Price, payable in lawful money of the United
States of America to be paid upon the exercise hereof. The exercise of this Warrant shall be subject to the provisions, limitations and restrictions herein contained, and may be exercised in whole or in part. 
 SECTION 1. Definitions. 
 For all
purposes of this Warrant, the following terms shall have the meanings indicated: 
 Contingent Warrant Shares – shall mean
shares of Common Stock purchasable hereunder at each time the Company borrows money directly from the Holder pursuant to section 2.2.1 of the Loan Agreement, dated March 30, 2001, between the Company and the Holder (a
“Borrowing”). For each Borrowing, the number of such Contingent Warrant Shares subject to this Warrant shall be equal to the amount of such Borrowing divided by 10 divided by the Warrant Price applicable to such Contingent Warrant
Shares. While the exercisability of Contingent Warrant Shares shall be automatic upon a Borrowing, the Company will execute when requested upon or after each Borrowing an acknowledgement to the Holder regarding such exercisability, the number of
Contingent Warrant Shares and the Warrant Price applicable thereto. 
 Common Stock - shall mean and include the Company’s
authorized Common Stock, $.001 par value, as constituted at the date hereof. 
 Current Market Price - shall mean, at any date
and with respect to one share of Common Stock, the average of the daily closing prices for the 30 consecutive business days ending five business days before the day in question (as adjusted for any stock dividend, split, combination or 

 reclassification that took effect during such 30 business day period). The closing price for each day shall be the last
reported sales price or, in case no such reported sales took place on such day, the average of the last reported bid and asked prices, in either case on the principal national securities exchange on which the Common Stock is listed or admitted to
trading or as reported by Nasdaq (or if the Common Stock is not at the time listed or admitted for trading on any such exchange or if prices of the Common Stock are not reported by Nasdaq then such price shall be equal to the average of the last
reported bid and asked prices on such day as reported by The National Quotation Bureau Incorporated or any similar reputable quotation and reporting service, if such quotation is not reported by The National Quotation Bureau Incorporated); provided,
however, that if the Common Stock is not traded in such manner that the quotations referred to herein are available for the period required hereunder, the Current Market Price shall be determined in good faith by the Board of Directors of the
Company or, if such determination cannot be made, by a nationally recognized independent investment banking firm selected by the Board of Directors of the Company (or if such selection cannot be made, by a nationally recognized independent
investment banking firm selected by the American Arbitration Association in accordance with its rules). 
 Exchange Act - shall
mean the Securities Exchange Act of 1934, as amended from time to time. 
 Securities Act - shall mean the Securities Act of
1933, as amended. 
 Term of this Warrant - shall mean the period beginning on the date of initial issuance hereof and ending
on March 30, 2011. 
 Warrant Price – shall mean:  
 (a) for the Initial Warrant Shares $1.50 per share, subject to adjustment in accordance with Section 5 hereof, and 
 (b) for each Contingent Warrant Share shall mean the greater of: 
 (i) $1.50 per share (the “Fixed Contingent Warrant Price”); or  
 (ii) at the time that such
Contingent Warrant Share becomes exercisable hereunder the greater of: 
 (x) the price, if applicable, at which shares of capital stock of
the Company were most recently issued by the Company in a private financing in which the Company received gross proceeds of at least $10,000,000; or 
 (y) the then lowest conversion price, if applicable, of Company convertible preferred stock then issued and outstanding, 
 and such Warrant Price as determined in this subsection (b) shall be subject to adjustment pursuant to Section 5 hereof. 
  

 -2- 

 Warrant Shares shall mean, collectively, the Initial Warrant Shares and the Contingent
Warrant Shares. 
  

 -3- 

 SECTION 2. Exercise of Warrant. 
 2.1. Procedure for Exercise of Warrant. To the extent exercisable, the Holder may exercise this Warrant in whole or in part (but not
as to any fractional share of Common Stock), by delivering to the Company at its office referred to in Section 14 hereof at any time and from time to time during the Term of this Warrant: (i) the Notice of Exercise in the form attached
hereto, (ii) cash, certified or official bank check payable to the order of the Company, wire transfer of funds to the Company’s account, or evidence of any indebtedness of the Company to the Holder (or any combination of any of the
foregoing) in the amount of the Warrant Price for each share being purchased, and (iii) this Warrant. Upon each such exercise, the Holder shall indicate whether it is exercising Initial Warrant Shares, Contingent Warrant Shares or a combination
thereof. In addition, the Holder shall have the right at any time after Contingent Warrant Shares become exercisable to cause the Company to replace this Warrant with separate warrants, one covering Initial Warrant Shares and the other(s) covering
each group of Contingent Warrant Shares having the same Warrant Price. 
 Notwithstanding any provisions herein to the contrary, if the Current Market Price
is greater than the applicable Warrant Price (at the date of calculation, as set forth below), in lieu of exercising this Warrant as hereinabove permitted, the Holder may elect to receive shares of Common Stock for each Warrant Share (such computed
shares then combined into an aggregate number of shares) equal to the value (as determined below) of each Warrant Share by surrender of this Warrant at the office of the Company referred to in Section 14 hereof, together with the Notice of
Exercise, in which event the Company shall issue to the Holder that number of shares of Common Stock computed using the following formula: 
 CS = (CMP-WP) 
   CMP 
 where: 
 CS
equals the number of shares of Common Stock to be issued to the Holder for each Warrant Share; 
 CMP equals the Current
Market Price (at the date of such calculation); and 
 WP equals the applicable Warrant Price (as adjusted to the date of such
calculation). 
 In the event of any exercise of the rights represented by this Warrant, a certificate or certificates for the shares of Common Stock so
purchased, registered in the name of the Holder or such other name or names as may be designated by the Holder, shall be delivered to the Holder hereof within a reasonable time, not exceeding fifteen days, after the rights represented by this
Warrant shall have been so exercised; and, unless this Warrant has expired, a new Warrant representing the number of shares (except a remaining fractional share), if any, with respect to which this Warrant shall not then have been exercised shall
also be issued to the Holder hereof within such time. The person in whose name any certificate for shares of Common Stock is issued upon exercise of this Warrant shall for all purposes be deemed to have become the holder of record of such shares on
the date on 
  

 -4- 

 which the Warrant was surrendered and payment of the applicable Warrant Price and any applicable taxes was made,
irrespective of the date of delivery of such certificate, except that, if the date of such surrender and payment is a date when the stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares
at the close of business on the next succeeding date on which the stock transfer books are open. 
 2.2. Transfer Restriction
Legend. Each certificate for Warrant Shares shall bear the following legend (and any additional legend required by (i) any applicable state securities laws and (ii) any securities exchange upon which such Warrant Shares may, at the
time of such exercise, be listed) on the face thereof unless at the time of exercise such Warrant Shares shall be registered under the Securities Act: 
 THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933. THESE SECURITIES MAY NOT BE SOLD OR TRANSFERRED IN THE ABSENCE OF SUCH
REGISTRATION OR AN EXEMPTION THEREFROM UNDER SAID ACT. 
 Any certificate issued at any time in exchange or substitution for any certificate bearing such
legend (except a new certificate issued upon completion of a public distribution under a registration statement of the securities represented thereby) shall also bear such legend unless, in the opinion of counsel for the holder thereof (which
counsel shall be reasonably satisfactory to counsel for the Company) the securities represented thereby are not, at such time, required by law to bear such legend. 
 SECTION 3. Covenants as to Common Stock. The Company covenants and agrees that all shares of Common Stock that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly
issued, fully paid and nonassessable, and free from all taxes (other than income taxes that may be payable by the Holder), liens and charges with respect to the issue thereof. Without limiting the generality of the foregoing, the Company covenants
that it will from time to time take all such action as may be requisite to assure that the stated or par value per share, if any, of the Common Stock is at all times equal to or less than the then Warrant Price. The Company further covenants and
agrees that it will pay when due and payable any and all federal and state taxes which may be payable in respect of the issue of this Warrant or any Common Stock or certificates therefor issuable upon the exercise of this Warrant. The Company
further covenants and agrees that the Company will at all times have authorized and reserved, free from preemptive rights, a sufficient number of shares of Common Stock to provide for the exercise of the rights represented by this Warrant. The
Company further covenants and agrees that if any shares of capital stock to be reserved for the purpose of the issuance of shares upon the exercise of this Warrant require registration with or approval of any governmental authority under any federal
or state law before such shares may be validly issued or delivered upon exercise, then the Company will in good faith and as expeditiously as possible endeavor to secure such registration or approval, as the case may be. If and so long as the Common
Stock issuable upon the exercise of this Warrant is listed on any national securities exchange, the Company will, if permitted by the rules of such exchange, list and keep listed on such exchange, upon official notice of issuance, all shares of such
Common Stock issuable upon exercise of this Warrant. The Company shall take no action which would cause any 
  

 -5- 

 changes in the Common Stock as to which an appropriate adjustment in the number of Warrant Shares and Warrant Price could
not be readily made pursuant to the intent of Sections 4 and 5 hereof. 
 SECTION 4. Adjustment of Number of Shares. Upon each adjustment of
each applicable Warrant Price as provided in Section 5, the Holder shall thereafter be entitled to purchase, at the Warrant Price resulting from such adjustment, the number of shares (calculated to the nearest tenth of a share) obtained by
multiplying the applicable Warrant Price in effect immediately prior to such adjustment by the number of shares purchasable pursuant hereto immediately prior to such adjustment and dividing the product thereof by the Warrant Price resulting from
such adjustment. 
 SECTION 5. Adjustment of Warrant Price. Each Warrant Price shall be subject to adjustment
from time to time as follows: 
 (i) Economic Diluting Issuances. 
 (i) If the Company shall at any time or from time to time during the Term of this Warrant issue shares of Common Stock other than Excluded Stock (as
hereinafter defined) without consideration or for a consideration per share less than the Warrant Price in effect immediately prior to the issuance of such Common Stock (a “Diluting Issuance”), the Warrant Price in effect
immediately prior to each such issuance or adjustment shall forthwith be adjusted to a price equal to the quotient obtained by dividing: 
 (A) an amount equal to the sum of 
 (x) the total number of shares of Common Stock outstanding (including any shares of Common Stock
deemed to have been issued pursuant to subdivision (3) of this clause (i) and to clause (ii) below) immediately prior to such issuance multiplied by the Warrant Price in effect immediately prior to such issuance, plus 
 (y) the consideration received by the Company upon such issuance, 
 by 
 (B) the total number of shares of Common Stock outstanding (including any shares of Common Stock deemed
to have been issued pursuant to subdivision (3) of this clause (i) and to clause (ii) below) immediately after the issuance of such Common Stock. 
 For the purposes of any adjustment of the Warrant Price pursuant to this clause (i), the following provisions shall be applicable: 
 1. In the case of the issuance of Common Stock for cash, the consideration shall be deemed to be the amount of cash paid therefor prior to deducting therefrom any discounts, commissions or other expenses allowed, paid or incurred by the
Company for any underwriting or otherwise in connection with the issuance and sale thereof. 
  

 -6- 

 2. In the case of the issuance of Common Stock for a consideration in whole or in part other than cash,
the consideration other than cash shall be deemed to be the fair market value thereof as determined by the Board of Directors of the Company, irrespective of any accounting treatment. 
 3. In the case of the issuance of (i) options to purchase or rights to subscribe for Common Stock, (ii) securities by their terms convertible
into or exchangeable for Common Stock or (iii) options to purchase or rights to subscribe for such convertible or exchangeable securities: 
 (A) the aggregate maximum number of shares of Common Stock deliverable upon exercise of such options to purchase or rights to subscribe for Common Stock shall be deemed to have been issued at the time such options or rights were issued and
for a consideration equal to the consideration (determined in the manner provided in subdivisions (1) and (2) above), if any, received by the Company upon the issuance of such options or rights plus the minimum purchase price provided in
such options or rights for the Common Stock covered thereby; 
 (B) the aggregate maximum number of shares of Common Stock deliverable upon
conversion of or in exchange for any such convertible or exchangeable securities or upon the exercise of options to purchase or rights to subscribe for such convertible or exchangeable securities and subsequent conversions or exchanges thereof shall
be deemed to have been issued at the time such securities were issued or such options or rights were issued and for a consideration equal to the consideration received by the Company for any such securities and related options or rights (excluding
any cash received on account of accrued interest or accrued dividends), plus the additional consideration, if any, to be received by the Company upon the conversion or exchange of such securities or the exercise of any related options or rights (the
consideration in each case to be determined in the manner provided in subdivisions (1) and (2) above); 
 (C) on any change in the
number of shares of Common Stock deliverable upon exercise of any such options or rights or conversion of or exchange for such convertible or exchangeable securities, other than a change resulting from the antidilution provisions thereof, the
Warrant Price shall forthwith be readjusted to such Warrant Price as would have obtained had the adjustment made upon the issuance of such options, rights or securities not converted prior to such change or options or rights related to such
securities not converted prior to such change being made upon the basis of such change; and 
 (D) on the expiration of any such options or
rights, the termination of any such rights to convert or exchange or the expiration of any options or rights related to such convertible or exchangeable securities, the Warrant Price shall 
  

 -7- 

 forthwith be readjusted to such Warrant Price as would have obtained had the adjustment made upon the
issuance of such options, rights, securities or options or rights related to such securities being made upon the basis of the issuance of only the number of shares of Common Stock actually issued upon the conversion or exchange of such securities or
upon the exercise of the options or rights related to such securities. 
 (ii) “Excluded Stock” shall mean shares of Common
Stock described in Section D.5.E. of Article IV of the Amended and Restated Certificate of Incorporation of the Company dated as of January 28, 2000, as amended October 16, 2000, as such Section D.5.E. may hereafter be amended. 

(iii) Stock Dividends, Subdivisions, Split-Ups. If, at any time during the Term of this Warrant, the number of shares of Common Stock
outstanding is increased by a stock dividend payable in shares of Common Stock or by a subdivision or split-up of shares of Common Stock (collectively a “Split”), then, following the record date fixed for the determination of
holders of Common Stock entitled to receive such Split, the Warrant Price shall be appropriately decreased so that the number of shares of Common Stock issuable upon the exercise hereof shall be increased in proportion to such increase in
outstanding shares. 
 (iv) Stock Combinations. If, at any time during the Term of this Warrant, the number of shares of Common
Stock outstanding is decreased by a combination of the outstanding shares of Common Stock (a “Combination”), then, following the record date for such Combination, the Warrant Price shall appropriately increase so that the number of
shares of Common Stock issuable upon the exercise hereof shall be decreased in proportion to such decrease in outstanding shares. 
 (v)
Certain Dividends. If, at any time during the Term of this Warrant, the Company shall declare a cash dividend upon its Common Stock payable otherwise than out of earnings or earned surplus or shall distribute to holders of its Common
Stock shares of its capital stock (other than Common Stock), stock or other securities of other persons, evidences of indebtedness issued by the Company or other persons, assets (excluding cash dividends and distributions) or options or rights
(excluding options to purchase and rights to subscribe for Common Stock or other securities of the Company convertible into or exchangeable for Common Stock) (collectively, “Dividend Issuance”), then, in each such case, immediately
following the record date fixed for the determination of the holders of Common Stock entitled to receive such Dividend Issuance, the Warrant Price in effect thereafter shall be determined by multiplying the Warrant Price in effect immediately prior
to such record date by a fraction of which the numerator shall be an amount equal to the difference of (x) the Current Market Price of one share of Common Stock minus (y) the fair market value (as determined by the Board of Directors of
the Company, whose determination shall be conclusive) of the stock, securities, evidences of indebtedness, assets, options or rights so distributed in respect of one share of Common Stock, and of which the denominator shall be such Current Market
Price. 
 (vi) All calculations under this Section 5 shall be made to the nearest cent or to the nearest one-tenth (1/10) of a
share, as the case may be. 
  

 -8- 

 (vii) Whenever either Warrant Price shall be adjusted as provided in Section 5, the Company shall
prepare a statement showing the facts requiring such adjustment and the Warrant Price that shall be in effect after such adjustment. The Company shall cause a copy of such statement to be sent by mail, first class postage prepaid, to each Holder of
this Warrant at its, his or her address appearing on the Company’s records. Where appropriate, such copy may be given in advance and may be included as part of the notice required to be mailed under the provisions of subsection (ix) of
this Section 5. 
 (viii) Adjustments made pursuant to clauses (iii), (iv) and (v) above shall be made on the date such
dividend, subdivision, split-up, combination or distribution, as the case may be, is made, and shall become effective at the opening of business on the business day next following the record date for the determination of stockholders entitled to
such dividend, subdivision, split-up, combination or distribution. 
 (ix) In the event the Company shall propose to take any action of the
types described in clauses (iii), (iv) or (v) of this Section 5, the Company shall forward, at the same time and in the same manner, to the Holder of this Warrant such notice, if any, which the Company shall give to the holders of
capital stock of the Company. 
 (x) In any case in which the provisions of this Section 5 shall require that an adjustment shall become
effective immediately after a record date for an event, the Company may defer until the occurrence of such event issuing to the Holder of all or any part of this Warrant which is exercised after such record date and before the occurrence of such
event the additional shares of capital stock issuable upon such exercise by reason of the adjustment required by such event over and above the shares of capital stock issuable upon such exercise before giving effect to such adjustment exercise;
provided, however, that the Company shall deliver to such Holder a due bill or other appropriate instrument evidencing such Holder’s right to receive such additional shares upon the occurrence of the event requiring such adjustment. 

(xi) The sale or other disposition of any Common Stock theretofore held in the treasury of the Company shall be deemed to be an issuance thereof.

 (xii) The adjustments provided for in this Section 5 by reason of a Diluting Issuance, a Dividend Issuance, a Combination or a Split
occurring prior to the time that Contingent Warrant Shares become exercisable shall be applicable only if the Warrant Price for such Contingent Warrant Shares is the Fixed Contingent Warrant Price (and whether the Warrant Price shall be the Fixed
Contingent Warrant Price shall be determined after the Fixed Contingent Warrant Price has been adjusted as provided in Section 5). 
 SECTION 6.
Ownership. 
 6.1. Ownership of This Warrant. The Company may deem and treat the person in whose name
this Warrant is registered as the holder and owner hereof (notwithstanding any notations of ownership or writing hereon made by anyone other than the Company) for all purposes 
  

 -9- 

 and shall not be affected by any notice to the contrary until presentation of this Warrant for registration of transfer
as provided in this Section 6. 
 6.2. Transfer and Replacement. Subject to the restrictions on transferability set
forth in the Amended and Restated Stockholders’ Agreement dated as of February 3, 2000 among the Company, the Holder and certain other parties, this Warrant and all rights hereunder are transferable in whole or in part upon the books of
the Company by the Holder hereof in person or by its duly authorized attorney, and a new Warrant or Warrants, of the same tenor as this Warrant but registered in the name of the transferee or transferees (and in the name of the Holder, if a partial
transfer is effected) shall be made and delivered by the Company upon surrender of this Warrant duty endorsed, at the office of the Company referred to in Section 14 hereof. Upon receipt by the Company of evidence reasonably satisfactory to it
of the loss, theft or destruction, and, in such case, of indemnity or security reasonably satisfactory to it, and upon surrender of this Warrant if mutilated, the Company will make and deliver a new Warrant of like tenor, in lieu of this Warrant;
provided that if the Holder hereof is an instrumentality of a state or local government or an institutional holder or a nominee for such an instrumentality or institutional holder an irrevocable agreement of indemnity by such Holder shall be
sufficient for all purposes of this Section 6, and no evidence of loss or theft or destruction shall be necessary. This Warrant shall be promptly cancelled by the Company upon the surrender hereof in connection with any transfer or replacement.
Except as otherwise provided above, in the case of the loss, theft or destruction of a Warrant, the Company shall pay all expenses, taxes and other charges payable in connection with any transfer or replacement of this Warrant, other than stock
transfer taxes (if any) payable in connection with a transfer of this Warrant, which shall be payable by the Holder. Holder will not transfer this Warrant and the rights hereunder except in compliance with federal and state securities laws.

 SECTION 7. Mergers, Consolidation, Sales. In the case of any proposed consolidation or merger of the Company with another entity, or
the proposed sale of all or substantially all of its assets to another person or entity, or any proposed reorganization or reclassification of the capital stock of the Company, then, as a condition of such consolidation, merger, sale, reorganization
or reclassification, lawful and adequate provision shall be made whereby the Holder of this Warrant shall thereafter have the right to receive upon the basis and upon the terms and conditions specified herein, in lieu of the shares of the Common
Stock of the Company immediately theretofore purchasable hereunder, such shares of stock, securities or assets as may (by virtue of such consolidation, merger, sale, reorganization or reclassification) be issued or payable with respect to or in
exchange for the number of shares of such Common Stock purchasable hereunder immediately before such consolidation, merger, sale, reorganization or reclassification. In any such case appropriate provision shall be made with respect to the rights and
interests of the Holder of this Warrant to the end that the provisions hereof shall thereafter be applicable as nearly as may be, in relation to any shares of stock, securities or assets thereafter deliverable upon the exercise of this Warrant. In
the case of any proposed consolidation or merger of the Company with another entity, or the proposed sale of all or substantially all of its assets to another person or entity, or any proposed reorganization or reclassification of the capital stock
of the Company in which the holders of the Company’s Common Stock are to receive assets in exchange for shares of Common Stock, then, as a condition of such consolidation, merger, sale, reorganization or reclassification, lawful and adequate
provision shall be made whereby the Holder of this Warrant shall have the opportunity to exercise this Warrant at the time of such consolidation, merger, sale, reorganization or reclassification and 
  

 -10- 

 receive upon the basis and upon the terms and conditions specified herein, in lieu of the shares of the Common Stock of
the Company immediately theretofore purchasable hereunder, such assets as may (by virtue of such consolidation, merger, sale, reorganization or reclassification) be issued or payable with respect to or in exchange for the number of shares of such
Common Stock purchasable hereunder immediately before such consolidation, merger, sale, reorganization or reclassification. 
  

 -11- 

 SECTION 8. Notice of Dissolution or Liquidation. In case of any distribution of the assets of the
Company in dissolution or liquidation (except under circumstances when the foregoing Section 7 shall be applicable), the Company shall give notice thereof to the Holder hereof and shall make no distribution to shareholders until the expiration
of thirty (30) days from the date of mailing of the aforesaid notice and, in any case, the Holder hereof may exercise this Warrant prior to the expiration date hereof within thirty (30) days from the date of the giving of such notice, and
all rights herein granted not so exercised within such thirty-day period shall thereafter become null and void. 
 SECTION 9. Notice of Extraordinary
Dividends. If the Board of Directors of the Company shall declare any dividend or other distribution on its Common Stock except out of earned surplus or by way of a stock dividend payable in shares of its Common Stock, the Company shall mail
notice thereof to the Holder hereof not less than 30 days prior to the record date fixed for determining shareholders entitled to participate in such dividend or other distribution, and the Holder hereof shall not participate in such dividend or
other distribution unless this Warrant is exercised prior to such record date. The provisions of this Section 9 shall not apply to distributions made in connection with transactions covered by Section 7. 
 SECTION 10. Fractional Shares. Fractional shares shall not be issued upon the exercise of this Warrant but in any case where the Holder would,
except for the provisions of this Section 10, be entitled under the terms hereof to receive a fractional share upon the complete exercise of this Warrant, the Company shall, upon the exercise of this Warrant for the largest number of whole
shares then called for, pay a sum in cash equal to the excess of the value of such fractional share (determined in such reasonable manner as may be prescribed in good faith by the Board of Directors of the Company) over the Warrant Price for such
fractional share. 
 SECTION 11. Special Arrangements of the Company. The Company covenants and agrees that during the Term of this
Warrant, unless otherwise approved by the Holder of this Warrant: 
 11.1. Will Not Amend Certificate. The Company will
not amend its Certificate of Incorporation to eliminate as an authorized class of capital stock that class denominated as “Common Stock” on the date hereof. 
 11.2. Will Bind Successors. This Warrant shall be binding upon any Company or other person or entity succeeding to the Company by merger, consolidation or acquisition of all or substantially all
of the Company’s assets. 
 SECTION 12. Registration Rights. The Company, the Holder and certain other parties have executed and
delivered a Registration Rights Agreement dated as of February 3, 2000 (the “Registration Rights Agreement”), pursuant to which the Company has granted certain registration and other rights to the other parties thereto.
The Company hereby agrees that the Warrant Shares shall be entitled to the same rights as Conversion Shares in the Registration Rights Agreement, as if the Warrant Shares were Conversion Shares, except that (a) the Warrant Shares shall not be
included in calculating the number of Conversion Shares for purposes of voting and exercising demand rights under the Registration Rights Agreement and shall not be entitled to vote or make a demand and (b) the Warrant Shares shall be reduced
from an underwritten public offering under the provisions of Section 5 of the Registration Rights Agreement prior to the reduction of any Conversion Shares. 
  

 -12- 

 SECTION 13. Put. The Company agrees that this Warrant and the Warrant Shares are securities covered
by and entitled to the rights contained in Section 5.37 of the Series B Convertible Preferred Stock Purchase Agreement dated as of February 3, 2000 among the Company, the Holder and certain other parties as if this Warrant and the Warrant
Shares were purchased thereunder. 
 SECTION 14. Notices. Any notice or other document required or permitted to be given or delivered to
the Holder shall be delivered at, or sent by certified or registered mail to, the Holder at 999 West Street, Rocky Hill, CT 06067 or to such other address as shall have been furnished to the Company in writing by the Holder. Any notice or other
document required or permitted to be given or delivered to the Company shall be delivered at, or sent by certified or registered mail to, the Company at 300 George Street New Haven, CT 06511 or to such other address as shall have been furnished in
writing to the Holder by the Company. Any notice so addressed and mailed by registered or certified mail shall be deemed to be given when so mailed. Any notice so addressed and otherwise delivered shall be deemed to be given when actually received
by the addressee. 
 SECTION 15. No Rights as Stockholder; Limitation of Liability. This Warrant shall not entitle the Holder to any of
the rights of a shareholder of the Company. No provision hereof, in the absence of affirmative action by the Holder to purchase shares of Common Stock, and no mere enumeration herein of the rights or privileges of the Holder, shall give rise to any
liability of the Holder for the Warrant Price hereunder or as a shareholder of the Company, whether such liability is asserted by the Company or by creditors of the Company. 
 SECTION 16. Acknowledgment of Continuing Obligation. The Company will, at the time of any exercise of this Warrant in whole or in part, upon request of the holder hereof, acknowledge in writing
its continuing obligation to such holder in respect of any rights (including without limitation any right to registration of the shares of Common Stock issued upon such exercise) to which such holder shall continue to be entitled after such exercise
in accordance with this Warrant; provided, however, that the failure of such holder to make any such request shall not affect the continuing obligation of the Company to such holder in respect of such rights. 
  

 -13- 

 SECTION 17. Representations and Warranties. The Company hereby represents and warrants to the holder
hereof as follows: 
 (a) The Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of
Delaware, has the corporate power and authority to conduct its business as presently conducted, has the corporate power and authority to execute, issue and deliver this Warrant and to perform its obligations under this Warrant, has the corporate
power and authority and legal right to own and lease its properties and is duly qualified and in good standing as a foreign corporation in each jurisdiction in which it owns or leases real property or in which the conduct of its business requires
such qualification, except where failure to be so qualified could not be reasonably expected to have a material adverse effect on the Company and its subsidiaries taken as a whole. 
 (b) The execution, delivery, issuance and performance by the Company of this Warrant and the issuance of the Warrant Shares upon exercise of this Warrant
have been duly authorized by all necessary corporate action and do not and will not violate, or result in a breach of, or constitute a default under, or require any consent under, or result in the creation of any lien, charge or encumbrance upon the
assets of the Company pursuant to, any law, statute, ordinance, rule, regulation, order or decree of any court, governmental body or regulatory authority or administrative agency having jurisdiction over the Company or its subsidiaries or any
contract, mortgage, loan agreement, note, lease or other instrument binding upon the Company or its subsidiaries or by which their properties are bound. 
 (c) This Warrant has been duly executed, issued and delivered by the Company and constitutes a legal, valid, binding and enforceable obligation of the Company. The Warrant Shares, when issued upon exercise of this
Warrant in accordance with the terms hereof, will be duly authorized, validly issued, fully paid and nonassessable shares of Common Stock, with no personal liability attaching to the ownership thereof. 
 (d) The Company has authorized capital stock consisting of (x) 27,000,000 shares of Common Stock, $.001 par value, of which 1,769,427 shares are
issued and outstanding, and (y) 31,883,332 shares of Preferred Stock, $.01 par value, of which (i) 250,000 shares are designated as Series A Convertible Preferred Stock, of which all shares are issued and outstanding, (ii) 15,816,666
shares are designated as Series B Convertible Preferred Stock, of which all shares are issued and outstanding and (iii) 15,816,666 shares are designated as Series B-l Convertible Preferred Stock, of which no shares are issued and outstanding.

 SECTION 18. Law Governing. This Warrant shall be governed by, and construed and enforced in accordance with, the laws of the State of
Connecticut, without giving effect to its conflict of laws principles. 
 SECTION 19. Miscellaneous. This Warrant and any provision
hereof may be changed, waived, discharged or terminated only by an instrument in writing signed by the party (or any predecessor in interest thereof) against which enforcement of the same is sought. The headings in this Warrant are for purposes of
reference only and shall not affect the meaning or construction of any of the provisions hereof. 
  

 -14- 

 IN WITNESS WHEREOF, the Company has caused this Warrant to be signed by its duly authorized
officer as of the date first written above. 
  

			
	ACHILLION PHARMACEUTICALS, INC.
		
	By:	 	 /s/ William G. Rice

		 	William G. Rice, Ph. D.
		 	 Its President
 Duly Authorized

  

 -15- 

 FORM OF NOTICE OF EXERCISE 
 [To be signed only upon exercise of the Warrant] 
 TO BE EXECUTED BY THE
REGISTERED HOLDER 
 TO EXERCISE THE WITHIN WARRANT 
 The undersigned hereby exercises the right to purchase                      shares of Common Stock which the
undersigned is entitled to purchase by the terms of the within Warrant according to the conditions thereof, and herewith makes payment of the Warrant Price of such shares in full. All shares to be issued pursuant hereto shall be issued in the name
of, and the initial address of such person to be entered on the books of the Company shall be: 
  

					
		 	  
 _________________________________
	 	
		 	  
 _________________________________
	 	
		 	  
 _________________________________
	 	

 The shares are to be issued in certificates of the following denominations: 
  

			
	  

	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     

 FORM OF ASSIGNMENT 
 (PARTIAL) 
 [To be signed only upon partial transfer of Warrant] 
 TO BE EXECUTED BY THE REGISTERED HOLDER 
 TO TRANSFER THE WITHIN WARRANT 
 FOR VALUE RECEIVED
                     hereby sells, assigns and transfers
unto                     (i) the rights of the undersigned to purchase          shares of
Common Stock under and pursuant to the within Warrant, and (ii) on a non-exclusive basis, all other rights of the undersigned under and pursuant to the within Warrant, it being understood that the undersigned shall retain, severally (and not
jointly) with the transferee(s) named herein, all rights assigned on such non-exclusive basis. The undersigned does hereby irrevocably constitute and
appoint                     Attorney to transfer the said Warrant on the books of the Company, with full power of substitution. 
  

			
	  
 
	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     
 NOTICE 

The signature to the foregoing Assignment must correspond to the name as written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever. 

 FORM OF ASSIGNMENT 
 (ENTIRE) 
 [To be signed only upon transfer of entire Warrant] 
 TO BE EXECUTED BY THE REGISTERED HOLDER 
 TO TRANSFER THE WITHIN WARRANT 
 FOR VALUE RECEIVED
                     hereby sells, assigns and transfers unto
                     all rights of the undersigned under and pursuant to the within Warrant, and the undersigned does hereby irrevocably
constitute and appoint                      Attorney to transfer the said Warrant on the books of the Company, with full power of
substitution. 
  

			
	  
 
	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     
 NOTICE 

The signature to the foregoing Assignment must correspond to the name as written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever. 

 FORM OF ASSIGNMENT 
 (PARTIAL) 
 [To be signed only upon partial transfer of Warrant] 
 TO BE EXECUTED BY THE REGISTERED HOLDER 
 TO TRANSFER THE WITHIN WARRANT 
 FOR VALUE RECEIVED
                     hereby sells, assigns and transfers unto
                     (i) the rights of the undersigned to purchase          shares of
Common Stock under and pursuant to the within Warrant, and (ii) on a non-exclusive basis, all other rights of the undersigned under and pursuant to the within Warrant, it being understood that the undersigned shall retain, severally (and not
jointly) with the transferee(s) named herein, all rights assigned on such non-exclusive basis. The undersigned does hereby irrevocably constitute and appoint
                     Attorney to transfer the said Warrant on the books of the Company, with full power of substitution. 
  

			
	  
 
	[Type Name of Holder]
		
	By:	 	  

		
	Title:	 	  

 Dated:
                     
 NOTICE 

The signature to the foregoing Assignment must correspond to the name as written upon the face of the within Warrant in every particular, without
alteration or enlargement or any change whatsoever.Action of Authorized Pricing Officers dated September 15, 2006

 Exhibit 4.1 
 CSX CORPORATION 
 Action of Authorized Pricing Officers 
 September 15, 2006 
 1. Pursuant to
(i) Section 301 of the Indenture, dated as of August 1, 1990, between CSX Corporation (the “Corporation”) and JPMorgan Chase Bank, N.A., formerly The Chase Manhattan Bank, as trustee (the “Trustee”), as heretofore
supplemented and amended (the “Indenture”), and (ii) resolutions duly adopted by the Board of Directors of the Corporation at a meeting duly called and held on December 8, 2004, the undersigned officers hereby establish a series
(as that term is used in Section 301 of the Indenture) of Securities to be issued under the Indenture, which series of Securities shall have the terms set forth in the Prospectus and the Prospectus Supplement attached as Exhibit A
(collectively, the “Prospectus”) and such other or different terms as may be set forth herein. The title of the Securities shall be the 6.000% Notes due 2036 (the “Notes”), and the Notes will be issued in fully registered form
only, in denominations of $2,000 and integral multiples of $1,000. Terms used herein and not defined shall have the meaning assigned to them in the Indenture or the Prospectus. 
 2. The form and terms of the Notes substantially in the form of Exhibit B attached hereto are hereby approved under the Indenture; and the
Chairman, President and Chief Executive Officer, any Executive Vice President, any Senior Vice President, any Vice President, the Treasurer, the Corporate Secretary, any Assistant Corporate Secretary or the Controller of the Corporation are, and
each of them with full power to act without the others hereby is, authorized, in the name and on behalf of the Corporation, to execute, manually or by facsimile signature, and in the manner provided in the Indenture, the Notes (and, in addition, to
replace lost, stolen, mutilated or destroyed Notes, all as provided in the Indenture) substantially in the form approved hereby, in both temporary and definitive form, with such changes, modifications and insertions therein as the officer executing
the Notes shall determine, such determination to be conclusively evidenced by the execution thereof by such officer, all in the manner and form required in, or contemplated by, the Indenture. 
 3. The signatures of the officers of the Corporation so authorized to execute the Notes may, but need not be, the facsimile signatures of the current or
any future such authorized officers imprinted or otherwise reproduced thereon, the Corporation for such purpose hereby adopting such facsimile signatures as binding upon it, notwithstanding that at the time any Notes shall be authenticated and
delivered or disposed of any officer so signing shall have ceased to be such authorized officer. 
 4. The form, terms and provisions of the
Indenture are hereby ratified and approved. 
 5. The form, terms and provisions of the Underwriting Agreement, dated September 15, 2006
(the “Underwriting Agreement”), between the Corporation and the Underwriters named on Schedule II thereto, providing for the issuance and sale of the 

 Notes are hereby approved; and the Chairman, President and Chief Executive Officer, any Executive Vice President, any
Senior Vice President, any Vice President, the Treasurer, any General Counsel or Assistant General Counsel, the Corporate Secretary, any Assistant Corporate Secretary or the Assistant Vice President, Treasury and Investor Relations of the
Corporation (each an “Authorized Officer” and collectively, the “Authorized Officers”) are, and each of them with full power to act without the others hereby is, authorized and directed to execute and deliver, in the name and on
behalf of the Corporation, the Underwriting Agreement with such changes therein as the officer of the Corporation executing the Underwriting Agreement shall approve, the execution thereof by such officer to be conclusive evidence of such approval.

 6. The form and terms of the Prospectus are hereby approved. 
 7. The Authorized Officers are, and each of them with full power to act without the others hereby is, authorized and empowered to take all actions, and
to execute and deliver any and all documents, in the name and on behalf of this Corporation as such officer or officers shall deem necessary or appropriate to effect or otherwise carry out the foregoing. 
 8. Any and all actions heretofore or hereafter taken by any officer or officers of the Corporation within the terms of the foregoing, including without
limitation, the filing of a registration statement and amendments, supplements and addenda thereto with the Securities and Exchange Commission with respect to the Notes and other securities which may be issued pursuant to the Indenture, are hereby
ratified and confirmed as the act of the Corporation. 
 9. The Notes may be authenticated by the Trustee and issued in accordance with the
Indenture. 

 Dated as of the date first set forth above. 
  

			
	By:	 	 /s/ Oscar Munoz

	Name:	 	Oscar Munoz
	Title:	 	Executive Vice President and Chief Financial Officer

			
		
	By:	 	 /s/ David A. Boor

	Name:	 	David A. Boor
	Title:	 	Vice President-Tax and Treasurer

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