Warrant to purchase shares of Common Stock issued to Alexandria Equities, LLC



 EXHIBIT 4.7 
 THIS WARRANT AND THE SECURITIES ISSUABLE UPON THE EXERCISE HEREOF HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR ANY STATE SECURITIES LAWS. THEY MAY
NOT BE SOLD, OFFERED FOR SALE, PLEDGED, HYPOTHECATED OR OTHERWISE TRANSFERRED IN THE ABSENCE OF A REGISTRATION STATEMENT IN EFFECT WITH RESPECT TO THE SECURITIES UNDER SUCH ACT OR AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT.

 Void after February 9, 2016 
 WARRANT FOR THE 
 PURCHASE OF SHARES OF COMMON STOCK 
 of 
 CODEXIS, INC. 
 INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE 
 THIS CERTIFIES THAT, for value received, Alexandria Equities, LLC, a Delaware limited liability company, together with its successors and
assigns (each, a “Holder”), is entitled to purchase up to that number of duly authorized, validly issued, fully paid and nonassessable shares of Common Stock par value $0.0001 per share, (the “Common Stock”) of
Codexis, Inc., a Delaware corporation (the “Company”), as set forth in Section 1.2 below, at the per share purchase price described in Section 1.3 below, subject to the provisions and upon the terms and conditions
hereinafter set forth. 
 1. Exercise of Warrant. The terms and conditions upon which this Warrant may be exercised, and
the Common Stock covered hereby may be purchased, are as follows: 
 1.1 Term; Put Right. 
 (a) The purchase right represented by this Warrant may be exercised in whole or in part at any time and from time to time from and after the
date hereof and on or before the tenth anniversary hereof; provided, that if the last day on which this Warrant may be exercised is not a Business Day (as defined in Section 12 hereof), this Warrant may be exercised prior to 5:00 p.m.
(New York time) on the next succeeding full Business Day with the same force and effect as if exercised on such last day specified herein. 
 (b) Notwithstanding anything herein to the contrary, in the event that on or prior to January 31, 2011 the Company has not consummated any Liquidity Event (as defined below), then on January 31,
2011 the Company shall repurchase from Holder, at Holder’s option (such option being the “Put Right”), this Warrant, at a price of $8.30 per share of Common Stock then issuable upon exercise of the Warrant. In the event Holder
does not elect to exercise Holder’s Put Right on or before 12:00 p.m. Pacific time on January 31, 2011, then the Put Right shall expire, and this Warrant shall survive and be governed by all the terms and conditions set forth herein. For
purposes hereof, “Liquidity Event” shall mean any sale, lease, license, transfer or other disposition of all or substantially all of the assets of the Company to any








 
other Person; any consolidation or merger involving the Company; or any firm commitment underwritten public offering of its Common Shares registered under the Act. 
 1.2 Number of Shares. This Warrant is initially exercisable for that number of shares of Common Stock, subject to adjustment pursuant
to Section 2 of this Warrant, equal to three thousand five hundred seventy-seven (3,577). 
 1.3 Purchase Price. The
initial per share purchase price for the shares of Common Stock to be issued upon exercise of this Warrant shall be $8.30, subject to adjustment as provided for herein (the “Warrant Price”). 
 1.4 Method of Exercise. The exercise of the purchase rights evidenced by this Warrant shall be effected by (a) the surrender of
this Warrant, together with a duly executed copy of the form of a subscription attached hereto, to the Company at its principal offices and the delivery of the purchase price (i) by check or bank draft payable to the Company’s order or by
wire transfer to the Company’s account for the number of shares for which the purchase rights hereunder are being exercised or any other form of consideration approved by the Company’s Board of Directors or (ii) pursuant to the
procedure set forth in Section 1.5. 
 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 herein or at such later date as may be specified in the executed form of subscription, and at such time the person or persons in
whose name or names any certificate or certificates for shares of Common Stock shall be issuable upon such exercise as provided herein shall be deemed to have become the Holder or Holders of record thereof. 
 1.5 Cashless Exercise. In addition to and without limiting the rights of the Holder hereof under the terms hereof, at the
Holder’s option this Warrant may be exercised in whole or in part at any time or from time to time prior to its expiration for a number of shares of Common Stock having an aggregate fair market value on the date of such exercise equal to the
difference between (a) the fair market value of the number of shares of Common Stock subject to this Warrant designated for exercise by the Holder hereof on the date of exercise and (b) the aggregate Warrant Price for such shares in effect
at such time. 
 The “fair market value” of shares of Common Stock shall be calculated on the basis of (a) if the
Common Stock is then traded on a securities exchange, the average of the closing prices of the Common Stock on such exchange over the 20 trading day period ending three (3) trading days prior to the date of exercise, (b) if the Common
Stock is then regularly traded over-the-counter, the average of the sale prices or, if sale prices for the Common Stock are not regularly and publicly reported, then the closing bid of the Common Stock over the 20 trading day period ending three
(3) trading days prior to the date of exercise, or (c) if there is no active public market for the Common Stock, the fair market value thereof shall be determined by a nationally recognized investment banking firm chosen in good faith by
the Company’s Board of Directors. If the Holder of this Warrant exercises this Warrant contingent upon the closing of a public offering, the “fair market value” of a share of Common Stock on the date of exercise shall be equal to the
initial price to the public specified in the final prospectus with respect to such public

  

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offering. The following formula illustrates how many shares would be issued upon exercise of this Warrant pursuant to the “cashless exercise” provisions of this Section 1.5:

  

							
	Let	  	FMV	  	=	  	Fair market value per share of Common Stock at date of exercise.
				
		  	PSP	  	=	  	Per share Warrant Price at date of exercise.
				
		  	N	  	=	  	Number of shares of Common Stock desired to be exercised.
				
		  	X	  	=	  	Number of shares of Common Stock issued upon exercise.
				
		  	X	  	=	  	(FMV)(N)-(PSP)(N)
		  		  		  	     FMV


 No payment of any cash or other consideration to the Company shall be required from
the Holder of this Warrant in connection with any exercise of this Warrant pursuant to this Section 1.5. Such exercise shall be effective upon the date of receipt by the Company of this Warrant surrendered for cancellation and a written request
from the Holder hereof that the exercise pursuant to this section be made, or at such later date as may be specified in such request. 
 1.6 Issuance of Shares. As soon as reasonably practicable after each exercise of this Warrant, in whole or in part, the Company at its expense (including the payment by it of any applicable issue taxes) shall cause to be issued in
the name of and delivered to the Holder hereof or as such Holder (upon payment by such Holder of any applicable transfer taxes) may direct, (a) a certificate or certificates for the number of duly authorized, validly issued, fully paid and
nonassessable shares of Common Stock to which such Holder shall be entitled upon such exercise, and (b) in case such exercise is in part only, a new Warrant or Warrants of like tenor representing in the aggregate the right to purchase the
number of shares of Common Stock equal (without giving effect to any adjustment thereof) to the number of such shares stated in this Warrant minus the number of such shares designated by the Holder upon such exercise as provided herein. 

2. Certain Adjustments. 
 2.1 Mergers, Consolidations or Sale of Assets. If after the date hereof there shall be a capital reorganization (other than a combination or subdivision of Common Stock otherwise provided for
herein), or spin-off, or a merger or consolidation of the Company with or into another corporation, a limited liability company, a partnership or other legal entity (each of the foregoing being referred to herein as a “Person”), or the
sale of all or substantially all of the Company’s properties and assets to any other Person, then, as a part of such transaction, lawful provision shall be made so that the Holder shall thereafter be entitled to receive upon exercise of this
Warrant, during the period specified in this Warrant and upon payment of the purchase price specified by this Warrant, the number of shares of stock or other securities, cash or property of the Company or the successor corporation or other Person
resulting from such transaction, to which a Holder of the Common Stock deliverable upon exercise of this Warrant would have been entitled under the provisions of the agreement in such transaction (or otherwise pursuant to such transaction) if this
Warrant had been exercised immediately before such transaction. In any

  

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such case, appropriate adjustment (as determined reasonably and in good faith by the Company’s Board of Directors) shall be made in the application of the provisions of this Warrant with
respect to the rights and interests of the Holder such that the provisions of this Warrant (including adjustment of the Warrant Price then in effect and the number of shares of Common Stock issuable upon exercise hereof) shall be applicable after
that event, as near as reasonably may be, in relation to any shares of stock or other property deliverable after that event upon exercise of this Warrant. 
 2.2 Splits and Subdivisions; Dividends. If the Company should effect or fix a record date for the effectuation of a split or subdivision of the outstanding shares of Common Stock or the
determination of the Holders of Common Stock entitled to receive a dividend or other distribution payable in additional shares of Common Stock or other securities or warrants, options or other rights convertible into, or entitling the Holder thereof
to receive directly or indirectly, additional shares of Common Stock (hereinafter referred to as “Common Stock Equivalents”) without payment of any consideration by such Holder for the additional shares of Common Stock or Common
Stock Equivalents (including the additional shares of Common Stock issuable upon conversion or exercise thereof), then, as of such record date (or the date of such distribution, split or subdivision if no record date is fixed), the per share Warrant
Price shall be appropriately decreased and the number of shares of Common Stock issuable upon exercise hereof shall be appropriately increased in proportion to such increase of outstanding shares. 
 2.3 Combination of Shares. If the number of shares of Common Stock outstanding at any time after the date hereof is decreased by a
combination of the outstanding shares of Common Stock, the per share Warrant Price shall be appropriately increased and the number of shares of Common Stock issuable upon exercise hereof shall be appropriately decreased in proportion to such
decrease in outstanding shares. 
 2.4 Adjustments for Other Distributions. In the event the Company shall declare a
distribution payable in securities of the Company (other than Common Stock or Common Stock Equivalents) or other Persons, evidences of indebtedness issued by the Company or other Persons, assets (including cash dividends) or options or rights not
referred to in subsection 2.2, then, in each such case, upon exercise of this Warrant the Holder hereof shall be entitled to a proportionate share of any such distribution as though such Holder was the holder of the number of shares of Common Stock
of the Company into which this Warrant may be exercised as of the record date fixed for the determination of the holders of Common Stock of the Company entitled to receive such distribution. 
 2.5 Issuance of Additional Common Stock. 
 (a) If, after the date hereof, the Company shall issue or sell 
  

	 	(i)	Additional Shares (defined below) without consideration or for a consideration per share that is less than the higher of (A) the Warrant Price and (B) the
fair market value of a share of Common Stock in effect immediately prior to such issue or sale, or 

  

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	 	(ii)	Common Stock Equivalents exercisable for Additional Shares with a minimum exercise or exchange price that is less than the higher of (A) the Warrant Price and
(B) the fair market value of a share of Common Stock in effect immediately prior to such issue or sale, 

 then, and in each
such case, the Warrant Price shall be reduced, concurrently with such issue or sale, to a price (calculated to the nearest .001 of a cent) determined by multiplying such Warrant Price by a fraction: 
  

	 	(iii)	the numerator of which shall be (A) the number of shares of Common Stock outstanding immediately prior to such issue or sale (including any shares of Common Stock
issuable upon conversion of all outstanding shares of preferred stock and issuable upon exercise of outstanding options, warrants or other convertible securities) plus (B) the number of shares of Common Stock that the aggregate consideration
received by the Company upon such issuance or sale (or, in the case of Common Stock Equivalents exercisable for Additional Shares, receivable by the Company upon exercise or exchange) would purchase at such Warrant Price, and


  

	 	(iv)	the denominator of which shall be the number of shares of Common Stock outstanding immediately after such issue or sale (assuming, in the case of Common Stock
Equivalents exercisable for Additional Shares, exercise or exchange of all such Common Stock Equivalents and including any shares of Common Stock issuable upon conversion of outstanding shares of preferred stock and issuable upon exercise of
outstanding options, warrants or other convertible securities). 

 (b) For the purposes of this Section 2.5,
the consideration for the issue or sale of Additional Shares shall, irrespective of the accounting treatment of such consideration, (i) insofar as it consists of cash, be computed at the net amount of cash received by the Company, and
(ii) insofar as it consists of property (including securities) other than cash, be computed at the fair market value thereof at the time of such issue or sale. In the event of a disagreement by the Holder as to the fair market value of any
consideration consisting of property proposed to be assigned to such consideration by the Company, the Company shall, at the option of the Holder, engage a consulting firm or investment banking firm mutually agreed to by the Holder and the Company
to prepare an independent appraisal of the fair market value of such property to be distributed. The expenses of such appraisal shall be borne by the Company. 
 (c) Notwithstanding anything contained herein to the contrary, the consideration for any Common Stock Equivalents shall be the total amount of consideration received by the Company for the issuance of
such Common Stock Equivalents plus the minimum

  

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amount of consideration payable to the Company upon exercise, conversion or exchange of Common Stock Equivalents (the “Net Consideration”) determined as of the date of issuance
of such Common Stock Equivalents. Any obligation, agreement or understanding to issue Common Stock Equivalents at any time in the future shall be deemed to be an issuance at the time such obligation or agreement is made or arises. No adjustment of
the Warrant Price shall be made under this Section 2.5 upon the issuance of any shares of Common Stock which are issued pursuant to the exercise, conversion or exchange of any Common Stock Equivalents if any adjustment shall previously have
been made upon the issuance of any such Common Stock Equivalents. 
 Should the Net Consideration for any such Common Stock
Equivalents be increased or decreased from time to time, then, upon the effectiveness of such change, the Warrant Price will be that which would have been obtained (i) had the adjustments made upon the issuance of such Common Stock Equivalents
been made upon the basis of the actual Net Consideration (as so increased or decreased) of such Common Stock Equivalents, and (ii) had adjustments to such Warrant Price since the date of issuance of such Common Stock Equivalents been made to
such Warrant Price as adjusted pursuant to (i) above. Any adjustment of the Warrant Price pursuant to this paragraph which relates to Common Stock Equivalents shall be disregarded if, as, and when all of such Common Stock Equivalents expire or
are canceled without being exercised, so that the Warrant Price effective immediately upon cancellation or expiration shall be equal to the Warrant Price in effect at the time of the issuance of the expired or canceled Common Stock Equivalents, with
such additional adjustments as would have been made to such Warrant Price had the expired or canceled Common Stock Equivalents not been issued. 
 (d) “Additional Shares” means all shares of Common Stock, whether or not subsequently reacquired or retired by the Company, other than shares of Common Stock issued or to be issued to
directors, officers, employees and consultants of the Company or any subsidiary pursuant to any bona fide qualified or non-qualified stock option plan or agreement, stock purchase plan or agreement, stock restriction agreement, or employee stock
ownership plan. 
 (e) The number of shares of Common Stock that the Holder of this Warrant shall be entitled to receive upon
each exercise hereof after any adjustment pursuant to this Section 2.5 shall be determined by multiplying (i) the number of shares of Common Stock that were issuable immediately prior to such adjustment, by (ii) the fraction of which
(A) the numerator is the Warrant Price immediately prior to such adjustment and (B) the denominator is the Warrant Price immediately following such adjustment. 
 2.6 Certificate as to Adjustments. In the case of each adjustment or readjustment of the Warrant Price pursuant to this Section 2, the Company at its expense shall promptly compute such
adjustment or readjustment in accordance with the terms hereof and cause a certificate, signed by the Company’s Chief Financial Officer, setting forth such adjustment or readjustment and showing in detail the facts upon which such adjustment or
readjustment is based to be delivered to the Holder of this Warrant. The Company shall furnish or cause to be furnished to such Holder a certificate setting forth (a) such adjustments and readjustments, (b) the Warrant Price in effect
after such adjustment and how it was calculated and (c) the number of shares of Common Stock issuable upon exercise hereof after such adjustment and the amount, if any, of other property at the time receivable upon the exercise of the Warrant.

  

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 2.7 Other Dilutive Events. If any event shall occur as to which the provisions of
Section 2 are not strictly applicable but the failure to make any adjustment would not fairly protect the purchase rights represented by this Warrant in accordance with the essential intent and principles of such sections, then, in each such
case, the Board of Directors of the Company shall make such adjustment, if any, on a basis consistent with the essential intent and principles established in Section 2, necessary to preserve, without dilution, the purchase rights represented by
this Warrant. The Company shall promptly notify the Holder of any such adjustments and shall take any actions that may be necessary to put the same into effect. 
 2.8 No Dilution or Impairment. The Company shall not, by amendment of its certificate or articles of incorporation, as applicable, or through any consolidation, merger, reorganization, transfer of
assets, 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 shall 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 Holder against dilution or other impairment. Without limiting the generality of the foregoing, the Company (a) shall not permit
the par value of any shares of stock receivable upon the exercise of this Warrant to exceed the amount payable therefor upon such exercise, (b) shall take all such action as may be necessary or appropriate in order that the Company may validly
and legally issue fully paid and nonassessable shares of stock on the exercise of the Warrants from time to time outstanding; and (c) shall not take any action which results in any adjustments of the Warrant Price if the total number of shares
of Common Stock issuable after the action upon the exercise of all of the Warrants would exceed the total number of shares of Common Stock then authorized by the Company’s certificate or articles of incorporation, as applicable, and available
for the purpose of issue upon such exercise. 
 2.9 Notices of Record Date etc. In the event of: 
 (a) any taking by the Company of a record of the holders of any class of securities of the Company for the purpose of determining the
holders thereof who are entitled to receive any dividend (other than a cash dividend payable out of earned surplus at the same rate as that of the last such cash dividend theretofore paid) or other distribution, or any right to subscribe for,
purchase or otherwise acquire any shares of stock of any class or any other securities or property, or to receive any other right; 
 (b) any capital reorganization of the Company, any reclassification or recapitalization of the capital stock of the Company or Liquidity Event; or 
 (c) any voluntary or involuntary dissolution, liquidation or winding-up of the Company, 
 the
Company shall mail to the Holder at least thirty (30) days prior to the earliest date specified below, a notice specifying: (i) the date on which any such record is to be taken for the purpose of such dividend, distribution or right, and
the amount and character of such dividend,

  

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distribution or right; and (ii) the date on which any such reorganization, reclassification, transfer, consolidation, merger, dissolution, liquidation or winding-up is expected to become
effective and the record date for determining stockholders entitled to vote thereon and the time, if any such time is to be fixed, as of which the holders of record of Common Stock shall be entitled to exchange their shares of Common Stock for the
securities or other property deliverable upon such reorganization, reclassification, recapitalization, consolidation, merger, transfer, dissolution, liquidation or winding-up. 
 3. Fractional Shares. No fractional shares shall be issued in connection with any exercise of this Warrant. In lieu of the issuance
of any fractional share, the Company shall make a cash payment equal to the then fair market value of such fractional share as determined in accordance with Section 1.5 hereof. 
 4. Representations and Warranties of the Company. 
 4.1 Authorization. The Company has full power and authority to enter into this Warrant. This Warrant has been duly authorized, executed and delivered by the Company and constitutes its valid and
legally binding obligation, enforceable in accordance with its terms. 
 4.2 Reservation of Common Stock. The Company
shall at all times reserve and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the exercise of this Warrant, such number of its shares of Common Stock, free from preemptive rights, as
shall from time to time be sufficient to effect the exercise of this Warrant, and if at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the exercise of the entire Warrant, in addition to such
other remedies as shall be available to the Holder, the Company shall take such action as may be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purposes. If any
shares of its Common Stock to be reserved for the purpose of issuance upon exercise of the Warrants require registration with or approval of any governmental authority under any applicable law before such shares of Common Stock may be validly issued
or delivered, then it shall secure such registration or approval, as the case may be, and maintain such registration or approval in effect so long as so required. 
 4.3 Adjustment in Number of Shares Issuable and Purchase Price. There has not been nor will there be any adjustment to the number of shares issuable or the purchase price payable upon the exercise
of any securities of the Company convertible into or exchangeable for shares of Common Stock resulting from the issuance or exercise of this Warrant. 
 4.4 Valid Issuance. This Warrant, when issued and delivered in accordance with the terms hereof will be duly authorized and validly issued, and the Common Stock issuable upon the exercise hereof,
when issued pursuant to the terms hereof and upon payment of the exercise price, shall, upon such issuance, be duly authorized, validly issued, fully paid and nonassessable. 
 5. Privilege of Stock Ownership. Prior to the exercise of this Warrant, the Holder shall not be entitled, by virtue of holding this
Warrant, to any rights of a stockholder of the Company, including (without limitation) the right to vote, receive dividends or other

  

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distributions, exercise preemptive rights or be notified of stockholder meetings, and such Holder shall not be entitled to any notice or other communication concerning the business or affairs of
the Company. Nothing in this Section 5, however, shall limit the right of the Holder to be provided the notices described in Section 2 hereof or to participate in distributions described in Section 2 hereof if the Holder ultimately
exercises this Warrant. 
 6. Limitation of Liability. In the absence of affirmative action by the Holder to purchase the
Common Stock in accordance herewith, no mere enumeration herein of the rights or privileges of the Holder hereof shall give rise to an obligation on such Holder to purchase any securities or any liability of such Holder for the purchase price or as
a stockholder of the Company, whether such obligation or liability is asserted by the Company or by creditors of the Company. 
 7. Representations and Warranties of the Holder. Holder hereby represents and warrants to the Company as follows: 
 7.1 Investment Experience. Holder represents that it can bear the economic risk of its investment and has such knowledge and experience in financial or business matters that it is capable of evaluating the merits and risks of the investment
in the Warrant and the Common Stock issuable upon exercise hereof. Holder also represents it has not been organized solely for the purpose of acquiring the Warrant or the Common Stock issuable upon exercise hereof. 
 7.2 Restricted Securities. Holder understands that the Warrant being issued hereunder and the Common Stock issuable upon exercise
hereof are characterized as “restricted securities” under the federal securities laws inasmuch as they are being acquired from the Company in a transaction not involving a public offering and have not been registered under the Act nor
qualified under applicable state securities laws and that under such laws and applicable regulations such securities may not be resold without registration under the Act, except in certain limited circumstances. In this connection, Holder represents
that it is familiar with Rule 144 promulgated under the Act (“Rule 144”), as presently in effect, and understands the resale limitations imposed thereby and by the Act. 
 7.3 Accredited Investor. Holder is an “accredited investor” within the meaning of Rule 501 of Regulation D promulgated
under the Act. 
 7.4 Legends. It is understood that the certificates evidencing the Common Stock issuable upon exercise
hereof may bear the following or a substantially similar legend: 
 “THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, HYPOTHECATED OR OTHERWISE TRANSFERRED IN THE ABSENCE OF A REGISTRATION STATEMENT IN EFFECT WITH RESPECT TO THE SECURITIES UNDER SUCH
ACT OR AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT.” 
  

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 8. Additional Agreements. 
 8.1 Confidentiality. In handling any confidential information provided to the Holder by the Company, the Holder shall exercise the
same degree of care that it exercises with respect to its own proprietary information of the same type to maintain the confidentiality thereof, except that disclosure of such information may be made (i) to the subsidiaries or affiliates of
Holder in connection with their present or prospective business relations with the Company, (ii) to prospective transferees or purchasers of any interest in this Warrant, provided that they have entered into a comparable confidentiality
agreement in favor of the Company, (iii) as may be required in connection with the examination, audit or similar investigation of Holder or (iv) if otherwise required by law. Confidential information hereunder shall mean non-public
proprietary information of the Company identified as such prior to disclosure to Holder but shall not include information that either: (a) is in the public domain or in the knowledge or possession of Holder when disclosed to Holder, or
(b) is disclosed to Holder by a third party unless Holder has actual knowledge that such third party is prohibited from disclosing such information. 
 9. Transfers and Exchanges. 
 9.1 Compliance with Act. Holder agrees
not to sell, hypothecate, pledge or otherwise dispose of any interest in the Warrant or the Common Stock issuable upon exercise hereof in the United States, its territories, possessions or any area subject to its jurisdiction, or to any person who
is a national thereof or resident therein (including any estate of such person), or any corporation, partnership or other entity created or organized therein, other than in accordance with the Act. 
 9.2 New Warrants. Upon presentation to the Company’s transfer agent of the form of Assignment attached hereto, a new Warrant
shall be issued to the new holder hereof. New Warrants issued in connection with transfers or exchanges shall not require the signature of the new Holder hereof and shall be identical in form and provisions to this Warrant except, as applicable, as
to the number of shares of Common Stock covered thereby. 
 9.3 Ownership of Warrants. The Company may treat the person
in whose name any Warrant is registered on the register kept at the office of the Company maintained pursuant to Section 9.4(a) as the owner and Holder thereof for all purposes, notwithstanding any notice to the contrary, except that, if and
when any Warrant is properly assigned in blank, the Company may (but shall not be obligated to) treat the bearer thereof as the owner of such Warrant for all purposes, notwithstanding any notice to the contrary. A Warrant, if properly assigned, may
be exercised by a new Holder without a new Warrant first having been issued. 
 9.4 Transfer and Exchange of Warrants.

 (a) The Company shall serve as its own transfer agent for purposes of this Warrant, to whom notices, presentations and
demands in respect of this Warrant may be made, until such time as the Company shall notify the Holders of the Warrants of any change in such transfer agent or in the designated office locations thereof; and 
 (b) Upon the surrender of any Warrant, properly endorsed, for registration of transfer or for exchange, the Company at its expense will
execute and deliver to or

  

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upon the order of the Holder thereof a new Warrant or Warrants of like tenor, in the name of such Holder or as such Holder (upon payment by such Holder of any applicable transfer taxes) may
direct, representing the right to purchase in the aggregate the number of shares of Common Stock stated in the Warrant or Warrants so surrendered. 
 10. Successors and Assigns. The terms and provisions of this Warrant shall be binding upon the Company and the Holder and their respective successors and assigns, subject at all times to the
restrictions set forth herein. 
 11. Loss, Theft, Destruction or Mutilation of Warrant. Upon receipt by the Company of
evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this Warrant, and in case of loss, theft or destruction, of indemnity or security reasonably satisfactory to the Company, and upon reimbursement to the Company
of all reasonable expenses incidental thereto, and upon surrender and cancellation of this Warrant, if mutilated, the Company will make and deliver a new warrant of like tenor and dated as of such cancellation, in lieu of this Warrant. 

12. Saturdays, Sundays, Holidays, etc. If the last or appointed day for the taking of any action or the expiration of any right
required or granted herein is not a Business Day, then such action may be taken or such right may be exercised on the next succeeding full Business Day. For purposes of this Warrant, a Business Day is a day that is not a Saturday or a Sunday, a
legal holiday or a day on which banking institutions doing business in the City of New York, or the State of California are authorized by law to close. 
 13. Amendments and Waivers. Any term of this Warrant may be amended and the observance of any term of this Warrant may be waived (either generally or in a particular instance and either
retroactively or prospectively), only with the written consent of the Company and the Holder. Any such amendment or waiver shall be binding on the parties. 
 14. Governing Law. The terms and conditions of this Warrant shall be governed by and construed in accordance with Delaware law, without regard to conflict of law provisions. 
 15. Notices. Except as otherwise provided in this Warrant, any requirement for a notice, demand or request under this Warrant will be
satisfied by a writing (a) hand delivered with receipt; (b) mailed by United States registered or certified mail or Express Mail, return receipt requested, postage prepaid; or (c) sent by Federal Express or any other nationally
recognized overnight courier service, and addressed as follows: if to the Holder, at its address as shown on the books of the Company, with a copy to Cooley Godward LLP, Five Palo Alto Square, 3000 El Camino Real, Palo Alto, CA 94306, Attn: Vincent
P. Pangrazio; and if to the Company, at 200 Penobscot Drive, Redwood City, CA 94063, Attn: Chief Executive Officer, with a copy to Latham & Watkins LLP, 140 Scott Drive, Menlo Park, CA 94025, Attn: Patrick A. Pohlen. All notices that are
sent in accordance with this Section 15 will be deemed received by the Holder or the Company on the earliest of the following applicable time period: (i) the date the return receipt is executed; or (ii) the date delivered as
documented by the overnight courier service or the hand delivery receipt. Either the Holder or the Company may designate a change of address by written notice to the other party. 
  

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 16. Registration Rights. The Company agrees that the Common Stock issuable upon
exercise of this Warrant shall have certain “piggyback” registration rights pursuant to and as set forth in the Fourth Amended and Restated Investor Rights Agreement, made and entered into as of November 13, 2007 (the “Investor
Rights Agreement”) as may be amended from time to time. Holder agrees to become a party to the Investor Rights Agreement for the purposes of this Section 16. 
 17. Remedies. The Company acknowledges and agrees that irreparable harm, for which there may be no adequate remedy at law and for which the ascertainment of damages would be difficult, would occur
in the event any of the provisions of this Warrant were not performed in accordance with its specific terms or were otherwise breached. The Company accordingly agrees that the Holders shall be entitled to an injunction or injunctions to prevent
breaches of the provisions of this Warrant and to enforce specifically the terms and provisions hereof in any court of the United States or any state thereof having jurisdiction, in each instance without being required to post bond or other security
and in addition to, and without having to prove the inadequacy of other remedies at law. 
 18. Securities Matters. In
order to make available the benefits of certain rules and regulations of the Commission, including without limitation Rule 144 and any successor rule or regulation of the Commission, that may at any time permit the sale of the shares of Common Stock
issuable upon exercise of this Warrant to the public without registration, the Company agrees (i) to file in a timely manner all reports, statements and other information and documents required to be filed by it pursuant to Section 13 or
15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and (ii) whether or not the Company is subject to the reporting and other filing requirements of Section 13 or 15(d) of the Exchange Act, to
file with the Commission and, within fifteen (15) days after the date it would be required to file such reports with the Commission if it were subject to such reporting and other filing requirements of the Exchange Act, to deliver to the Holder
of this Warrant all such reports, information and other documents as it would be required to file with the Commission if it were subject to the requirements of Section 13 or 15(d) of the Exchange Act and otherwise to make and keep publicly
available all such information concerning the Company as shall be necessary to enable the Holder to comply with the aforementioned rules and regulations of the Commission. 
 19. “Market Stand-Off” Agreement. Holder hereby agrees that Holder shall not sell, transfer, make any short sale of, grant
any option for the purchase of, or enter into any hedging or similar transaction with the same economic effect as a sale, any Common Stock (or other securities) of the Company held by Holder (other than those included in the registration and Common
Stock purchased by Holder in the open market after the effective date of such registration statement) for a period specified by the representative of the underwriters of Common Stock (or other securities) of the Company not to exceed one hundred
eighty (180) days following the effective date of a registration statement of the Company filed under the Securities Act (or such longer period, not to exceed eighteen (18) days after the expiration of the 180-day period as the
underwriters or the Company shall request in order to facilitate compliance with National Association of Securities Dealers Rule 2711); provided that: 
 19.1 such agreement shall apply only to the Company’s Initial Offering; and 
  

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 19.2 all executive officers and directors of the Company and holders of at least one percent
(1%) of the Company’s capital stock (on an as converted basis) and all other persons with registration rights (whether or not pursuant to this Agreement) enter into similar agreements. 
 [signature page follows] 
  

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 [Warrant for the Purchase of Shares of Common Stock of Codexis, Inc.] 
  

			
	CODEXIS, INC.,
	a Delaware corporation
		
	By:	 	  

	Name:	 	Alan Shaw
	Title:	 	President and Chief Executive Officer
		
	Dated:	 	
	
	ACCEPTED AND AGREED:
	
	 ALEXANDRIA EQUITIES, LLC,
 a Delaware limited liability company

		
	By:	 	Alexandria Real Estate Equities, Inc
		 	a Maryland corporation,
		 	its managing member
		
	By:	 	  

	Name:	 	Joel S. Marcus
	Title:	 	Chief Executive Officer
		
	Dated:	 	March 27, 2008









 SUBSCRIPTION 
 Codexis, Inc. 
 Ladies and Gentlemen: 
 The undersigned,
                            , hereby elects to purchase, pursuant to the [cashless
exercise] provisions of the Warrant, dated July 17, 2007 held by the undersigned,
                                 shares of the Common Stock of Codexis, Inc., a
Delaware corporation[, and tenders herewith payment of the purchase price of such shares in full]. 
 In
exercising its rights to purchase such Common Stock, the undersigned hereby confirms the investment representations made in Section 7 and the agreements made in Section 8 of such Warrant. 
 Dated:                  200    .

  

			
	  

		
	By:	 	  

	Address:	 	  



  

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 [FORM OF ASSIGNMENT] 
 The undersigned hereby assigns this Warrant to 
  

	
	  

	
	  

	
	  

	(Print or type name, address and zip code of assignee)

 Please insert Social Security or other 
 identifying number of assignee 
 and irrevocably appoints
                                        
as agent to transfer this Warrant on the books of the Company. The agent may substitute another to act for him or it. 
  

							
	Dated:                     	 		 	Signed:	 	  


  

	
	  

	(Sign exactly as name appears on the front of this Warrant)

  

							
	Dated:                     	 		 	Signed:	 	  

		 		 	Name:	 	  

		 		 	Title:	 	  


  

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