Document:

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 
  

 12 

 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] 
  

 13 

 [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:	 	  

  

 15 

 [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:	 	  

  

 16Registration Rights Agreement

 Exhibit 4.8 
 A. 
 REGISTRATION RIGHTS AGREEMENT 
 This Registration Rights Agreement (the “Agreement”) is entered into by and among Codexis, Inc., a Delaware corporation (the
“Company”) and the shareholders of JFC—Jülich Fine Chemicals GmbH (“JFC”), Dr. Matthias Arnold, Dr. Thomas Daußmann, Dr. Thomas Drescher, Dr. Karl Rix, Dr. Falk Schneider, Mr. Horst Leutenberg and
Mr. Thomas Kalthoff (including their successors and assigns, each a “Holder” and collectively, the “Holders”). 
 RECITALS 
 WHEREAS, the Holders and the Company are parties to that certain Stock Purchase
Agreement recorded today under the role of deeds [•]/2005 of the notary public Dr. Marc Hermanns, Cologne, Germany (the “Purchase Agreement”), pursuant to which the Company is acquiring from the Holders the outstanding shares
of capital stock of JFC and in consideration therefore, among other things, the Company has agreed, upon the terms and subject to the conditions of the Purchase Agreement, to issue 312,500 shares (the “Shares”) of the Company’s
common stock (the “Common Stock”) to such Holders; and 
 WHEREAS, in connection with the consummation of the transaction
contemplated by the Purchase Agreement, the parties desire to enter into this Agreement in order to grant “piggyback” registration rights to the Holders as set forth below. 
 NOW, THEREFORE, in consideration of the representations, warranties, covenants and agreements contained in this Agreement and for other good and valuable consideration, the receipt and sufficiency of
which are hereby acknowledged, the parties hereto agree as follows: 
 SECTION 1. 
 GENERAL 
  

	 	1.1	Definitions. As used in this Agreement the following terms shall have the following respective meanings: 

  

	 	(a)	“Affiliate” means shall mean any corporation or other entity that is directly or indirectly controlling, controlled by or under the common control with
a party hereto. For the purpose of this definition, “control” shall mean the direct or indirect ownership of at least fifty percent (50%) of the outstanding shares or other voting rights of the subject entity to elect directors or
equivalent governing body, or if not meeting the preceding, any entity owned or controlled by or owning or controlling at the maximum control or ownership right permitted in the country where such entity exists. 

  

	 	(b)	“Exchange Act” means the United States Securities Exchange Act of 1934, as amended 

  

 1 

	 	(c)	“Investor Rights Agreement” shall mean the Second Amended and Restated Investor Rights Agreement, dated July 26, 2004, by and among the Company
and the investors listed on Exhibit A thereto, as the same may be amended, modified • or supplemented in accordance with its terms after the date hereof 

  

	 	(d)	“Investors” shall have the meaning given such term in the investor Rights Agreement. 

  

	 	(e)	“Initial Offering” means the Company’s first firm commitment underwritten public offering of its Common Stock registered under the Securities Act
that results in the Company’s preferred stock being converted into Common Stock. 

  

	 	(f)	“register”, “registered”, and “registration” refer to a registration effected by preparing and filing a
registration statement in compliance with the Securities Act, and the declaration or ordering of effectiveness of such registration statement or document. 

  

	 	(g)	“Registrable Securities” means (a) the Shares and (b) any Common Stock of the Company issued as (or issuable upon the conversion or exercise
of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for or in replacement of, such above-described securities. Notwithstanding the foregoing, Registrable Securities shall not
include any securities sold by a person to the public either pursuant to a registration statement or Rule 144 or sold in a private transaction in which the transferor’s rights under Section 2 of this Agreement are not assigned.

  

	 	(h)	“Registration Expenses” shall mean all expenses incurred by the Company in complying with Section 2.1 hereof, including, without limitation, all
registration and filing fees, printing expenses, fees and disbursements of counsel for the Company, blue sky fees and expenses and the expense of any special audits incident to or required by any such registration (but excluding the compensation of
regular employees of the Company, which shall be paid in any event by the Company). 

  

	 	(i)	“Securities Act” shall mean the United States Securities Act of 1933, as amended. 

  

	 	(j)	“Selling Expenses” shall mean all underwriting discounts and selling commissions applicable to the sale, and the fees and disbursements of counsel for
the Holders, if any. 

  

 2 

 SECTION 2. 
 REGISTRATION RIGHTS 
  

	 	2.1	Piggyback Registrations. The Company shall notify all Holders in writing at least fifteen (15) days prior to the filing of any registration statement under
the Securities Act for purposes of a public offering of securities of the Company (including, but not limited to, registration statements relating to secondary offerings of securities of the Company, but excluding a registration statement
(i) relating to any employee benefit plan or (ii) with respect to any corporate reorganization or transaction under Rule 145 of the Securities Act, including any registration statements related to the resale of securities issued in such a
transaction or (iii) related to stock issued upon conversion of debt securities) and will afford each such Holder an opportunity to include in such registration statement all or part of such Registrable Securities held by such Holder. Each
Holder desiring to include in any such registration statement all or any part of the Registrable Securities held by it shall, within seven (7) days after the above-described notice from the Company, so notify the Company in writing. Such notice
shall state the intended method of disposition of the Registrable Securities by such Holder. If a Holder decides not to include all of its Registrable Securities in any registration statement thereafter filed by the Company, or if the Holder’s
Registrable Securities are excluded therefrom by the provisions of Section 2.1(a), such Holder shall nevertheless continue to have the right to include any Registrable Securities in any subsequent registration statement or registration
statements as may be filed by the Company with respect to offerings of its securities, all upon the terms and conditions set forth herein. 

  

	 	(a)	 Underwriting. If the registration statement under which the Company gives notice under this Section 2.1 is for an underwritten offering,
the Company shall so advise the Holders. In such event, the right of any such Holder to be included in a registration pursuant to this Section 2.1 shall be conditioned upon such Holder’s participation in such underwriting and the inclusion
of such Holder’s Registrable Securities in the underwriting to the extent provided herein. All Holders proposing to distribute their Registrable Securities through such underwriting shall enter into an underwriting agreement in customary form
with the underwriter or underwriters selected for such underwriting by the Company. Notwithstanding any other provision of this Agreement, if the underwriter determines in good faith that marketing factors require a limitation of the number of
shares to be underwritten, the number of shares that may be included in the underwriting shall be allocated, first, to the Company; second, to the Investors in accordance with the terms of the Investor Rights Agreement; third, to the Holders on a
pro rata basis based on the total number of Registrable Securities held by the Holders; and fourth, to any other stockholder of the Company (other than an Investor or a Holder) on a pro rata basis. No such reduction shall reduce the
amount of securities of the selling Holders included in the registration below twenty-five percent (25%) of the total amount of securities included in such

  

 3 

	 	 
registration; provided, however, that if such registration does not include shares of any stockholder of the Company other than Investors any or all of the Registrable Securities of
the Holders may be excluded in accordance with the immediately preceding sentence. If any Holder disapproves of the terms of any such underwriting, such Holder may elect to withdraw therefrom by written notice to the Company and the underwriter,
delivered at least ten (10) business days prior to the effective date of the registration statement. Any Registrable Securities excluded or withdrawn from such underwriting shall be excluded and withdrawn from the registration. For any Holder
that is a partnership or corporation, the partners, retired partners and stockholders of such Holder, or the estates and family members of any such partners and retired partners and any trusts for the benefit of any of the foregoing person shall be
deemed to be a single “Holder,” and any pro rata reduction with respect to such “Holder” shall be based upon the aggregate amount of shares carrying registration rights owned by all entities and individuals included in
such “Holder,” as defined in this sentence. 

  

	 	(b)	Right to Terminate Registration. The Company shall have the right to terminate or withdraw any registration initiated by it under this Section 2.1 prior to
the effectiveness of such registration whether or not any Holder has elected to include securities in such registration. The Registration Expenses of such withdrawn registration shall be borne by the Company in accordance with Section 2.2
hereof. 

  

	 	2.2	Expenses of Registration. Except as specifically provided herein, all Registration Expenses incurred in connection with any registration, qualification or
compliance pursuant to Section 2.1 shall be borne by the Company. All Selling Expenses incurred in connection with any registrations hereunder, shall be borne by the holders of the securities so registered pro rata on the basis of the number of
shares so registered. 

  

	 	2.3	Termination of Registration Rights. All registration rights granted under this Section 2 shall terminate and be of no further force and effect five
(5) years after the date of the Company’s Initial Offering. In addition, a Holder’s registration rights shall expire if (a) the Company has completed its Initial Offering and is subject to the provisions of the Exchange Act, and
(b) the requirements of paragraphs (c), (e), (f) and (h) of Rule 144 promulgated under the Securities Act do not apply to Registrable Securities held by and issuable to such Holder (and its affiliates) as a result of Rule 144(k)
promulgated under the Securities Act. 

  

	 	2.4	Delay of Registration; Furnishing Information. 

  

	 	(a)	No Holder shall have any right to obtain or seek an injunction restraining or otherwise delaying any such registration as the result of any controversy that might arise
with respect to the interpretation or implementation of this Section 2. 

  

 4 

	 	(b)	It shall be a condition precedent to the obligations of the Company to take any action pursuant to Section 2.1 above that the selling Holders shall furnish to the
Company such information regarding themselves, the Registrable Securities held by them and the intended method of disposition of such securities as shall be required to effect the registration of their Registrable Securities.

  

	 	2.5	Assignment of Registration Rights. The rights to cause the Company to register Registrable Securities pursuant to this Section 2 may be assigned by a Holder
to a transferee or assignee of Registrable Securities that (a) is a subsidiary, parent, general partner, limited partner, retired partner, member or retired member of a Holder, (b) is a Holder’s family member or trust for the benefit
of an individual Holder, or (c) acquires at least fifty thousand (50,000) shares of Registrable Securities (as adjusted for stock splits and combinations); or (d) is an Affiliate of such Holder provided, however, that
(i) the transferor shall, within ten (10) days after such transfer, furnish to the Company written notice of the name and address of such transferee or assignee and the securities with respect to which such registration rights are being
assigned, and (ii) such transferee shall agree to be subject to all restrictions set forth in this Agreement. 

  

	 	2.6	“Market Stand-Off” Agreement. Each Holder hereby agrees that such 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 such Holder (other than those included in the registration) 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;
provided that: 

  

	 	i.	such agreement shall apply only to the Company’s Initial Offering; and 

  

	 	ii.	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. 

  

	 	2.7	 Agreement to Furnish Information. Each Holder agrees to execute and deliver such other agreements as may be reasonably requested by the Company
or the underwriter that are consistent with the Holder’s obligations under Section 2.6 or that are necessary to give further effect thereto. In addition, if requested by the Company or the representative of the underwriters of Common Stock
(or other securities) of the Company, each Holder shall provide, within ten (10) days of such request, such information as may be required by the Company or such representative in connection with the completion of any public offering of the

  

 5 

	 	 
Company’s securities pursuant to a registration statement filed under the Securities Act. The obligations described in Section 2.6 above and this Section 2.7 shall not apply to a
registration statement (i) relating to any employee benefit plan or (ii) with respect to any corporate reorganization or transaction under Rule 145 of the Securities Act, including any registration statements related to the resale of
securities issued in such a transaction or (iii) related to stock issued upon conversion of debt securities. The Company may impose stop-transfer instructions with respect to the shares of Common Stock (or other securities) subject to the
foregoing restriction until the end of the one hundred eighty (180) day period. Each Holder agrees that any transferee of any shares of Registrable Securities shall be bound by Sections 2.6 and 2.7. The underwriters of the Company’s stock
are intended third party beneficiaries of Sections 2.6 and 2.7 and shall have the right, power and authority to enforce the provisions hereof as though they were a party hereto. 

  

	 	2.8	Stock Milestone Shares. In the event that the Company in 2006 issues additional shares of Common Stock to the Holders or any of their transferees as a 2005 stock
milestone payment pursuant to Section 2.5(c) of the Purchase Agreement (the “2005 Stock Milestone Shares”), the provisions of this Agreement as applicable to the Shares shall also be applicable to such 2005 Stock Milestone
Shares. 

  

	 	2.9	Indemnification. In the event any Registrable Securities are included in a registration statement under Section 2.1: 

  

	 	(a)	 To the extent permitted by law, the Company will indemnify and hold harmless each Holder, the partners, officers and directors of each Holder, any
underwriter (as defined in the Securities Act) for such Holder and each person, if any, who controls such Holder or underwriter within the meaning of the Securities Act or the Exchange Act, against any losses, claims, damages, or liabilities (joint
or several) to which they may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages or liabilities (or actions in respect thereof) arise out of or are based upon any of the
following statements, omissions or violations (collectively a “Violation”) by the Company: (1) any untrue statement or alleged untrue statement of a material fact contained in such registration statement, including any
preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto, (ii) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements
therein not misleading, or (iii) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation promulgated under the Securities Act, the Exchange Act or any state
securities law in connection with the offering covered by such registration statement; and the Company will pay as incurred to each such Holder, partner, officer, director, underwriter or controlling person for any legal or other expenses reasonably
incurred by them in connection with investigating or defending

  

 6 

	 	 
any such loss, claim, damage, liability or action; provided, however, that the indemnity agreement contained in this Section 2.9(a) shall not apply to amounts paid in
settlement of any such loss, claim, damage, liability or action if such settlement is effected without the consent of the Company, which consent shall not be unreasonably withheld, nor shall the Company be liable in any such case for any such loss,
claim, damage, liability or action to the extent that it arises out of or is based upon a Violation that occurs in reliance upon and in conformity with written information furnished expressly for use in connection with such registration by such
Holder, partner, officer, director, underwriter or controlling person of such Holder. 

  

	 	(b)	To the extent permitted by law, each Holder will, if Registrable Securities held by such Holder are included in the securities as to which such registration
qualifications or compliance is being effected, indemnify and hold harmless the Company, each of its directors, its officers and each person, if any, who controls the Company within the meaning of the Securities Act, any underwriter and any other
Holder selling securities under such registration statement or any of such other Holder’s partners, directors or officers or any person who controls such Holder, against any losses, claims, damages or liabilities (joint or several) to which the
Company or any such director, officer, controlling person, underwriter or other such Holder, or partner, director, officer or controlling person of such other Holder may become subject under the Securities Act, the Exchange Act or other federal or
state law, insofar as such losses, claims, damages or liabilities (or actions in respect thereto) arise out of or are based upon any Violation, in each case to the extent (and only to the extent) that such Violation occurs in reliance upon and in
conformity with written information furnished by such Holder under an instrument duly executed by such Holder and stated to be specifically for use in connection with such registration; and each such Holder will pay as incurred any legal or other
expenses reasonably incurred by the Company or any such director, officer, controlling person, underwriter or other Holder, or partner, officer, director or controlling person of such other Holder in connection with investigating or defending any
such loss, claim, damage, liability or action if it is judicially determined that there was such a Violation; provided, however, that the indemnity agreement contained in this Section 2.9(b) shall not apply to amounts paid in
settlement of any such loss, claim, damage, liability or action if such settlement is effected without the consent of the Holder, which consent shall not be unreasonably withheld; provided further, that in no event shall any indemnity
under this Section 2.9 exceed the proceeds from the offering received by such Holder. 

  

	 	(c)	 Promptly after receipt by an indemnified party under this Section 2.9 of notice of the commencement of any action (including any governmental
action), such indemnified party will, if a claim in respect thereof is to be

  

 7 

	 	 
made against any indemnifying party under this Section 2.9, deliver to the indemnifying party a written notice of the commencement thereof and the indemnifying party shall have the right to
participate in, and, to the extent the indemnifying party so desires, jointly with any other indemnifying party similarly noticed, to assume the defense thereof with counsel mutually satisfactory to the parties; provided, however, that
an indemnified party shall have the right to retain its own counsel, with the fees and expenses to be paid by the indemnifying party, if representation of such indemnified party by the counsel retained by the indemnifying party would be
inappropriate due to actual or potential differing interests between such indemnified party and any other party represented by such counsel in such proceeding. The failure to deliver written notice to the indemnifying party within a reasonable time
of the commencement of any such action, if materially prejudicial to its ability to defend such action, shall relieve such indemnifying party of any liability to the indemnified party under this Section 2.9, but the omission so to deliver
written notice to the indemnifying party will not relieve it of any liability that it may have to any indemnified party otherwise than under this Section 2.9. 

  

	 	(d)	If the indemnification provided for in this Section 2.9 is held by a court of competent jurisdiction to be unavailable to an indemnified party with respect to any
losses, claims, damages or liabilities referred to herein, the indemnifying party, in lieu of indemnifying such indemnified party thereunder, shall to the extent permitted by applicable law contribute to the amount paid or payable by such
indemnified party as a result of such loss, claim, damage or liability in such proportion as is appropriate to reflect the relative fault of the indemnifying party on the one hand and of the indemnified party on the other in connection with the
Violation(s) that resulted in such loss, claim, damage or liability, as well as any other relevant equitable considerations. The relative fault of the indemnifying party and of the indemnified party shall be determined by a court of law by reference
to, among other things, whether the untrue or alleged untrue statement of a material fact or the omission to state a material fact relates to information supplied by the indemnifying party or by the indemnified party and the parties’ relative
intent, knowledge, access to information and opportunity to correct or prevent such statement or omission; provided, that in no event shall any contribution by a Holder hereunder exceed the proceeds from the offering received by such Holder.

  

	 	(e)	 The obligations of the Company and Holders under this Section 2.9 shall survive completion of any offering of Registrable Securities in a
registration statement and the termination of this Agreement. No indemnifying party, in the defense of any such claim or litigation, shall, except with the consent of each indemnified party, consent to entry of any judgment or enter into any
settlement which does not include as an unconditional term thereof the giving by the claimant or plaintiff to such

  

 8 

	 	 
indemnified party of a release from all liability in respect to such claim or litigation. 

  

	 	2.10	Rule 144 Reporting. With a view to making available to the Holders the benefits of certain rules and regulations of the United States Securities and Exchange
Commission (the “Commission”) that may permit the sale of the Registrable Securities to the public without registration, the Company agrees to use its reasonable best efforts to: 

  

	 	(a)	Make and keep public information available, as those terms are understood and defined in Commission Rule 144 or any similar or analogous rule promulgated under the
Securities Act, at all times after the effective date of the first registration filed by the Company for an offering of its securities to the general public; 

  

	 	(b)	File with the Commission, in a timely manner, all reports and other documents required of the Company under the Exchange Act; and 

  

	 	(c)	So long as a Holder owns any Registrable Securities, furnish to such Holder forthwith upon request: a written statement by the Company as to its compliance with the
reporting requirements of Rule 144 of the Securities Act, and of the Exchange Act (at any time after it has become subject to such reporting requirements); a copy of the most recent annual or quarterly report of the Company; and such other reports
and documents as a Holder may reasonably request in availing itself of any rule or regulation of the Commission allowing it to sell any such securities without registration. 

 SECTION 3. 
 MISCELLANEOUS 
  

	 	3.1	Governing Law. This Agreement shall be governed by and construed under the laws of the State of California, United States of America, as applied to agreements
among California residents entered into and to be performed entirely within California. 

  

	 	3.2	Successors and Assigns. Except as otherwise expressly provided herein, the provisions hereof shall inure to the benefit of, and be binding upon, the successors,
assigns, heirs, executors, and administrators of the parties hereto and shall inure to the benefit of and be enforceable by each person who shall be a holder of Registrable Securities from time to time; provided, however, that prior to
the receipt by the Company of adequate written notice of the transfer of any Registrable Securities specifying the full name and address of the transferee, the Company may deem and treat the person listed as the holder of such shares in its records
as the absolute owner and holder of such shares for all purposes, including the payment of dividends or any redemption price. 

  

 9 

	 	3.3	Entire Agreement. This Agreement constitutes the full and entire understanding and agreement between the parties with regard to the subject matter hereof and no
party shall be liable or bound to any other in any manner by any representations, warranties, covenants and agreements except as specifically set forth herein and therein. 

  

	 	3.4	Severability. In the event one or more of the provisions of this Agreement should, for any reason, be held to be invalid, illegal or unenforceable in any
respect, such invalidity, illegality, or unenforceability shall not affect any other provisions of this Agreement, and this Agreement shall be construed as if such invalid, illegal or unenforceable provision had never been contained herein.

  

	 	3.5	Amendment and Waiver. 

  

	 	(a)	Except as otherwise expressly provided, this Agreement may be amended or modified only upon the written consent of (i) the Company and (ii) the holders of at
least a majority of the Shares. 

  

	 	(b)	Except as otherwise expressly provided, the obligations of the Company and the rights of the Holders under this Agreement may be waived only with the written consent of
(i) the Company and (ii) the holders of at least a majority of the Shares. 

  

	 	(c)	For the purposes of determining the number of Holders entitled to vote or exercise any rights hereunder, the Company shall be entitled to rely solely on the list of
record holders of its stock as maintained by or on behalf of the Company. 

  

	 	3.6	Notices. 

  

	 	(a)	All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the Company or to the
Holders’ Agent (as defined below under (b)) if to be given to any or all of the Holders, (b) when sent by confirmed facsimile if sent during normal business hours of the Company or the Holders’ Agent, respectively; if not, then on the
next business day, (c) five (5) days after having been sent to the Company or the Holders’ Agent, respectively, by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit
with an overnight courier, specifying next day delivery to the Company or the Holders’ Agent, respectively, with written verification of receipt. All communications shall be sent to the party to be notified, in the case of any or all of the
Holders to the Holders’ Agent, at the address as set forth below under (c) or at such other address as the Company or the Holders’ Agent, as the case may be, may designate by ten (10) days advance written notice to the relevant
other party hereto. 

  

	 	(b)	 The Holders hereby jointly appoint Dr. Thomas Drescher as their agent (the “Holders’ Agent”), until they notify the Company in
writing of the

  

 10 

	 	 
appointment of another Holder as new Holders’ Agent; until receipt of that notification Dr. Drescher will be considered the appointed Holders’ Agent for purposes of this Agreement. The
Holders authorize Dr. Drescher to receive on their behalf all notices, declarations and documents. The Holders hereby release the Holders’ Agent from the restrictions of self dealing (including those restrictions under Sec. 181 of the German
Civil Code (BGB)). 

  

	 	(c)	The initial addresses for service of notices and other declarations to either the Company or the Holders’ Agent in accordance with (a) above shall be as
follows: 

 in the case of the Holders: 
 Dr. Thomas Drescher (as Holders’ Agent) 
 c/o JFC - Jülich Fine Chemicals GmbH 
 Prof.-Rehm-Str. 1 
 52428 Jülich/Germany 
 FAX: +49 (2461) 980-116;

 in the case of the Company: 
 Codexis, Inc. 
 Attention: Tassos Gianakakos 
 200 Penobscot Drive 
 Redwood City, CA 94063 / U.S.A. 
 FAX: +1 (650) 2985449 
  

	 	3.7	Titles and Subtitles. The titles of the sections and subsections of this Agreement are for convenience of reference only and are not to be considered in
construing this Agreement. 

  

	 	3.8	Aggregation of Stock. All shares of Registrable Securities held or acquired by Affiliates or persons or entities under common management or control shall be
aggregated together for the purpose of determining the availability of any rights under this Agreement. 

  

	 	3.9	Attorneys’ Fees. In the event that any suit or action is instituted to enforce any provision in this Agreement, the prevailing party in such dispute shall
be entitled to recover from the losing party all fees, costs and expenses of enforcing any right of such prevailing party under or with respect to this Agreement, including without limitation, such reasonable fees and expenses of attorneys and
accountants, which shall include, without limitation, all fees, costs and expenses of appeals. 

  

 11 

 Cologne, February 11, 2005 
  

					
			
	/s/ Thomas Daußmann	 		 	/s/ Thomas Drescher
	(Dr. Thomas Daußmann)	 		 	(Dr. Thomas Drescher)
			
	/s/ Matthias Arnold	 		 	/s/ Karl Rix
	(Dr. Matthias Arnold)	 		 	(Dr. Karl Rix)
			
	/s/ Falk Schneider	 		 	/s/ Horst Leutenberg
	(Dr. Falk Schneider)	 		 	(Horst Leutenberg)
			
	/s/ Thomas Kalthoff	 		 	/s/ Roland Maaß
	(Thomas Kalthoff)	 		 	(Codexis, Inc.)
			
		 		 	 —     on the basis of power of attorney
          dated February 7, 2005

  

 12

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