Document:

Form of Warrant to purchase shares of Series D Preferred Stock

 Exhibit 4.6 
 NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. SUBJECT TO SECTION 6 BELOW, NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE
WITH RULE 144 UNDER SAID ACT OR WITHOUT (I) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (II) AN OPINION OF COUNSEL FOR HOLDER, SATISFACTORY TO COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR (III) RECEIPT OF A
NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. 
 WARRANT TO PURCHASE SHARES OF SERIES D CONVERTIBLE PREFERRED STOCK

 September 28, 2007 
 THIS CERTIFIES
THAT, for value received,                                 
(“Holder”) is entitled to subscribe for and purchase the Specified Number (as defined below) of shares of fully paid and nonassessable Series D Convertible Preferred Stock of Codexis, Inc., a Delaware corporation (the
“Company”), at the Warrant Price (as hereinafter defined), subject to the provisions and upon the terms and conditions hereinafter set forth. As used herein, the term “Series D Preferred” shall mean Company’s presently
authorized Series D Convertible Preferred Stock, $.0001 par value per share, and any stock into which such Series D Preferred may hereafter be converted or exchanged and the term “Warrant Shares” shall mean the shares of Series D Preferred
which Holder may acquire pursuant to this Warrant and any other shares of stock into which such shares of Series D Preferred may hereafter be converted or exchanged. 
 1. Warrant Price and Specified Number. 
 (a) The “Warrant Price” shall initially be
                     (            ) per share, subject to adjustment as
provided in Section 7 below. 
 (b) The “Specified Number” shall initially be
                     (            ) shares on the date hereof, subject to
adjustment as provided in Section 7 below. Further, the “Specified Number” shall increase by                     
(            ) shares for each One Million Dollars ($1,000,000) of additional loans made by the Holder to Company after the date hereof pursuant to that certain Loan and Security
Agreement, dated as of the date hereof, by and among the Company, the Holder, the other lenders party thereto, and General Electric Capital Corporation, as agent; provided, however, that in no event shall the “Specified Number”
exceed                      (            ) shares. 
 2. Conditions to Exercise. The purchase right represented by this Warrant may be exercised at any time, or from time to time, in whole or in part during the term
commencing on the date hereof and ending at 5:00 P.M. Pacific time on the later of (a) the tenth anniversary of the date of this Warrant and (b) the fifth anniversary of the date of an initial public offering (the “Initial Public
Offering”) of Company (such later date, the “Expiration Date”). 

 3. Method of Exercise or Conversion; Payment; Issuance of Shares; Issuance of New Warrant. 
 (a) Cash Exercise. Subject to Section 2 hereof, the purchase right represented by this Warrant may be exercised by Holder hereof, in whole or
in part, by the surrender of the original of this Warrant (together with a duly executed Notice of Exercise in substantially the form attached hereto) at the principal office of Company (as set forth in Section 19 below) and by payment to
Company, by certified or bank check, or wire transfer of immediately available funds, of an amount equal to the then applicable Warrant Price per share multiplied by the number of Warrant Shares then being purchased. In the event of any exercise of
the rights represented by this Warrant, certificates for the shares of stock so purchased shall be in the name of, and delivered to, Holder hereof, or as such Holder may direct (subject to the terms of transfer contained herein and upon payment by
such Holder hereof of any applicable transfer taxes). Such delivery shall be made within 30 days after exercise of this Warrant and at Company’s expense and, unless this Warrant has been fully exercised or expired, a new Warrant having terms
and conditions substantially identical to this Warrant and representing the portion of the Warrant Shares, if any, with respect to which this Warrant shall not have been exercised, shall also be issued to Holder hereof within 30 days after exercise
of this Warrant. 
 (b) Conversion. In lieu of exercising this Warrant as specified in Section 3(a), Holder may from time to time
convert this Warrant, in whole or in part, into Warrant Shares by surrender of the original of this Warrant (together with a duly executed Notice of Exercise in substantially the form attached hereto) at the principal office of Company, in which
event Company shall issue to Holder the number of Warrant Shares computed using the following formula: 
  

																			
	X	 	=	 	 Y (A-B)
	 		 		 		 		 		 		 	
		 		 	A	 		 		 		 		 		 		 	

 Where: 
 X = the number of Warrant Shares to be issued to Holder. 
 Y = the number of Warrant Shares purchasable under
this Warrant (at the date of such calculation). 
 A = the Fair Market Value of one share of Company’s Series D Preferred (at the date of
such calculation). 
 B = Warrant Price (as adjusted to the date of such calculation). 
 (c) Fair Market Value. For purposes of this Section 3, Fair Market Value of one share of Company’s Series D Preferred shall mean:

 (i) In the event of an exercise in connection with an Initial Public Offering, the per share Fair Market Value for the Series D Preferred
shall be the offering price at which the underwriters initially sell common stock of Company (“Common Stock”) to the public multiplied by the number of shares of Common Stock into which each share of Series D Preferred is then convertible;

  

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 (ii) The average of the closing bid and asked prices of Common Stock quoted in the Over-The-Counter
Market Summary, the last reported sale price quoted on the Nasdaq Stock Market or on any other exchange on which the Common Stock is listed, whichever is applicable, as published in the Western Edition of the Wall Street Journal for the three
(3) trading days prior to the date of determination of Fair Market Value, multiplied by the number of shares of Common Stock into which each share of Series D Preferred is then convertible; 
 (iii) In the event of an exercise in connection with a merger, acquisition or other consolidation in which Company is not the surviving entity, the per
share Fair Market Value for the Series D Preferred shall be the value to be received per share of Series D Preferred by all holders of the Series D Preferred in such transaction as determined by the Board of Directors; or 
 (iv) In any other instance, the per share Fair Market Value for the Series D Preferred shall be as determined in the reasonable good faith judgment of
Company’s Board of Directors. 
 In the event of 3(c)(iii) or 3(c)(iv), above, Company’s Board of Directors shall prepare a
certificate, to be signed by an authorized officer of Company, setting forth in reasonable detail the basis for and method of determination of the per share Fair Market Value of the Series D Preferred. The Board of Directors will also certify to
Holder that this per share Fair Market Value will be applicable to all holders of Company’s Series D Preferred. Such certification must be made to Holder at least thirty (30) business days prior to the proposed effective date of the
merger, consolidation, sale, or other triggering event as defined in 3(c)(iii) or 3(c)(iv). 
 (d) Automatic Exercise. To the extent
this Warrant is not previously exercised, it shall be deemed to have been automatically converted in accordance with Sections 3(b) and 3(c) hereof (even if not surrendered) as of immediately before its expiration, involuntary termination or
cancellation if the then-Fair Market Value of a Warrant Share exceeds the then-Warrant Price, unless Holder notifies Company in writing to the contrary prior to such automatic exercise. 
 4. Representations and Warranties of Holder and Company. 
 (a) Representations and Warranties by
Holder. Holder represents and warrants to Company with respect to this purchase as follows: 
 (i) Evaluation. Holder has
substantial experience in evaluating and investing in private placement transactions of securities of companies similar to Company so that Holder is capable of evaluating the merits and risks of its investment in Company and has the capacity to
protect its interests. 
  

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 (ii) Resale. Except for transfers to an affiliate of Holder, Holder is acquiring this Warrant and
the Warrant Shares issuable upon exercise of this Warrant (collectively the “Securities”) for investment for its own account and not with a view to, or for resale in connection with, any distribution thereof. Holder understands that the
Securities have not been registered under the Securities Act of 1933, as amended (the “Act”) by reason of a specific exemption from the registration provisions of the Act which depends upon, among other things, the bona fide nature of the
investment intent as expressed herein. 
 (iii) Rule 144. Holder acknowledges that the Securities must be held indefinitely unless
subsequently registered under the Act or an exemption from such registration is available. Holder is aware of the provisions of Rule 144 promulgated under the Act. 
 (iv) Accredited Investor. Holder is an “accredited investor” within the meaning of Regulation D promulgated under the Act. 
 (v) Opportunity To Discuss. Holder has had an opportunity to discuss Company’s business, management and financial affairs with its management and an opportunity to review Company’s facilities. Holder
understands that such discussions, as well as the written information issued by Company, were intended to describe the aspects of Company’s business and prospects which Company believes to be material but were not necessarily a thorough or
exhaustive description. 
 (b) Representations and Warranties by Company. Company hereby represents and warrants to Holder that the
statements in the following paragraphs of this Section 4(b) are true and correct (a) as of the date hereof and (b) except where any such representation and warranty relates specifically to an earlier date, as of the date of any
exercise of this Warrant. 
 (i) Corporate Organization and Authority. Company (a) is a corporation duly organized, validly
existing, and in good standing in its jurisdiction of incorporation, (b) has the corporate power and authority to own and operate its properties and to carry on its business as now conducted and as proposed to be conducted; and (c) is
qualified as a foreign corporation in all jurisdictions where such qualification is required. 
 (ii) Corporate Power. Company has all
requisite legal and corporate power and authority to execute, issue and deliver this Warrant, to issue the Warrant Shares issuable upon exercise or conversion of this Warrant, and to carry out and perform its obligations under this Warrant and any
related agreements. 
 (iii) Authorization; Enforceability. All corporate action on the part of Company, its officers, directors and
shareholders necessary for the authorization, execution, delivery and performance of its obligations under this Warrant and for the authorization, issuance and delivery of this Warrant and the Warrant Shares 

  

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issuable upon exercise of this Warrant has been taken and this Warrant constitutes the legally binding and valid obligation of Company enforceable in
accordance with its terms. 
 (iv) Valid Issuance of Warrant and Warrant Shares. This Warrant has been validly issued and is free of
restrictions on transfer other than restrictions on transfer set forth herein and under applicable state and federal securities laws. The Warrant Shares issuable upon conversion of this Warrant, when issued, sold and delivered in accordance with the
terms of this Warrant for the consideration expressed herein, will be duly and validly issued, fully paid and nonassessable, and will be free of restrictions on transfer other than restrictions on transfer under this Warrant and under applicable
state and federal securities laws. Subject to applicable restrictions on transfer, the issuance and delivery of this Warrant and the Warrant Shares issuable upon exercise or conversion of this Warrant are not subject to any preemptive or other
similar rights or any liens or encumbrances except as specifically set forth in Company’s Certificate of Incorporation or this Warrant. The offer, sale and issuance of the Warrant Shares, as contemplated by this Warrant, are exempt from the
prospectus and registration requirements of applicable United States federal and state security laws, and neither Company nor any authorized agent acting on its behalf has or will take any action hereafter that would cause the loss of such
exemption. 
 (v) No Conflict. The execution, delivery, and performance of this Warrant will not result in (a) any violation of,
be in conflict with, or constitute a default under, with or without the passage of time or the giving of notice (1) any provision of Company’s Certificate of Incorporation or by-laws; (2) any provision of any judgment, decree, or
order to which Company is a party, by which it is bound, or to which any of its material assets are subject; (3) any contract, obligation, or commitment to which Company is a party or by which it is bound; or (4) any statute, rule, or
governmental regulation applicable to Company, or (b) the creation of any lien, charge or encumbrance upon any assets of Company. 
 (vi)
Capitalization. The capitalization table of Company attached hereto as Annex A is complete and accurate as of the date hereof (after giving effect to the issuance of this Warrant) and reflects (a) all outstanding capital stock of Company
and (b) all outstanding warrants, options, conversion privileges, preemptive rights or other rights or agreements to purchase or otherwise acquire or issue any equity securities or convertible securities of Company. Company has reserved
11,154,802 shares of Common Stock for issuance upon conversion of the Series D Preferred. 
 5. Legends. 
 (a) Legend. Each certificate representing the Warrant Shares shall be endorsed with substantially the following legend: 
  

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 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”). NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH THE ACT AND ANY REGULATIONS PROMULGATED THEREUNDER OR WITHOUT (I) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (II) AN OPINION OF COUNSEL FOR HOLDER
SATISFACTORY TO THE ISSUER THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR (III) RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. 
 Company need not enter into its stock records a transfer of Warrant Shares unless the conditions specified in the foregoing legend are satisfied. Company may also instruct its transfer agent not to allow the transfer
of any of the Warrant Shares unless the conditions specified in the foregoing legend are satisfied. 
 (b) Removal of Legend and Transfer
Restrictions. The legend relating to the Act endorsed on a certificate pursuant to paragraph 5(a) of this Warrant shall be removed and Company shall issue a certificate without such legend to Holder if (i) the Securities are registered
under the Act and a prospectus meeting the requirements of Section 10 of the Act is available or (ii) Holder provides to Company an opinion of counsel for Holder reasonably satisfactory to Company, a no-action letter or interpretive
opinion of the staff of the Securities and Exchange Commission (“SEC”) reasonably satisfactory to Company, or other evidence reasonably satisfactory to Company, to the effect that public sale, transfer or assignment of the Securities may
be made without registration and without compliance with any restriction such as Rule 144. 
 6. Condition of Transfer or Exercise of Warrant. It
shall be a condition to any transfer or exercise of this Warrant that at the time of such transfer or exercise, Holder (with respect to an exercise) or transferee (with respect to a transfer) shall provide Company with a representation in writing
that Holder or transferee is acquiring this Warrant and the shares of Series D Preferred to be issued upon exercise for investment purposes only and not with a view to any sale or distribution, or will provide Company with a statement of pertinent
facts covering any proposed distribution. As a further condition to any transfer of this Warrant or any or all of the shares of Series D Preferred issuable upon exercise of this Warrant, other than a transfer registered under the Act, Company may
request a legal opinion, in form and substance satisfactory to Company and its counsel, reciting the pertinent circumstances surrounding the proposed transfer and stating that such transfer is exempt from the registration and prospectus delivery
requirements of the Act. Company shall not require Holder to provide an opinion of counsel if the transfer is to an affiliate of Holder or without payment or promise of consideration. As further condition to each transfer, at the request of Company,
Holder shall surrender this Warrant to Company and the transferee shall receive and accept a Warrant, of like tenor and date, executed by Company. 
 7.
Adjustment for Certain Events. The number and kind of securities purchasable upon the exercise of this Warrant and the Warrant Price shall be subject to adjustment from time to time upon the occurrence of certain events, as follows:

  

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 (a) Reclassification, Merger or Sale. (i) In the event of (A) any reclassification or
change of securities of the class issuable upon exercise of this Warrant (other than a change in par value, or from par value to no par value, or from no par value to par value, or as a result of a subdivision or combination) or
(B) (1) any merger of Company with or into another corporation (other than a merger with another corporation in which Company is the acquiring and the surviving corporation and which does not result in any reclassification or change of
outstanding securities issuable upon exercise of this Warrant) (herein called a “Merger”) or (2) any sale of all or substantially all of the assets of Company (herein called a “Sale”), and if on the record date for such
Merger or Sale the fair market value of a share of Series D Preferred (or other securities issuable upon exercise of this Warrant) based on the amount to be paid to holders of the Warrant Shares if the Warrant had been exercised, is less than 300%
of the Warrant Price, Company, or such successor or purchasing corporation, as the case may be, shall duly execute and deliver to Holder a new Warrant (in form and substance satisfactory to Holder of this Warrant), or Company shall make appropriate
provision without the issuance of a new Warrant, so that Holder shall have the right to receive, at a total purchase price not to exceed that payable upon the exercise of the unexercised portion of this Warrant, and in lieu of the Warrant Shares
theretofore issuable upon exercise or conversion of this Warrant, the kind and amount of shares of stock, other securities, money and property receivable upon such reclassification, change, Merger or Sale by a holder of the number of shares of
Series D Preferred then purchasable under this Warrant, or in the case of such Merger or Sale in which the consideration paid consists all or in part of assets other than securities of the successor or purchasing corporation, at the option of
Holder, the securities of the successor or purchasing corporation having a value at the time of the transaction equivalent to the value of the Warrant Shares purchasable upon exercise of this Warrant at the time of the transaction. Any new Warrant
shall provide for adjustments that shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section 7. Subject to Sections 7(a)(ii) and 7(a)(iii) below, the provisions of this subparagraph (a) shall
similarly apply to successive reclassifications, changes, Mergers and Sales. 
 (ii) In the event of a Merger or Sale where, on the record
date for such Merger or Sale, the fair market value of a share of Series D Preferred (or other securities issuable upon exercise of this Warrant) based on the amount to be paid to holders of the Warrant Shares if the Warrant had been exercised, is
equal to or greater than 300% of the Warrant Price, Holder may either (A) exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Merger or Sale or
(B) subject to Section 3(d) above, permit the Warrant to expire upon the consummation of such Merger or Sale. 
 (iii)
Notwithstanding anything in this Section 7(a) to the contrary, in the event of a Sale where 80% or more of the aggregate consideration for such Sale is comprised of cash, Holder may either (A) exercise its conversion or purchase right
under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Sale or (B) subject to Section 3(d) above, permit the Warrant to expire upon the consummation of such Sale. 
  

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 (iv) Company shall provide Holder with written notice of any proposed Merger or Sale together with such
reasonable information as Holder may request in connection with such contemplated Merger or Sale giving rise to such notice, which is to be delivered to Holder not less than ten (10) business days prior to the closing of the proposed Merger or
Sale. 
 (b) Subdivision or Combination of Shares. If Company at any time while this Warrant remains outstanding and unexpired shall
subdivide or combine its outstanding shares of Series D Preferred, the Warrant Price shall be proportionately decreased and the number of Warrant Shares issuable hereunder shall be proportionately increased in the case of a subdivision and the
Warrant Price shall be proportionately increased and the number of Warrant Shares issuable hereunder shall be proportionately decreased in the case of a combination. 
 (c) Stock Dividends and Other Distributions. If Company at any time while this Warrant is outstanding and unexpired shall (i) pay a dividend with respect to Series D Preferred payable in Series D
Preferred, then the Warrant Price shall be adjusted, from and after the date of determination of shareholders entitled to receive such dividend or distribution, to that price determined by multiplying the Warrant Price in effect immediately prior to
such date of determination by a fraction (A) the numerator of which shall be the total number of shares of Series D Preferred outstanding immediately prior to such dividend or distribution, and (B) the denominator of which shall be the
total number of shares of Series D Preferred outstanding immediately after such dividend or distribution; or (ii) make any other distribution with respect to Series D Preferred (except any distribution specifically provided for in Sections 7(a)
and 7(b)), then, in each such case, provision shall be made by Company such that Holder shall receive upon exercise of this Warrant a proportionate share of any such dividend or distribution as though it were Holder of the Warrant Shares as of the
record date fixed for the determination of the shareholders of Company entitled to receive such dividend or distribution. 
 (d) Adjustment
of Number of Shares. Upon each adjustment in the Warrant Price, the number of Warrant Shares purchasable hereunder shall be adjusted, to the nearest whole share, to the product obtained by multiplying the number of Warrant Shares purchasable
immediately prior to such adjustment in the Warrant Price by a fraction, the numerator of which shall be the Warrant Price immediately prior to such adjustment and the denominator of which shall be the Warrant Price immediately thereafter.

 (e) Adjustment for Dilutive Issuance. The number of shares of Common Stock issuable upon conversion of the Warrant Shares, shall be
subject to adjustment, from time to time in the manner set forth in Company’s Certificate of Incorporation as if the Warrant Shares were issued and outstanding on and as of the date of any such required adjustment. The provisions set forth for
the Warrant Shares in Company’s Certificate of Incorporation relating to the above in effect as of the date hereof may not be amended, modified or waived, without the prior written consent of Holder unless such amendment, modification or waiver
affects the rights associated with the Warrant Shares in the same manner as such amendment, modification or waiver affects the rights associated with all other shares of the same series and class as the Warrant Shares. 
  

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 (f) Adjustment for Pay-to-Play Transaction. In the event that Company’s Certificate of
Incorporation provides, or is amended to so provide, for the amendment or modification of the rights, preferences or privileges of the Series D Preferred, or the reclassification, conversion or exchange of the Series D Preferred, in the event that a
holder thereof fails to participate in an equity financing transaction (a “Pay-to-Play Provision”), and in the event that such Pay-to-Play Provision becomes operative, this Warrant shall automatically and without any action required become
exercisable for that number and type of shares of equity securities as would have been issued or exchanged, or would have remained outstanding, in respect of the Warrant Shares issuable hereunder had this Warrant been exercised in full prior to such
event, and had Holder participated in the equity financing to the maximum extent permitted. 
 (g) Adjustments Upon Conversion of Series D
Preferred. If all of the Series D Preferred is converted into shares of Common Stock (including without limitation pursuant to the automatic conversion provisions of Company’s certificate of incorporation providing for the conversion of the
Series D Preferred into Common Stock in connection with a qualified initial public offering of Company’s securities), then this Warrant shall automatically become exercisable for that number of shares of Common Stock equal to the number of
shares of Common Stock that would have been received if this Warrant had been exercised in full and the shares of Series D Preferred received thereupon had been simultaneously converted into shares of Common Stock immediately prior to such event,
and the Warrant Price shall be automatically adjusted to equal the amount obtained by dividing the then existing Warrant Price by the number of shares of Common Stock into which one share of Series D Preferred is converted. For avoidance of doubt,
the aggregate Warrant Price shall not be adjusted in connection with any adjustments pursuant to this Section 7(g). 
 8. Notice of Adjustments.
Whenever any Warrant Price or the kind or number of securities issuable under this Warrant shall be adjusted pursuant to Section 7 hereof, Company shall prepare a certificate signed by an officer of Company setting forth, in reasonable detail,
the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the Warrant Price and number or kind of shares issuable upon exercise of this Warrant after giving effect to such adjustment,
and shall cause copies of such certificate to be mailed (by certified or registered mail, return receipt required, postage prepaid) within thirty (30) days of such adjustment to Holder as set forth in Section 19 hereof. 
 9. Reserved. 
 10. Transferability of Warrant. This Warrant is
transferable on the books of Company at its principal office by the registered Holder hereof upon surrender of this Warrant properly endorsed, subject to compliance with Section 6 and applicable federal and state securities laws. Company shall
issue and deliver to the transferee a new Warrant representing the Warrant so transferred. Upon any partial transfer, Company will issue and deliver to Holder a new Warrant with respect to the Warrant not so transferred. Holder shall not have any
right to transfer any portion of this Warrant to any direct competitor of Company. 
  

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 11. Investor and Co-Sale Rights. Company grants to Holder the rights granted to other holders of the Series D
Preferred under that certain Third Amended and Restated Investor Rights Agreement dated August 22, 2006 (the “Investor Rights Agreement”) and that certain Second Amended and Restated Right of First Refusal and Co-Sale Agreement dated
August 22, 2006 (the “ROFR/Co-Sale Agreement”) and agrees that Holder shall be added as a party to the Investor Rights Agreement and ROFR/Co-Sale Agreement, and that the Warrant Shares shall be “Registrable Securities” under
the Investor Rights Agreement. Holder further agrees to be bound by the terms and conditions of the market standoff agreement, currently section 2.12, of the Investor Rights Agreement, as it may be amended from time to time (but only to the extent
that such Investor Rights Agreement is not amended in a manner that treats the Holder differently than any other holder of the Series D Preferred). 
 12.
No Fractional Shares. No fractional share of Series D Preferred will be issued in connection with any exercise or conversion hereunder, but in lieu of such fractional share Company shall make a cash payment therefor upon the basis of the
Warrant Price then in effect. 
 13. Charges, Taxes and Expenses. Issuance of certificates for shares of Series D Preferred upon the exercise or
conversion of this Warrant shall be made without charge to Holder for any United States or state of the United States documentary stamp tax or other incidental expense with respect to the issuance of such certificate, all of which taxes and expenses
shall be paid by Company, and such certificates shall be issued in the name of Holder. 
 14. No Shareholder Rights Until Exercise. Except as
expressly provided herein, this Warrant does not entitle Holder to any voting rights or other rights as a shareholder of Company prior to the exercise hereof. 
 15. Registry of Warrant. Company shall maintain a registry showing the name and address of the registered Holder of this Warrant. This Warrant may be surrendered for exchange or exercise, in accordance with its terms, at such office
or agency of Company, and Company and Holder shall be entitled to rely in all respects, prior to written notice to the contrary, upon such registry. 
 16.
Loss, Theft, Destruction or Mutilation of Warrant. Upon receipt by Company of evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this Warrant, and, in the case of loss, theft, or destruction, of indemnity
reasonably satisfactory to it, and, if mutilated, upon surrender and cancellation of this Warrant, Company will execute and deliver a new Warrant, having terms and conditions substantially identical to this Warrant, in lieu hereof. 
 17. Miscellaneous. 
 (a) Issue Date. The
provisions of this Warrant shall be construed and shall be given effect in all respect as if it had been issued and delivered by Company on the date hereof. 
 (b) Successors. This Warrant shall be binding upon any successors or assigns of Company. 
 (c)
Headings. The headings used in this Warrant are used for convenience only and are not to be considered in construing or interpreting this Warrant. 
  

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 (d) Saturdays, Sundays, Holidays. If the last or appointed day for the taking of any action or the
expiration of any right required or granted herein shall be a Saturday or a Sunday or shall be a legal holiday in the State of Connecticut, then such action may be taken or such right may be exercised on the next succeeding day not a legal holiday.

 (e) Attorney’s Fees. In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the
party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorney’s fees. 
 18. No Impairment. Company will not, by amendment of its Certificate of Incorporation or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms of this Warrant, but will at all times in
good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of Holder hereof against impairment. Without limiting the breadth of the foregoing,
Company will not cause the Series D Preferred into which this Warrant is exercisable or convertible to be converted into Common Stock unless such conversion is effected as part of the conversion of all Company’s outstanding series of Series D
Preferred and other senior securities into Common Stock. 
 19. Addresses. Any notice required or permitted hereunder shall be in writing and shall be
mailed by overnight courier, registered or certified mail, return receipt requested, and postage prepaid, or otherwise delivered by hand or by messenger, addressed as set forth below, or at such other address as Company or Holder hereof shall have
furnished to the other party in accordance with the delivery instructions set forth in this Section 19. 
  

			
	If to Company:	  	Codexis Inc.
		  	Chief Financial Officer
		  	200 Penobscot Drive
		  	Redwood City, CA 94063
		  	Attention: Mr. Robert Breuil
		  	Phone: (650) 421-8120
		  	Facsimile: (650) 298-5837
		
		  	Codexis, Inc.
		  	General Counsel
		  	200 Penobscot Drive
		  	Redwood City, CA 94063
		  	Attention: Mr. Doug Sheehy
		  	Phone: (650) 421-8160
		  	Facsimile: (650) 421-8108
		
	If to Holder:	  	_________________

 If mailed by registered or certified mail, return receipt requested, and postage prepaid, notice shall be deemed
to be given five (5) days after being sent, and if sent by overnight courier, by hand or by messenger, notice shall be deemed to be given when delivered (if on a business day, and if not, on the next business day). 
  

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 20. WAIVER OF JURY TRIAL. EACH OF THE PARTIES HERETO HEREBY WAIVES TO THE FULLEST EXTENT PERMITTED BY APPLICABLE
LAW, ANY RIGHT IT MAY HAVE TO A TRIAL BY JURY IN RESPECT OF ANY LITIGATION DIRECTLY OR INDIRECTLY ARISING OUT OF, UNDER OR IN CONNECTION WITH THIS WARRANT OR THE WARRANT SHARES. 
 21. GOVERNING LAW. THIS WARRANT SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK. 
 [Remainder of page intentionally left blank] 
  

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 IN WITNESS WHEREOF, Company has caused this Warrant to be executed by its officer thereunto duly
authorized. 
  

			
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	Alan Shaw
	Title:	 	President and Chief Executive Officer

 Dated as of September 28, 2007. 
  

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 NOTICE OF EXERCISE 
 To: 
 Codexis, Inc. 
 200
Penobscot Drive 
 Redwood City, California 04063 
 Attn: General
Counsel 
 1. The undersigned Warrantholder (“Holder”) elects to acquire shares of the Series D Convertible Preferred Stock (the “Series D
Preferred”) of Codexis, Inc. (the “Company”), pursuant to the terms of the Stock Purchase Warrant dated [                    ,
20    ] (the “Warrant”). 
 2. Holder exercises its rights under the Warrant as set forth below: 
  

			
	(        )	  	Holder elects to purchase                      shares of Series D Preferred as
provided in Section 3(a) and tenders herewith a check in the amount of $             as payment of the purchase price.
		
	(        )	  	Holder elects to convert the purchase rights into shares of Series D Preferred as provided in Section 3(b) of the Warrant.

 3. Holder surrenders the Warrant with this Notice of Exercise. 
 Holder represents that it is acquiring the aforesaid shares of Series D Preferred for investment and not with a view to or for resale in connection with distribution and
that Holder has no present intention of distributing or reselling the shares. 
 Please issue a certificate representing the shares of the Series D Preferred
in the name of Holder or in such other name as is specified below: 
  

															
		 		 	Name:	 	  
	 		 		 	
							
		 		 	Address:	 	  
	 		 		 	
							
		 		 	Taxpayer I.D.:	 	  
	 		 		 	
							
		 		 		 		 	[NAME OF HOLDER]	 		 	
								
		 		 		 		 	By:	 	  
	 		 	
		 		 		 		 	Name:	 	  
	 		 	
		 		 		 		 	Title:	 	  
	 		 	
						
		 		 		 		 	Date:                          ,
200    	 	

 ANNEX A 
 CAPITALIZATION TABLE 
 [SEE ATTACHED]Registration Rights Agreement dated February 11, 2005

 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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