Document:

Form of Warrant to purchase shares of Common Stock

 Exhibit 4.3 
 THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “1933 ACT”), OR ANY APPLICABLE STATE SECURITIES LAWS, AND MAY NOT BE SOLD OR TRANSFERRED UNLESS SUCH
SALE OR TRANSFER IS IN ACCORDANCE WITH THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS OR SOME OTHER EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS IS AVAILABLE WITH RESPECT THERETO. 
 COMMON STOCK PURCHASE WARRANT 
  

			
	Warrant No.                     	  	Number of Shares:                     

 CODEXIS, INC. 
 Effective as of February 12, 2004 
 Void after February 12, 2011 
 1. Issuance. This Common Stock Purchase
Warrant (the “Warrant”) is issued to
                                        
 by CODEXIS, INC., a Delaware corporation (hereinafter with its successors called the “Company”). 
 2. Purchase Price; Number of Shares. The registered holder of this Warrant (the “Holder”), commencing on the date hereof, is entitled upon surrender of this Warrant with the
subscription form annexed hereto duly executed, at the principal office of the Company, to purchase from the Company at a price per share of              (the “Purchase
Price”),                      fully paid and nonassessable shares of Common Stock, $0.0001 par value, of the Company (the
“Common Stock”). 
 Until such time as this Warrant is exercised in full or expires, the Purchase Price and the securities
issuable upon exercise of this Warrant are subject to adjustment as hereinafter provided. The person or persons in whose name or names any certificate representing shares of Common Stock is issued hereunder shall be deemed to have become the holder
of record of the shares represented thereby as at the close of business on the date this Warrant is exercised with respect to such shares, whether or not the transfer books of the Company shall be closed. 
 3. Payment of Purchase Price. The Purchase Price may be paid (a) in cash or by check, or (b) by any combination of the
foregoing. 
 4. Net Issue Election. The Holder may elect to receive, without the payment by the Holder of any additional
consideration, shares of Common Stock equal to the value of this Warrant or any portion hereof by the surrender of this Warrant or such portion to the Company, with the net issue election notice annexed hereto duly executed, at the principal office
of the Company. Thereupon, the Company shall issue to the Holder such number of fully paid and nonassessable shares of Common Stock as is computed using the following formula: 
  

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		 	 X
	 	 =
	 	 Y (A-B)
	 	
		 	 	 	A	 	

  

					
	where:	 	X =	 	the number of shares of Common Stock to be issued to the Holder pursuant to this Section 4.
			
		 	Y =	 	the number of shares of Common Stock covered by this Warrant in respect of which the net issue election is made pursuant to this Section 4.
			
		 	A =	 	the Fair Market Value (defined below) of one share of Common Stock as determined at the time the net issue election is made pursuant to this Section 4.
			
		 	B =	 	the Purchase Price in effect under this Warrant at the time the net issue election is made pursuant to this Section 4.

 “Fair Market Value” of a share of Common Stock as of the date that
the net issue election is made (the “Determination Date”) shall mean: 
 (i) If the net issue election is
made in connection with and contingent upon the closing of the sale of the Company’s Common Stock to the public in a public offering pursuant to a Registration Statement under the 1933 Act (a “Public Offering”), and if the
Company’s Registration Statement relating to such Public Offering (“Registration Statement”) has been declared effective by the Securities and Exchange Commission, then the initial “Price to Public” specified in the
final prospectus with respect to such offering. 
 (ii) If the net issue election is not made in connection with and
contingent upon a Public Offering, then as follows: 
 (a) If traded on a securities exchange or the Nasdaq National
Market, the fair market value of the Common Stock shall be deemed to be the average of the closing or last reported sale prices of the Common Stock on such exchange or market over the five day period ending five trading days prior to the
Determination Date; 
 (b) If otherwise traded in an over-the-counter market, the fair market value of the Common Stock
shall be deemed to be the average of the closing ask prices of the Common Stock over the five day period ending five trading days prior to the Determination Date; and 
 (c) If there is no public market for the Common Stock, then fair market value shall be determined in good faith by the Company’s Board of Directors. 
 5. Partial Exercise. This Warrant may be exercised in part, and the Holder shall be entitled to receive a new warrant, which shall be
dated as of the date of this Warrant, covering the number of shares in respect of which this Warrant shall not have been exercised. 
 6. Fractional Shares. In no event shall any fractional share of Common Stock be issued upon any exercise of this Warrant. If, upon exercise of this Warrant in its entirety, the

  

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Holder would, except as provided in this Section 6, be entitled to receive a fractional share of Common Stock, then the Company shall pay cash equal to the product of such fraction
multiplied by the Common Stock’s fair market value (as determined by the Board of Directors) on the date of exercise. 
 7. Expiration Date; Automatic Exercise. This Warrant shall expire at the close of business on February 12, 2011, and shall be void thereafter. Notwithstanding the foregoing, this Warrant shall automatically be deemed to be
exercised in full pursuant to the provisions of Section 4 hereof, without any further action on behalf of the Holder, immediately prior to the time this Warrant would otherwise expire pursuant to the preceding sentence. 
 8. Reserved Shares; Valid Issuance. The Company covenants that it will at all times from and after the date hereof reserve and keep
available such number of its authorized shares of Common Stock, free from all preemptive or similar rights therein, as will be sufficient to permit the exercise of this Warrant in full. The Company further covenants that such shares as may be issued
pursuant to such exercise will, upon issuance in accordance with the terms hereof, be duly and validly issued, fully paid and nonassessable and free from all taxes, liens and charges with respect to the issuance thereof. 
 9. Stock Splits and Dividends. If after the date hereof the Company shall subdivide the Common Stock, by split-up or otherwise, or
combine the Common Stock, or issue additional shares of Common Stock in payment of a stock dividend on the Common Stock, the number of shares of Common Stock issuable on the exercise of this Warrant shall forthwith be proportionately increased in
the case of a subdivision or stock dividend, or proportionately decreased in the case of a combination, and the Purchase Price shall forthwith be proportionately decreased in the case of a subdivision or stock dividend, or proportionately increased
in the case of a combination. 
 10. Antidilution Rights. The other antidilution rights applicable to the Common Stock of
the Company are set forth in the Amended and Restated Certificate of Incorporation, as amended from time to time (the “Articles”), a true and complete copy in its current form which is attached hereto as
Exhibit A. Such rights shall not be restated, amended or modified in any manner which affects the Holder differently than the holders of Common Stock without such Holder’s prior written consent. The Company shall promptly
provide the Holder hereof with any restatement, amendment or modification to the Articles promptly after the same has been made. 
 11. Dissolutions, Liquidations, Mergers or Changes in Control. 
 (a) Dissolution or Liquidation.
In the event of the proposed dissolution or liquidation of the Company, the Company shall notify the Holder as soon as practicable prior to the effective date of such proposed transaction. To the extent it has not been previously exercised, the
Warrant will terminate immediately prior to the consummation of such proposed action. 
 (b) Merger or Change in
Control. In the event of a merger of the Company with or into another corporation, or a Change in Control, the Warrant shall be assumed or an equivalent warrant substituted by the successor corporation or a parent or subsidiary of the

  

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successor corporation. In the event that the successor corporation or parent or subsidiary of the successor corporation in a merger or Change in Control refuses to assume or substitute for the
Warrant, then the Company shall notify the Holder in accordance with the provisions of Section 13 hereof of the pending Change of Control and Holder may then elect to exercise the Warrant not less than three (3) days prior to the
effective date of the Change of Control. 
 (c) “Change in Control” means the occurrence of any of the
following events: 
 (i) Any “person” (as such term is used in Sections 13(d) and 14(d) of the Securities
Exchange Act of 1934, as amended (the “Exchange Act”)) becomes the “beneficial owner” (as defined in Rule 13d-3 of the Exchange Act), directly or indirectly, of securities of the Company representing fifty percent
(50%) or more of the total voting power represented by the Company’s then outstanding voting securities; or 
 (ii) The consummation of the sale or disposition by the Company of all or substantially all of the Company’s assets; or 
 (iii) The consummation of a merger or consolidation of the Company with any other corporation, other than a merger or consolidation which would result in the voting securities of the Company
outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting securities of the surviving entity or its parent) at least fifty percent (50%) of the total voting power
represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately after such merger or consolidation. 
 12. Certificate of Adjustment. Whenever the Purchase Price is adjusted, as herein provided, the Company shall promptly deliver to the Holder a certificate of the Company’s chief financial
officer setting forth the Purchase Price after such adjustment and setting forth a brief statement of the facts requiring such adjustment. 
 13. 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 for the purpose of determining the holders thereof who are entitled to receive any dividend or other distribution, or any right to subscribe for, purchase, sell or otherwise acquire
or dispose of any shares of stock of any class or any other securities or property, or to receive any other right; 
 (b)
any reclassification of the capital stock of the Company, capital reorganization of the Company, consolidation or merger involving the Company, or sale or conveyance of all or substantially all of its assets; or 
 (c) any voluntary or involuntary dissolution, liquidation or winding-up of the Company; 
 then in each such event the Company will provide or cause to be provided to the Holder a written notice thereof. Such notice shall be provided at least ten
(10) days prior to the date specified in such notice on which any such action is to be taken. 
  

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 14. Representations, Warranties and Covenants. This Warrant is issued and delivered
by the Company and accepted by each Holder on the basis of the following representations, warranties and covenants made by the Company as of the date of issuance of this initial Warrant to the initial Holder: 
 (a) The Company has all necessary authority to issue, execute and deliver this Warrant and to perform its obligations hereunder. This
Warrant has been duly authorized issued, executed and delivered by the Company and is the valid and binding obligation of the Company, enforceable against the Company in accordance with its terms. 
 (b) The shares of Common Stock issuable upon the exercise of this Warrant have been duly authorized and reserved for issuance by the
Company and, when issued in accordance with the terms hereof, will be validly issued, fully paid and nonassessable. 
 (c)
The issuance, execution and delivery of this Warrant do not, and the issuance of the shares of Common Stock upon the exercise of this Warrant in accordance with the terms hereof will not, (i) violate or contravene the Company’s
Articles or by-laws, or any law, statute, regulation, rule, judgment or order applicable to the Company, (ii) violate, contravene or result in a breach or default under any contract, agreement or instrument to which the Company is a party or by
which the Company or any of its assets are bound or (iii) require the consent or approval of or the filing of any notice or registration with any person or entity. 
 (d) As long as obligations under the                      (the “Loan
Agreement”) are outstanding, the Company will provide to the Holder the financial and other information described in the Loan Agreement. 
 (e) As of the date hereof, the authorized capital stock of the Company consists of (i) 18,500,000 shares of Common Stock, of which 1,003,427 shares are issued and outstanding, 2,996,573 shares
are reserved for issuance upon the exercise of options issued pursuant to the Company’s 2002 Stock Plan and 46,176 shares are reserved for issuance upon the exercise of warrant, (ii) 6,000,000 shares of Series A Preferred Stock, of which
6,000,000 are issued and outstanding shares, and (iii) 8,101,102 shares of Series B Redeemable Preferred Stock, of which 8,101,101 are issued and outstanding shares. Attached hereto as Exhibit B is a capitalization table
summarizing the capitalization of the Company. At Holder’s request, not more than once per calendar quarter, the Company will provide Holder with a current capitalization table indicating changes, if any, to the number of outstanding shares of
common stock and preferred stock. 
 15. Amendment. The terms of this Warrant may be amended, modified or waived only
with the written consent of the Holder and the Company. 
 16. Representations and Covenants of the Holder. This Common
Stock Purchase Warrant has been entered into by the Company in reliance upon the following representations, warranties and covenants of the Holder, which by its execution hereof each Holder hereby confirms: 
 (a) Investment Purpose. The right to acquire Common Stock contained herein will be acquired for investment and not with a view to the
sale or distribution of any part thereof, and the Holder has no present intention of selling or engaging in any public distribution of the same except pursuant to a registration or exemption. 
  

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 (b) Accredited Investor. Holder is an “accredited investor” within the
meaning of the Securities and Exchange Rule 501 of Regulation D, as presently in effect. 
 (c) Private Issue. The Holder
understands (i) that the Common Stock issuable upon exercise of the Holder’s rights contained herein is not registered under the 1933 Act or qualified under applicable state securities laws on the ground that the issuance contemplated by
this Warrant will be exempt from the registration and qualifications requirements thereof, and (ii) that the Company’s reliance on such exemption is predicated on the representations set forth in this Section 16. 
 (d) Financial Risk. The Holder has such knowledge and experience in financial and business matters as to be capable of evaluating the
merits and risks of its investment and has the ability to bear the economic risks of its investment. 
 17. Notices,
Transfers, Etc. 
 (a) Any notice or written communication required or permitted to be given to the Holder may be
given by certified mail or delivered to the Holder at the address most recently provided by the Holder to the Company. 
 (b)
Subject to compliance with applicable federal and state securities laws, this Warrant may be transferred by the Holder with respect to any or all of the shares purchasable hereunder. Upon surrender of this Warrant to the Company, together with
the assignment notice annexed hereto duly executed, for transfer of this Warrant as an entirety by the Holder, the Company shall issue a new warrant of the same denomination to the assignee. Upon surrender of this Warrant to the Company, together
with the assignment hereof properly endorsed, by the Holder for transfer with respect to a portion of the shares of Common Stock purchasable hereunder, the Company shall issue a new warrant to the assignee, in such denomination as shall be requested
by the Holder hereof, and shall issue to such Holder a new warrant covering the number of shares in respect of which this Warrant shall not have been transferred. 
 (c) In case this Warrant shall be mutilated, lost, stolen or destroyed, the Company shall issue a new warrant of like tenor and denomination and deliver the same (i) in exchange and
substitution for and upon surrender and cancellation of any mutilated Warrant, or (ii) in lieu of any Warrant lost, stolen or destroyed, upon receipt of an affidavit of the Holder or other evidence reasonably satisfactory to the Company of the
loss, theft or destruction of such Warrant. 
 18. No Impairment. The Company will not, by amendment of its Articles or
through any reclassification, capital reorganization, consolidation, merger, sale or conveyance of assets, dissolution, liquidation, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance of performance of
any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the Holder. 
  

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 19. Governing Law. The provisions and terms of this Warrant shall be governed by and
construed in accordance with the internal laws of the State of California. 
 20. Successors and Assigns. This Warrant
shall be binding upon the Company’s successors and assigns and shall inure to the benefit of the Holder’s successors, legal representatives and permitted assigns. 
 21. Business Days. If the last or appointed day for the taking of any action required of the expiration of any rights granted herein
shall be a Saturday or Sunday or a legal holiday in California, then such action may be taken or right may be exercised on the next succeeding day which is not a Saturday or Sunday or such a legal holiday. 
 22. Value. The Company and the Holder agree that the value of this Warrant on the date of grant is $50. 
  

			
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

  

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 Subscription 
  

									
	To:	 	  
	 		 	Date:	 	  

 The undersigned hereby subscribes for
                     shares of Common Stock covered by this Warrant. The certificate(s) for such shares shall be issued in the name of the
undersigned or as otherwise indicated below: 
  

	
	  

	Signature
	
	  

	Name for Registration
	
	  

	Mailing Address

 Net Issue Election Notice 
  

									
	To:	 	  
	 		 	Date:	 	  

 The undersigned hereby elects under Section 4 to surrender the right to
purchase                      shares of Common Stock pursuant to this Warrant. The certificate(s) for such shares issuable upon such net issue
election shall be issued in the name of the undersigned or as otherwise indicated below: 
  

	
	  

	Signature
	
	  

	Name for Registration
	
	  

	Mailing Address

 Assignment 
 For value received _______________________________________ hereby sells, assigns and transfers unto _______________ 
 __________________________________________________________________________________________________________ 
 __________________________________________________________________________________________________________ 
 [Please print or typewrite name and address of Assignee] 
 the within Warrant, and does hereby irrevocably constitute and appoint _________________________________________________ 
 its attorney
to transfer the within Warrant on the books of the within named Company with full power of substitution on the premises. 
  

			
	Dated:	 	  

	
	In the Presence of:Warrant to purchase shares of Common Stock

 Exhibit 4.4 
 COMMON STOCK PURCHASE WARRANT 
  
 NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY
NOT BE TRANSFERRED UNLESS COVERED BY AN EFFECTIVE REGISTRATION STATEMENT UNDER SAID ACT, A “NO ACTION” LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER MEETING THE REQUIREMENTS OF RULE 144 OF THE
SECURITIES AND EXCHANGE COMMISSION, OR AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY TO THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 WARRANT TO PURCHASE 9,100 SHARES OF COMMON STOCK 
 Dated: October 25, 2005 
 THIS CERTIFIES THAT, for value received, Oxford Finance Corporation, (“Holder”) is entitled
to subscribe for and purchase Nine Thousand One Hundred (9,100) shares of the fully paid and non-assessable shares of Common Stock (“the Shares”) 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 “Common Stock” shall mean the Company’s currently authorized Common Stock, and any stock into which
such Common Stock may hereafter be exchanged. 
 1. Warrant Price. The Warrant Price shall initially be seventy one-hundredths dollars
($.70) per share, subject to adjustment as provided in Section 7 below. 
 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 on the earlier of: 
  

	 	(a)	5:00 P.M. Eastern Standard time on the seventh annual anniversary of this Warrant Agreement; or 

  

	 	(b)	the earlier termination of this Warrant pursuant to Section 3(e). 

 In the event that, although the Company shall have given notice of a transaction pursuant to subparagraph (b) hereof, the transaction does not close within 60 days after the day specified by the
Company, unless otherwise elected by the Holder any exercise of the Warrant subsequent to the giving of such notice shall be rescinded and the Warrant shall again be exercisable until terminated in accordance with this Paragraph 2. 
 3. Method of Exercise; 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 the Holder hereof, in whole
or in part, by the surrender of this Warrant (with a duly executed Notice of Exercise in the form attached hereto) at the principal office of the Company (as set forth in Section 19 below) and by payment to the Company, by check, of an amount
equal to the then applicable Warrant Price per share multiplied by the number of 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, the 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 promptly after
exercise of the Warrant and at the Company’s

  

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 COMMON STOCK PURCHASE WARRANT 
  
  

	 	 
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 Shares,
if any, with respect to which this Warrant shall not have been exercised, shall also be issued to the Holder hereof promptly after exercise of the Warrant. 

  

	 	(b)	Net Issue Exercise. In lieu of exercising this Warrant pursuant to Section 3(a), Holder may elect to receive shares equal to the value of this Warrant (or
of any portion thereof remaining unexercised) by surrender of this Warrant at the principal office of the Company together with notice of such election, in which event the Company shall issue to Holder the number of shares of the Company’s
Common Stock computed using the following formula: 

  

																			
	X	 	=	 	 Y (A-B)
	 		 		 		 		 		 		 	
		 		 	A	 		 		 		 		 		 		 	

 Where : 
 X = the number of shares of Common Stock to be issued to Holder in connection with the applicable net issue exercise. 
 Y = the number of shares of Common Stock purchasable under this Warrant (at the date of such calculation). 
 A = the Fair Market Value (defined below) of one share of the Company’s Common Stock (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 the Company’s Common Stock shall mean: 

(i) Subject to (iv) below, if the Common Stock is publicly traded, the average, over the ten (10) trading days prior to the
date of determination of fair market value, of (x) the average of the closing bid and asked prices of the Common Stock quoted in the Over-The-Counter Market Summary, or (y) the last reported sale price of the Common Stock or the closing
price quoted on the Nasdaq National Market System (“NMS”) or on any exchange on which the Common Stock is listed, whichever is applicable (with respect to both (x) or (y), as published in The Wall Street Journal; or 

(ii) [paragraph intentionally omitted] 
 (iii) Subject to (iv) below, if the Common Stock is not publicly traded, the per share fair market value of the Common Stock as determined in good faith by the Company’s Board of Directors.

 (iv) In the event of an exercise in connection with the Company’s initial public offering, the per share public offering
price as set forth on the cover page of the final prospectus relating to such offering (prior to underwriter discounts, commissions, concessions and expenses). 
 In the event of 3(c)(iii), above, the Company shall deliver to the Holder a certificate, to be signed by an authorized officer of the Company, setting forth the per share Fair

  

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 COMMON STOCK PURCHASE WARRANT 
  
  

 
Market Value of the Common Stock as determined by the Company’s Board of Directors. In connection with a proposed Acquisition (as defined in Section 3(e), such certification of the Fair
Market Value must be made to Holder at least ten (10) business days prior to the proposed closing of such Acquisition. 
  

	 	(d)	Automatic Exercise. To the extent this Warrant is not previously exercised, it shall be automatically exercised in accordance with Sections 3(b) and 3(c) hereof
(even if not surrendered) immediately before its expiration. 

  

	 	(e)	Treatment of Warrant Upon Acquisition of Company. 

 (i) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition (as defined below) in which the sole consideration is cash, either (a) Holder shall exercise its
conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) if Holder elects not to exercise the Warrant, this Warrant will expire upon the closing
of such Acquisition. The Company shall provide the Holder with written notice of its request relating to the foregoing (together with such reasonable information as the Holder may request in connection with such contemplated Acquisition giving rise
to such notice), which is to be delivered to Holder not less than ten (10) days prior to the closing of the proposed Acquisition. 
 (ii) Upon written request of the Company, Holder agrees that, in the event of a stock for stock Acquisition of the Company by a publicly traded acquirer if, on the record date for the Acquisition, the fair market value of the Shares (or
other securities issuable upon exercise of this Warrant) is equal to or greater than three (3x) times the Warrant Price, Company may require the Warrant to be deemed automatically exercised and the Holder shall participate in the Acquisition as
a holder of the Shares (or other securities issuable upon exercise of the Warrant) on the same terms as other holders of the same class of securities of the Company. 
 (iii) Upon the closing of any Acquisition other than those particularly described in subsections (i) or (ii) above, the successor entity shall assume the obligations of the Warrant, and the
Warrant shall be exercisable for the same securities, cash, and property as would be payable for the Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the record date for the Acquisition
and subsequent closing. The Warrant Price and/or number of Shares shall be adjusted accordingly. 
 (iv) For the purpose of this
Warrant, “Acquisition” means any sale, license, or other disposition of all or substantially all of the assets of the Company, or any reorganization, consolidation, or merger of the Company where the holders of the Company’s
securities before the transaction beneficially own less than 50% of the outstanding voting securities of the surviving entity after the transaction, other than in connection with an initial public offering. 
 4. Representations and Warranties of Holder and Restrictions on Transfer Imposed by the Securities Act of 1933. 
  

	 	(a)	Representations and Warranties of Holder. The Holder represents and warrants to the Company with respect to this purchase as follows: 

 

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 COMMON STOCK PURCHASE WARRANT 
  
  

 (i) The Holder has substantial experience in evaluating and investing in private
placement transactions of securities of companies similar to the Company so that the Holder is capable of evaluating the merits and risks of its investment in the Company and has the capacity to protect its interests. 
 (ii) The Holder is acquiring the Warrant and the Shares of Common Stock issuable upon exercise of the 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. The 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. In this connection, the Holder
understands that, in the view of the Securities and Exchange Commission (the “SEC”), the statutory basis for such exemption may be unavailable if this representation was predicated solely upon a present intention to hold the Securities for
the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the Securities or for a period of one year or any other fixed period in the future. 
 (iii) The Holder acknowledges that the Securities must be held indefinitely unless subsequently registered under the Act or an exemption
from such registration is available. The Holder is aware of the provisions of Rule 144 promulgated under the Act (“Rule 144”) which permits limited resale of securities purchased in a private placement subject to the satisfaction of
certain conditions, including, in case the securities have been held for more than one but less than two years, the existence of a public market for the shares, the availability of certain public information about the Company, the resale occurring
not less than one year after a party has purchased and paid for the security to be sold, the sale being through a “broker’s transaction” or in a transaction directly with a “market maker” (as provided by Rule 144(f)) and the
number of shares or other securities being sold during any three-month period not exceeding specified limitations. 
 (iv) The
Holder further understands that at the time the Holder wishes to sell the Securities there may be no public market upon which such a sale may be effected, and that even if such a public market exists, the Company may not be satisfying the current
public information requirements of Rule 144 and that in such event, the Holder may be precluded from selling the Securities under Rule 144 unless a) a one-year minimum holding period has been satisfied and b) the Holder was not at the time of the
sale nor at any time during the three-month period prior to such sale an affiliate of the Company. 
 (v) The Holder has had an
opportunity to discuss the Company’s business, management and financial affairs with its management and an opportunity to review the Company’s facilities. The Holder understands that such discussions, as well as the written information
issued by the Company, were intended to describe the aspects of the Company’s business and prospects which it believes to be material but were not necessarily a thorough or exhaustive description. 
  

	 	(b)	Legends. Each certificate representing the Shares issuable upon exercise of this Warrant, or upon any transfer of such Shares (other than a transfer registered
under the Act), shall be endorsed with the following legend: 

  

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 COMMON STOCK PURCHASE WARRANT 
  
  

 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED,
AND MAY NOT BE TRANSFERRED UNLESS COVERED BY AN EFFECTIVE REGISTRATION STATEMENT UNDER SAID ACT, A “NO ACTION” LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER MEETING THE REQUIREMENTS OF RULE
144 OF THE SECURITIES AND EXCHANGE COMMISSION, OR AN OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY TO THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 The Company need not enter into its stock register a transfer of Securities unless the conditions specified in the foregoing legend are
satisfied. The Company may also instruct its transfer agent not to register the transfer of any of the Shares unless the conditions specified in the foregoing legend are satisfied. 
  

	 	(c)	Removal of Legend and Transfer Restrictions. The legend relating to the Act endorsed on a certificate pursuant to paragraph 4(b) of this Warrant and the stop
transfer instructions with respect to the Securities represented by such certificate shall be removed and the Company shall issue a certificate without such legend to the Holder of the Securities 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) the Holder provides to the Company an opinion of counsel for the Holder in form and substance satisfactory to the Company, or a no-action letter or
interpretive opinion of the staff of the SEC reasonably satisfactory to the 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. 

 5. 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, the Holder (with respect to any exercises) or the transferee (with respect to any transfer) shall provide the Company with a representation in writing that the Holder or transferee is acquiring this
Warrant (as applicable) and the shares of Common Stock to be issued upon exercise, for investment purposes only and not with a view to any sale or distribution, or will provide the 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 Common Stock issuable upon exercise of this Warrant, other than a transfer registered under the Act, the Company must have received a legal opinion,
in form and substance satisfactory to the 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.

 As further condition to each transfer, the Holder shall surrender this Warrant to the Company and the transferee shall receive and accept a
Warrant, of like tenor and date, executed by the Company. 
 6. [paragraph intentionally omitted] 
 7. Stock Fully Paid; Reservation of Shares. All Shares, which may be issued upon the exercise of the rights represented by this Warrant, will, upon
issuance, be fully paid and non-assessable, and free from all taxes, liens, and charges with respect to the issue thereof. During the period within which the rights represented by this Warrant may be exercised, the Company will at all times have
authorized, and reserved for issuance upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its Common Stock to provide for the exercise of the rights represented by this Warrant. 
  

 Page 5 of 9 

 COMMON STOCK PURCHASE WARRANT 
  
  

 8. (a) Adjustment for Certain Events. In the event of changes in the outstanding Common Stock by
reason of stock dividends, split-ups, recapitalizations, reclassifications, mergers, consolidations, combinations or exchanges of shares, separations, reorganizations, liquidations, or the like, the number and class of shares available under the
Warrant in the aggregate and the Warrant Price shall be correspondingly adjusted, as appropriate, by the Board of Directors of the Company. The adjustment shall be such as will give the Holder of this Warrant upon exercise for the same aggregate
Warrant Price the total number, class and kind of shares as it would have owned had the Warrant been exercised prior to the event and had it continued to hold such shares until after the event requiring adjustment. 
 (b) [paragraph intentionally omitted] 
 9. Notice of Adjustments. Whenever any Warrant Price shall be adjusted pursuant to Section 8 hereof, the Company shall prepare a certificate signed by its chief financial officer 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 of shares issuable upon exercise of the 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 the Holder of this Warrant as set forth in Section 19 hereof. 
 10. “Market Stand-Off” Agreement. Holder hereby agrees that for a period of up to 180 days following the effective date of the first
registration statement of the Company covering common stock (or other securities) to be sold on behalf of the Company in an underwritten public offering, it will not, to the extent requested by the Company and any underwriter, sell or otherwise
transfer or dispose of (other than to designees or transferees who agree to be similarly bound) any of the Shares at any time during such period except common stock included in such registration. Upon request by the underwriters of such offering,
Holder agrees to enter into an agreement with such underwriters providing for “market stand-off” or “lockup” restrictions substantially similar to all officers and directors of the Company who hold securities of the Company or
options to acquire securities of the Company and all holders of one percent (1%) or more of the Company’s capital stock, on an as-converted to Common Stock basis. 
 11. Transferability of Warrant. This Warrant is transferable on the books of the Company at its principal office by the registered Holder hereof upon surrender of this Warrant properly endorsed,
subject to compliance with Section 5 and applicable federal and state securities laws. The Company shall issue and deliver to the transferee a new Warrant representing the Warrant so transferred. Upon any partial transfer, the 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 the Company. 
 12. No Fractional Shares. No fractional share of Common Stock will be issued in connection with any exercise hereunder, but in lieu of such
fractional share the 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 Common Stock upon the exercise of this Warrant shall be made without charge to the 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 the Company, and such certificates shall be issued in the name of the Holder. 
 14. No Stockholder Rights Until Exercise. This Warrant does not entitle the Holder hereof to any voting rights or other rights as a stockholder of the Company prior to the exercise hereof.

  

 Page 6 of 9 

 COMMON STOCK PURCHASE WARRANT 
  
  

 15. Registry of Warrant. The 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 the Company, and the 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 the 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, the 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 the Company on
the date hereof. 

  

	 	(b)	Successors. This Warrant shall be binding upon any successors or assigns of the Company. 

  

	 	(c)	Governing Law. This Warrant shall be governed by and construed in accordance with the laws of the State of California. 

  

	 	(d)	Headings. The headings used in this Warrant are used for convenience only and are not to be considered in construing or interpreting this Warrant.

  

	 	(e)	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 California, then such action may be taken or such right may be exercised on the next succeeding day not a legal holiday. 

 18. No Impairment. The Company shall not by any action including, without limitation, amending its certificate of incorporation or by-laws, any
reorganization, transfer of assets, consolidation, merger, share exchange 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 the Warrants or impair the
ability of the Holder(s) to realize upon the intended economic value hereof, 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 to protect the
rights of the Holder(s) hereof against impairment. 
 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 required, and postage prepaid, or otherwise delivered by hand or by messenger, addressed as set forth below, or at such other address as the Company or the Holder
hereof shall have furnished to the other party. 
  

			
	If to the Company:	  	 Codexis, Inc.
 200 Penobscot
Drive
 Redwood City, CA 94063

		  	Attn: Finance Director
		
	If to the Holder:	  	 Oxford Finance Corporation
 133 N. Fairfax Street
 Alexandria, VA 22314

		  	Attn: Chief Financial Officer

  

 Page 7 of 9 

 COMMON STOCK PURCHASE WARRANT 
  
  

 IN WITNESS WHEREOF, Codexis, Inc. has caused this Warrant to be executed by its officers thereunto duly
authorized. 
 Dated as of October 25, 2005. 
  

			
	Codexis, Inc.
		
	By:	 	 /s/ Tassos Gianakakos

	Name:	 	Tassos Gianakakos
	Title:	 	Senior Vice President

  

 Page 8 of 9 

 COMMON STOCK PURCHASE WARRANT 
  
  

 NOTICE OF EXERCISE 
  

							
	TO:	 	  
	 		 	
		 	  
	 		 	
		 	  
	 		 	

 1. The undersigned, Oxford Finance Corporation (“Holder”) elects to acquire shares of the
Common Stock of Codexis, Inc. (the “Company”), pursuant to the terms of the Common Stock Purchase Warrant dated October 25, 2005 (the “Warrant”). 
 2. The Holder exercises its rights under the Warrant as set forth below: 
  

	 	(    )	The Holder elects to purchase                      shares of
Common Stock as provided in Section 3(a) and 3(c) of the Warrant and tenders herewith a check in the amount of $             as payment of the purchase price.

  

	 	(    )	The Holder elects to convert the purchase rights into shares of Common Stock as provided in Section 3(b) and 3(c) of the Warrant. 

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

							
	Name:	 	  
	 		 	
				
	Address:	 	  
	 		 	
				
	Taxpayer I.D.:	 	  
	 		 	

 Oxford Finance Corporation 
  

			
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  

		
	Date:	 	  

  

 Page 9 of 9

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