Document:

Warrant to purchase shares of Common Stock issued to Oxford Finance Corporation

 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otherwise elected by the Holder any exercise of the Warrant subsequent to the giving of such notice shall be rescinded and the Warrant shall again be exercisable until terminated in accordance with this Paragraph 2. 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 

  

 Page 2 of 9 

 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. 
  

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 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. 
  

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 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

  

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 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 9Form of Warrant to purchase shares of Series D Preferred Stock

 Exhibit 4.5 
 THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT THE PRIOR WRITTEN CONSENT OF THE COMPANY OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF
COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. 
 THE SALE OF THESE SECURITIES HAS NOT BEEN QUALIFIED WITH ANY STATE SECURITIES AUTHORITIES. THE RIGHTS OF ALL PARTIES TO THIS WARRANT ARE EXPRESSLY CONDITIONED UPON SUCH QUALIFICATION BEING OBTAINED UNLESS THE SALE IS
SO EXEMPT. 
 THIS WARRANT MAY NOT BE EXERCISED EXCEPT IN COMPLIANCE WITH ALL APPLICABLE FEDERAL AND STATE SECURITIES LAWS TO THE REASONABLE SATISFACTION OF
THE COMPANY AND LEGAL COUNSEL FOR THE COMPANY. 
 Void after May 25, 2013 
 CODEXIS, INC. 
 STOCK PURCHASE WARRANT 
 THIS CERTIFIES THAT, for value received,
                     and its registered assigns (hereinafter called the “Holder”) is entitled to purchase from Codexis, Inc.,
a Delaware corporation (the “Company”) whose address is 200 Penobscot Drive, Redwood City, California 94063, at any time after the date specified in Section 1 hereof and ending at 5:00 p.m. Pacific Standard Time on the
Expiration Date, as such term is defined in Section 1 hereof, a number of shares of the Company’s New Preferred Stock (the “Warrant Shares”) equal to the quotient obtained by dividing (A) the product of (i) 0.30
and (ii) the Note Amount, by (B) the Effective Price (for purposes herein, the “Warrant Price”). This Warrant is a “Warrant” as defined in that certain Bridge Loan Agreement (the “Loan
Agreement”), dated as of May 25, 2006 by and among the Company and the investors set forth therein. This Warrant may be exercised in whole or in part, at the option of the Holder of this Warrant. Unless otherwise defined herein,
defined terms in this Warrant shall have the meanings ascribed to them in the Loan Agreement. 
 1. Term. This Warrant shall be
exercisable through May 25, 2013 (the “Expiration Date”). 
 2. Method of Exercise; Payment; Issuance of New
Warrant. Subject to Section 1 hereof, the purchase right represented by this Warrant may be exercised by the Holder, in whole or in part, by: 
 2.1 The surrender of this Warrant (with the notice of exercise form attached hereto as Attachment A and the Investment Representation Statement attached hereto as Attachment B duly executed) at the
principal office of the Company; and 

 2.2 The payment to the Company, by check, wire transfer, forgiveness of indebtedness, or any combination
of the foregoing of an amount equal to the then applicable Warrant Price per share multiplied by the number of Warrant Shares then being purchased. 
 If
this Warrant should be exercised in part only, the Company shall, upon surrender of this Warrant, execute and deliver a new Warrant evidencing the rights of the Holder thereof to purchase the balance of the Warrant Shares purchasable hereunder. Upon
receipt by the Company of this Warrant and such notice of exercise, together with, if applicable, the aggregate Warrant Price, at such office, or by the stock transfer agent or warrant agent of the Company at its office, the Holder shall be deemed
to be the holder of record of the applicable Warrant Shares, notwithstanding that the stock transfer books of the Company shall then be closed or that certificates representing such Warrant Shares shall not then be actually delivered to the Holder.
The Company shall pay any and all documentary stamp or similar issue or transfer taxes payable in respect of the issue or delivery of the Warrant Shares. 
 2.3 Net Exercise. 
 (a) In addition to and without limiting the rights of the Holder under the terms
of this Warrant, the Holder may elect to convert this Warrant or any portion thereof (the “Conversion Right”) into Warrant Shares, the aggregate value of which Warrant Shares shall be equal to the value of this Warrant or the portion
thereof being converted. The Conversion Right may be exercised by the Holder by surrender of this Warrant at the principal office of the Company together with notice of the Holder’s intention to exercise the Conversion Right, in which event the
Company shall issue to the Holder a 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 the holder upon exercise of Conversion Right.
		
	Y-  	  	The number of Warrant Shares issuable upon exercise of this Warrant (or such lesser number as are being exercised).
		
	A-  	  	The fair market value of one Warrant Share as at the time the Conversion Right is exercised pursuant to this Section 2.
		
	B-  	  	Effective Price for one Warrant Share under this Warrant (as adjusted to the date of such calculations).

 Notwithstanding the foregoing, the Warrant shall be deemed to have converted into Warrant Shares pursuant to this
Section 2.3(a) upon the Expiration Date if not previously exercised or converted before such date. 
  

 2 

 (b) Fair Market Value. For purposes of Section 2.3, “fair market value of one Warrant
Share” shall mean, as of any date: 
 (i) the last closing price per share of the Company’s Common Stock on the principal national
securities exchange on which the Common Stock is listed or admitted to trading; 
 (ii) the last reported sales price per share of the
Company’s Common Stock on the Nasdaq National Market or the Nasdaq Small-Cap Market (collectively, “Nasdaq”) if the Company’s Common Stock is not listed or traded on any such exchange; 
 (iii) the average of the bid and asked price per share as reported in the “pink sheets” published by the National Quotation Bureau, Inc. (the
“pink sheets”) if the Company’s Common Stock is not listed or traded on any exchange or Nasdaq; or 
 (iv) if such quotations
are not available, the fair market value per share of the New Preferred Stock issued in the Next Financing on the date such notice was received by the Company, as reasonably determined in good faith by the Board of Directors of the Company.

 3. Stock Fully Paid; Reservation of Warrant Shares. All shares of stock which may be issued upon the exercise of the rights
represented by this Warrant will, upon issuance, be fully paid and nonassessable, 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 the purpose of issue upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its stock to provide for the exercise of the rights represented by
this Warrant. In the event that there is an insufficient number of Warrant Shares reserved for issuance pursuant to the exercise of this Warrant, the Company will take appropriate action to authorize an increase in its capital stock to allow for
such issuance or similar issuance acceptable to the Holder. 
 4. Adjustment of Warrant Price and Number of Warrant Shares. The
number and kind of Warrant Shares 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: 
 4.1 Reclassification; Merger. In case of any reclassification or change of outstanding 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 in case of any consolidation or merger of the Company with or into another
corporation (other than a merger with another corporation in which the Company is a continuing corporation and which does not result in any reclassification or change of outstanding securities issuable upon exercise of this Warrant), or any other
corporate reorganization in which the Company shall not be the continuing or surviving entity of such consolidation, merger or reorganization, or any transaction in which in excess of 50% of the Company’s voting power is transferred, or any
sale of all or substantially all of the stock or assets of the Company, the Company shall, as condition precedent to such transaction, execute a new Warrant or cause such successor or purchasing corporation, as the case may be, to execute 

  

 3 

 
a new Warrant, providing that the Holder shall have the right to exercise such new Warrant and upon such exercise to receive, in lieu of each share of stock
theretofore issuable upon exercise of this Warrant, the kind and amount of shares of stock, other securities, money and property receivable upon such reclassification, change, merger or acquisition by a holder of one share of stock theretofore
issuable upon the exercise of this Warrant. Such new Warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section 4. The provisions of this Section 4.1
shall similarly apply to successive reclassifications, changes, mergers, and acquisitions. 
 4.2 Subdivision or Combination of Warrant
Shares. If the Company at any time while this Warrant remains outstanding and unexpired shall subdivide or combine its stock, the Warrant Price shall be proportionately decreased in the case of a subdivision or increased in the case of a
combination. 
 4.3 Stock Dividends. If the Company at any time while this Warrant is outstanding and unexpired shall pay a dividend
with respect to stock payable in, or make any other distribution with respect to stock (except any distribution specifically provided for in the foregoing Sections 4.1 and 4.2) of, stock, 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 (i) the numerator of
which shall be the total number of shares of stock outstanding immediately prior to such dividend or distribution, and (ii) the denominator of which shall be the total number of shares of stock outstanding immediately after such dividend or
distribution. 
 4.4 Adjustment of Number of Warrant Shares. Upon each adjustment in the Warrant Price, the number of shares of stock
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. 
 5. Fractional Warrant Shares. No fractional Warrant Shares will be issued in connection with any exercise hereunder, but in lieu of such fractional shares the Company shall make a cash payment therefor upon the basis of the
Warrant Price then in effect. 
 6. Compliance with Securities Act; Non-transferability of Warrant; Disposition of Shares of
Stock. 
 6.1 Compliance with Securities Act. The Holder, by acceptance hereof, agrees that this Warrant and the Warrant
Shares are being acquired for investment and that he, she or it will not offer, sell or otherwise dispose of this Warrant or any Warrant Shares except under circumstances which will not result in a violation of the Securities Act of 1933, as amended
(the “Act”). Upon exercise of this Warrant, the Holder hereof shall confirm in writing, in a form attached hereto as Attachment B, that the Warrant Shares so purchased are being acquired for investment and not with a view
toward distribution or resale. In addition, the Holder shall provide such additional information regarding such Holder’s financial and investment 

  

 4 

 
background, as the Company may reasonably request, as is relevant for purposes of determining the Holder’s suitability with respect to a purchase of the
Warrant Shares. This Warrant and all Warrant Shares (unless registered under the Act) shall be stamped or imprinted with a legend in substantially the following form: 
 THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT THE PRIOR WRITTEN CONSENT OF THE COMPANY AND WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED
THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION. 
 6.2 This Warrant may not be transferred or assigned in whole or in part without compliance with all applicable federal and state securities laws by the
transferor and the transferee (including the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, if such are requested by the Company). Notwithstanding the foregoing, no investment representation
letter or opinion of counsel shall be required for any transfer of this Warrant (or any portion thereof) or any shares of New Preferred Stock issued upon exercise hereof (or shares of Common Stock issuable upon conversion thereof) (i) in
compliance with customary transactions pursuant to Rule 144 or Rule 144A of the Act, or (ii) by gift, will or intestate succession by the Holder to his or her spouse or lineal descendants or ancestors or any trust for any of the foregoing or by
the Holder to its managers, partners, members, affiliates (as defined under Rule 404 promulgated under the Act) or subsidiaries, as applicable; provided, that in each of the foregoing cases, the transferee agrees in writing to be subject to the
terms of this Section 6.2. In addition, if the holder of the Warrant (or any portion thereof) or any New Preferred Stock issued upon exercise hereof delivers to the Company an unqualified opinion of counsel that no subsequent transfer of such
Warrant or New Preferred Stock shall require registration under the Act, the Company shall, upon such contemplated transfer, promptly deliver new documents/certificates for such Warrant or New Preferred Stock that do not bear the legend set forth in
Section 6.1 above. Subject to the provisions of this Warrant with respect to compliance with the Act, title to this Warrant may be transferred by endorsement (by the Holder executing an assignment form) and delivery in the same manner as a
negotiable instrument transferable by endorsement and delivery. Notwithstanding the foregoing, with respect to any offer, sale or other disposition of this Warrant or of securities into which this Warrant may be converted or for which it may be
exercised, the Holder will give written notice to the Company, describing briefly the manner thereof. Unless the Company reasonably determines that such transfer would violate applicable securities laws, and notifies the Holder thereof within ten
(10) business days after receiving notice of the transfer, the Holder may effect such transfer. Each Warrant thus transferred and each certificate representing the securities thus transferred shall bear a legend as to the applicable
restrictions on transferability in order to ensure compliance with the Act, unless in the opinion of counsel for the Company, such legend is not required in order to ensure compliance with the Act. The Company may issue stop transfer instructions to
its transfer agent in connection with such restrictions. 
  

 5 

 6.3 Disposition of Warrant Shares. Upon exercise of the Warrant Shares, the Holder will be
entitled to any registration rights granted to all holders of the New Preferred Stock issued in the Next Financing. With respect to any offer, sale or other disposition of any Warrant Shares prior to registration of such shares, the Holder and each
subsequent Holder of this Warrant agrees to give written notice to the Company prior thereto, describing briefly the manner thereof, together with a written opinion of such Holder’s counsel, if reasonably requested by the Company, to the effect
that such offer, sale or other disposition may be effected without registration or qualification (under the Act as then in effect or any federal or state law then in effect) of such Warrant Shares and indicating whether or not under the Act
certificates for such shares to be sold or otherwise disposed of require any restrictive legend as to applicable restrictions on transferability in order to ensure compliance with the Act; provided, however, that no such opinion of counsel or
no-action letter shall be necessary for a transfer without consideration by a Holder which is a partnership to a partner of such partnership, so long as such transfer is made pursuant to the terms of the partnership agreement, or to the transfer by
gift, will or intestate succession by the Holder to his or her spouse or lineal descendants or ancestors or any trust for the benefit of any of the foregoing if the transferee agrees in writing to be subject to the terms hereof to the same extent as
if he/she were an original Holder hereunder. Notwithstanding the foregoing, such Warrant Shares may be offered, sold or otherwise disposed of in accordance with Rule 144. 
 7. Rights of Shareholders. No Holder of this Warrant shall be entitled to vote or receive dividends or be deemed the holder of stock or any other securities of the Company which may at any time be
issuable on the exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon the Holder of this Warrant, as such, any of the rights of a shareholder of the Company or any right to vote for the election of
directors or upon any matter submitted to shareholders at any meeting thereof, or to give or withhold consent to any corporate action (whether upon any recapitalization, issuance of stock, reclassification of stock, change of par value or change of
stock to no par value, consolidation, merger, conveyance, or otherwise) or to receive notice of meetings, or to receive dividends or subscription rights or otherwise until this Warrant has been exercised and the Warrant Shares shall have become
deliverable, as provided herein. 
 8. Governing Law. The terms and conditions of this Warrant and all acts and transactions
pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with California law, without giving effect to principles of conflicts of law. 
 9. Miscellaneous. The headings in this Warrant are for purposes of convenience and reference only, and shall not be deemed to constitute a
part hereof. Neither this Warrant nor any term hereof may be changed, waived, discharged or terminated orally, but only by an instrument in writing signed by the Company and the registered Holder. Upon any Acquisition (as defined in the Restated
Certificate), or any stock dividend, combination, stock split, reclassification or recapitalization of the capital stock of the Company, or the Company’s initial public offering of its Common Stock, the Company shall provide to each Holder at
such time, ten (10) days’ prior 
  

 6 

 
notice to the closing of such events; provided, however, that the Majority Holders may waive such notice on behalf of all Holders. All notices and other
communications from the Company to the Holder shall be delivered by hand or mailed by first class registered or certified mail, postage prepaid, to the address furnished to the Company in writing by the Holder. 
 10. Loan Agreement. This Warrant is a Warrant referred to in the Loan Agreement and is entitled to all the benefits provided therein.

 (Remainder of Page Intentionally Left Blank) 
  

 7 

 IN WITNESS WHEREOF, the Company has caused this
Warrant to be duly executed by its officers, thereunto duly authorized this 25th day of May, 2006. 
  

			
	CODEXIS INC.
		
	By:	 	  

 SIGNATURE PAGE TO WARRANT 

 ATTACHMENT A 
 NOTICE OF EXERCISE 
 TO: CODEXIS, INC. 
 1. The undersigned hereby elects to purchase                      shares of New Preferred Stock of CODEXIS,
INC. as defined in and pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full, together with all applicable transfer taxes, if any. 
 1. The undersigned hereby elects to convert the attached Warrant into Warrant Shares in the manner specified in Section 2.3 of the Warrant. This
conversion is exercised with respect to                      of the Shares covered by the Warrant. 
 [Strike paragraph above that does not apply] 
 2. Please issue a certificate or certificates representing said shares of stock in the name of the undersigned or in such other name as is specified below: 
  

							
	Name:	 	  
	 	 	  	  
				
	Address:	 	  
	 		  	
				
		 	  
	 		  	
				
		 	  
	 		  	

 3. The undersigned represents that the aforesaid shares of stock are being acquired for the
account of the undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares. In support thereof, the
undersigned has executed an Investment Representation Statement attached hereto as Attachment B. 
  

			
	WARRANTHOLDER
	
	  

	(signature)
	
	  

	(title)
		
	Date:	 	  

 ATTACHMENT B 
 INVESTMENT REPRESENTATION STATEMENT 
  

					
	PURCHASER	 	:	  	
			
	COMPANY	 	:	  	CODEXIS, INC.
			
	SECURITY	 	:	  	
			
	AMOUNT	 	:	  	
			
	DATE	 	:	  	

 In connection with the purchase of the above-listed securities and underlying stock (the
“Securities”), I, the Purchaser, represent to the Company the following: 
 (a) I am purchasing these Securities for my own
account for investment purposes only and not with a view to, or for the resale in connection with, any “distribution” thereof for purposes of the Securities Act of 1933 (“Act”). 
 (b) I understand that the Securities have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends
upon, among other things, the bona fide nature of my investment intent as expressed herein. In this connection, I understand that, in the view of the Securities and Exchange Commission (“SEC”), the statutory basis for such exemption
may be unavailable if my representation was predicated solely upon a present intention to hold these 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. 
 (c) I further understand that the
Securities must be held indefinitely unless subsequently registered under the Act or unless an exemption from registration is otherwise available. Moreover, I understand that the Company is under no obligation to register the Securities. In
addition, I understand that the certificate evidencing the Securities will be imprinted with a legend which prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel for the
Company. 
 (d) I am aware of the provisions of Rule 144, promulgated under the Act, which, in substance, permits limited public resale of
“restricted securities” acquired, directly or indirectly, from the issuer thereof (or from an affiliate of such issuer), in a non-public offering subject to the satisfaction of certain conditions. 

 (e) I further understand that at the time I wish to sell the Securities there may be no public market
upon which to make such a sale. 
  

			
	  

	WARRANTHOLDER
	
	  

	(signature)
	
	  

	(title)
		
	Date:

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