First Amendment to Loan and Security Agreement



 [*] Certain information in this document has been omitted and filed separately with the Securities and
Exchange Commission. Confidential treatment has been requested with respect to the omitted portions. 
 EXHIBIT 10.1B 

 FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT 
 THIS FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”) is dated as of November 9, 2007 (the
“Amendment Date”), by and among CODEXIS, INC., a Delaware corporation (“Borrower”), WASABI ACQUISITION LLC, a Delaware limited liability company (“Wasabi”), GENERAL ELECTRIC CAPITAL CORPORATION, a
Delaware corporation acting in its capacity as agent (the “Agent”) for the lenders under the Credit Agreement (as defined below) (the “Lenders”), and the Lenders. 
 W I T N E S S E T H: 
 WHEREAS, Borrower, the Lenders and Agent are parties to that certain Loan and Security Agreement, dated as of September 28, 2007 (as the same may be amended, supplemented and modified from
time to time, the “Credit Agreement”; capitalized terms used herein have the meanings given to them in the Credit Agreement except as otherwise expressly defined herein), pursuant to which Lenders have agreed to provide to Borrower
certain loans and other extensions of credit in accordance with the terms and conditions thereof; 
 WHEREAS, Borrower
has requested that Agent and Lenders amend certain provisions of the Credit Agreement, in each case in accordance with and subject to the terms and conditions set forth herein. 
 NOW, THEREFORE, in consideration of the premises, the covenants and agreements contained herein, and other good and valuable
consideration, the receipt and adequacy of which are hereby acknowledged, Borrower, the Lenders and Agent hereby agree as follows: 
 1. Acknowledgment of Obligations. Borrower hereby acknowledges, confirms and agrees that as of the close of business on the Amendment Date, Borrower is indebted to the Lenders in respect of the Term Loans in the aggregate
principal amount of $15,000,000. All such Term Loans, together with interest accrued and accruing thereon, and fees, costs, expenses and other charges owing by Borrower to Agent and Lenders under the Credit Agreement and the other Debt Documents,
are unconditionally owing by Borrower to Agent and Lenders, without offset, defense or counterclaim of any kind, nature or description whatsoever except as may be limited by applicable bankruptcy, insolvency, reorganization, moratorium or other
similar laws relating to or affecting creditor’s rights generally. 
 2. Amendments to Credit Agreement.
Subject to the terms and conditions of this Amendment (including, without limitation, the conditions to effectiveness set forth in Section 6 below), and effective as of the Effective Date (as such term is defined in Section 6
below), the Credit Agreement is hereby amended as follows: 
 (a) The penultimate paragraph in Section 3.1 of the
Credit Agreement is hereby amended by (1) deleting the word “or” at the end of clause (b) thereof, (2) deleting the period at








 
the end of clause (c) thereof and inserting, in lieu thereof, the language “; or”, and (3) inserting the following new clause (d) at the end thereof: 
 “(d) all funds from time to time on deposit in that certain deposit account number [*] maintained with Wells Fargo Bank, N.A. (such
funds, the “WF Collateral”, and such account, the “WF Cash Collateral Account”); provided, however, that only $1,750,000 in WF Collateral deposited in the WF Cash Collateral Account shall be subject to
exclusion from the Collateral under this clause (d).” 
 (b) Section 5.7 of the Credit Agreement is hereby
deleted in its entirety and the following new Section 5.7 is hereby inserted in lieu thereof: 
 “    5.7. Collateral. Borrower is, and will remain, the sole and lawful owner, and in possession of, the Collateral, and has the sole right and lawful authority to grant the security interest described in
this Agreement. The Collateral is, and will remain, free and clear of all liens, claims and encumbrances of any kind whatsoever, except for (a) liens in favor of Agent, on behalf of itself and Lenders, to secure the Obligations, (b) liens
(i) with respect to the payment of taxes, assessments or other governmental charges or (ii) of suppliers, carriers, materialmen, warehousemen, workmen or mechanics and other similar liens, in each case imposed by law and arising in the
Ordinary Course of Business, and securing amounts that are not yet due or that are being contested in good faith by appropriate proceedings diligently conducted and with respect to which adequate reserves or other appropriate provisions are
maintained on the books of Borrower or its Subsidiaries in accordance with GAAP and which do not involve, in the judgment of Agent, any risk of the sale, forfeiture or loss of any of the Collateral (a “Permitted Contest”),
(c) zoning restrictions, easements, rights of way, encroachments or other restrictions on the use of, and other minor defects or irregularities in title with respect to, any real property of Borrower or its Subsidiaries so long as the same do
not materially impair the use of such real property by Borrower or such Subsidiary, (d) purported liens evidenced by the filing of precautionary UCC financing statements relating solely to operating leases of personal property entered into in
the Ordinary Course of Business, (e) liens in favor of customs and revenue authorities arising as a matter of law to secure payment of customs duties in connection with the importation of goods, (f) liens existing on the date hereof and
set forth on Schedule B hereto, (g) liens securing Indebtedness (as defined below) permitted under Section 7.2(c) below, provided that (i) such liens exist prior to the acquisition of, or attach substantially simultaneous with,
or within 20 days after the, acquisition, repair, improvement or construction of, such property financed by such Indebtedness and (ii) such liens do not extend to any property of Borrower or its Subsidiaries other than the property (and

  

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Exchange Commission. Confidential treatment has been requested with respect to the omitted portions 







 
proceeds thereof) acquired or built, or the improvements or repairs, financed by such Indebtedness, (h) licenses described in Section 7.3(b) below, and (i) liens of Wells Fargo
Bank, N.A. in the WF Collateral maintained in the WF Cash Collateral Account securing the Indebtedness permitted under Section 7.2(i) (all of such liens described in the foregoing clauses (a) through (i) are called “Permitted
Liens”). “Ordinary Course of Business” means, with respect to Borrower and its Subsidiaries, the operation of the business of Borrower and its Subsidiaries consistent with Borrower’s business plan as of the Closing Date, it
being understood and acknowledged by the Lenders that the business of Borrower and/or its Subsidiaries involves entering into corporate collaborations in the fields of energy, chemicals, carbon management and pharmaceuticals pursuant to exclusive
and non-exclusive licenses of Intellectual Property.” 
 (c) Section 7.2 of the Credit Agreement is hereby
amended by (1) deleting the word “and” at the end of clause (g) thereof, (2) deleting the period at the end of clause (h) thereof and inserting, in lieu thereof, the language “; and”, and (3) inserting
the following new clause (i) thereto: 
 “(i) Indebtedness consisting of reimbursement obligations owing to Wells Fargo
Bank, N.A. for one or more standby letters of credit issued from time to time in favor of Borrower in a face amount not to exceed $1,750,000 in the aggregate at any time.” 
 (d) Section 7.10 of the Credit Agreement is hereby deleted in its entirety and the following new Section 7.10 is
hereby inserted in lieu thereof: 
 “    7.10. Deposit Accounts and Securities Accounts. Other
than with respect to (1) deposit accounts used solely to fund payroll and withholding taxes and (2) the WF Cash Collateral Account, Borrower will not directly or indirectly maintain or establish any deposit account or securities account,
unless Agent, Borrower and the depository institution or securities intermediary at which the account is or will be maintained enter into a deposit account control agreement or securities account control agreement, as the case may be (an
“Account Control Agreement”), in form and substance satisfactory to Agent (which agreement shall provide that such depository institution or securities intermediary shall comply with all instructions of Agent without further consent
of Borrower, including, without limitation, an instruction by Agent to follow a notice of exclusive control or similar notice (such notice, a “Notice of Exclusive Control”)), prior to or concurrently with the establishment of such
deposit account or 
  

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securities account (or in the case of any such deposit account or securities account maintained as of the date hereof, prior to or concurrently with the entering into this Agreement). Agent may
give a Notice of Exclusive Control with respect to any deposit account or securities account at any time at which an Event of Default has occurred and is continuing. Borrower hereby agrees that it shall not maintain at any time in the WF Cash
Collateral Account funds in excess of the lesser of (a) $1,750,000 and (b) 105% of the aggregate outstanding face amount at such time of all standby letters of credit issued by Wells Fargo Bank, N.A. in favor of Borrower in accordance with
the terms and conditions of Section 7.2(i).” 
 3. Amendment to Perfection Certificate and Post Closing
Obligation Letter. 
 (a) Subject to the terms and conditions of this Amendment (including, without limitation, the
conditions to effectiveness set forth in Section 6 below), and effective as of the Effective Date (as such term is defined in Section 6 below), Section 6 and Section 7 of the Perfection Certificate shall be amended
in the manner described on Schedule A hereto. 
 (b) Subject to the terms and conditions of this Amendment (including,
without limitation, the conditions to effectiveness set forth in Section 6 below), and effective as of the Effective Date (as such term is defined in Section 6 below), Paragraph 4 of that certain Post Closing Obligations
Letter, dated as of September 28, 2007, by and among the parties hereto, is amended to delete the reference to deposit account number [*] maintained by Borrower with Wells Fargo Bank, N.A. 
 4. No Other Amendments. Except for the amendments set forth and referred to in Section 2 and Section 3
above, the Credit Agreement and the Perfection Certificate shall remain unchanged and in full force and effect. Nothing in this Amendment is intended, or shall be construed, to constitute a novation or an accord and satisfaction of any of
Borrower’s Obligations or to modify, affect or impair the perfection or continuity of Agent’s security interests in, security titles to or other liens, for the benefit of itself and the Lenders, on any Collateral for the Obligations.

 5. Representations and Warranties. To induce Agent and Lenders to enter into this Amendment, Borrower does
hereby warrant, represent and covenant to Agent and Lenders that after giving effect to this Amendment (i) each representation or warranty of the Borrower set forth in the Credit Agreement is hereby restated and reaffirmed as true and correct
in all material respects on and as of the Amendment Date as if such representation or warranty were made on and as of the date hereof (except to the extent that any such representation or warranty expressly relates to a prior specific date or
period), (ii) no Default or Event of Default has occurred and is continuing as of the date hereof and (iii) Borrower has the power and is duly authorized to enter into, deliver and perform this Amendment and this Amendment is the legal,
valid and binding obligation of the Borrower enforceable against the Borrower in accordance with its terms. 
 6.
Condition Precedent to Effectiveness of this Amendment. This Amendment shall become effective as of the Amendment Date, and the amendments set forth in Section 2 and Section 3 hereof shall be deemed to be effective
as of September 28, 2007 (the “Effective Date”), upon the receipt by Agent of each of the following, in each case in form and substance 
  

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satisfactory to Agent and Lenders: 
 (a) one or more counterparts of this
Amendment duly executed and delivered by the Borrower, Agent and Lenders; and 
 (b) one or more counterparts of the attached
Confirmation duly executed and delivered by Wasabi. 
 7. Release. 
 (a) In consideration of the agreements of Agent and Lenders contained herein and for other good and valuable consideration, the receipt and
sufficiency of which is hereby acknowledged, Borrower and Wasabi (by executing the Confirmation attached hereto), on behalf of themselves and their successors, assigns, and other legal representatives, hereby absolutely, unconditionally and
irrevocably release, remise and forever discharge Agent and Lenders and their respective successors and assigns, and their respective present and former shareholders, affiliates, subsidiaries, divisions, predecessors, directors, officers, attorneys,
employees, the agents and other representatives (Agent and Lenders, and all such other Persons being hereinafter referred to collectively as the “Releasees” and individually as a “Releasee”), of and from all
demands, actions, causes of action, suits, covenants, contracts, controversies, agreements, promises, sums of money, accounts, bills, reckonings, damages and any and all other claims, counterclaims, defenses, rights of set-off, demands and
liabilities whatsoever (individually, a “Claim” and collectively, “Claims”) of every name and nature, known or unknown, suspected or unsuspected, both at law and in equity, which Borrower or Wasabi or any of their
respective successors, assigns, or other legal representatives may now or hereafter own, hold, have or claim to have against the Releasees or any of them for, upon, or by reason of any circumstance, action, cause or thing whatsoever which arises at
any time on or prior to the day and date of this Amendment, for or on account of, or in relation to, or in any way in connection with this Amendment or transactions thereunder or related thereto. 
 (b) Each of Borrower and Wasabi (by executing the Confirmation attached hereto) understands, acknowledges and agrees that its release set
forth above may be pleaded as a full and complete defense and may be used as a basis for an injunction against any action, suit or other proceeding which may be instituted, prosecuted or attempted in breach of the provisions of such release.

 (c) Each of Borrower and Wasabi (by executing the Confirmation attached hereto)agrees that no fact, event, circumstance,
evidence or transaction which could now be asserted or which may hereafter be discovered shall affect in any manner the final, absolute and unconditional nature of the release set forth above. 
 8. Covenant Not To Sue. Each of Borrower and Wasabi (by executing the Confirmation attached hereto), on behalf of themselves
and their respective successors, assigns, and other legal representatives, hereby absolutely, unconditionally and irrevocably, covenant and agree with and in favor of each Releasee that it will not sue (at law, in equity, in any regulatory

  

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proceeding or otherwise) any Releasee on the basis of any Claim released, remised and discharged by Borrower or Wasabi pursuant to Section 7 above. If Borrower or Wasabi or any of
their respective successors, assigns or other legal representatives violates the foregoing covenant, Borrower and Wasabi, for itself and its successors, assigns and legal representatives, jointly and severally agrees to pay, in addition to such
other damages as any Releasee may sustain as a result of such violation, all attorneys’ fees and costs incurred by any Releasee as a result of such violation. 
 9. Advice of Counsel. Each of the parties represents to each other party hereto that it has discussed this Amendment with its counsel. 
 10. Severability of Provisions. In case any provision of or obligation under this Amendment shall be invalid, illegal or
unenforceable in any applicable jurisdiction, the validity, legality and enforceability of the remaining provisions or obligations, or of such provision or obligation in any other jurisdiction, shall not in any way be affected or impaired thereby.

 11. Counterparts. This Amendment may be executed in multiple counterparts, each of which shall be deemed to be
an original and all of which when taken together shall constitute one and the same instrument. 
 12. GOVERNING
LAW. THIS AGREEMENT SHALL BE GOVERNED BY, AND CONSTRUED IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE STATE OF NEW YORK APPLICABLE TO CONTRACTS MADE AND PERFORMED IN SUCH STATE WITHOUT REGARD TO THE PRINCIPLES THEREOF REGARDING CONFLICTS OF
LAWS. 
 13. Entire Agreement. The Credit Agreement as and when amended through this Amendment embodies the entire
agreement between the parties hereto relating to the subject matter thereof and supersedes all prior agreements, representations and understandings, if any, relating to the subject matter thereof. 
 14. No Strict Construction, Etc. The parties hereto have participated jointly in the negotiation and drafting of this
Amendment. In the event an ambiguity or question of intent or interpretation arises, this Amendment shall be construed as if drafted jointly by the parties hereto and no presumption or burden of proof shall arise favoring or disfavoring any party by
virtue of the authorship of any provisions of this Amendment. Time is of the essence for this Amendment. 
 15. Costs and
Expenses. Borrower absolutely and unconditionally agree to reimburse Agent for all reasonable and documented out-of-pocket fees, costs and expenses, including all reasonable fees and expenses of one counsel or the allocated cost of internal
legal staff, incurred in the preparation, negotiation, execution and delivery of this Amendment and any other Debt Documents or other agreements prepared, negotiated, executed or delivered in 
  

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connection with this Amendment or transactions contemplated hereby. 
 [Signature Page to Follow] 
  

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 IN WITNESS WHEREOF, the parties hereto have caused this First Amendment to Loan and
Security Agreement to be duly executed and delivered as of the day and year specified at the beginning hereof. 
  

			
	 BORROWER:
  
 CODEXIS, INC.

		
	By:	 	/s/ Alan Shaw
	Name:	 	Alan Shaw
	Title:	 	President & CEO


  
 [Additional signature pages to follow] 
  
 SIGNATURE PAGE 
 FIRST AMENDMENT 








			
	 AGENT AND LENDER:
  
 GENERAL ELECTRIC CAPITAL CORPORATION

		
	By:	 	/s/ Daniela Gjenero
	Name:	 	Daniela Gjenero
	Title:	 	Duly Authorized Signatory


  
  

			
	 LENDER:
  
 OXFORD FINANCE CORPORATION

		
	By:	 	/s/ T.A. Lex
	Name:	 	T.A. Lex
	Title:	 	COO


  
 SIGNATURE PAGE 
 FIRST AMENDMENT 







 CONFIRMATION 
 The undersigned Guarantor hereby acknowledges and agrees to the terms and performance of the within and foregoing First Amendment to Loan
and Security Agreement, and hereby ratifies all the provisions of the Credit Agreement, its Guaranty and any other Debt Documents to which it is a party and confirms that all provisions of each such documents are in full force and effect.

 IN WITNESS WHEREOF, the undersigned has executed this Confirmation as of the day and year first above set forth. 
  

			
	WASABI ACQUISITION LLC
		
	By:	 	/s/ Alan Shaw
	Name:	 	Alan Shaw
	Title:	 	President & CEO


  
 SIGNATURE PAGE 
 CONFIRMATION AGREEMENT 







 Schedule A 
 Amendments to Perfection Certificate 
 Section 6 of the Perfection Certificate
is amended by adding the following disclosure: 
 Indebtedness of the Borrower arising under the Standby Letter of Credit
Agreement, dated as of June 8, 2007 by and between the Borrower and Wells Fargo Bank, National Association and any modifications, replacement, refinancing, refunding, renewal or extension thereof. 
 Section 7 of the Perfection Certificate is amended by adding the following disclosure: 
  

					
	Name of Holder of
Lien/Encumbrance	 	Description of Property
Encumbered	 	Borrower/Subsidiary
	Wells Fargo Bank, National Association	 	Cash	 	Codexis, Inc