Document:

Exhibit

Exhibit 10.4

June 28, 2019

John Nicols
200 Penobscot Drive
Redwood City, CA 94063

Re:     Amendment to Employment Agreement
Dear John,
You and Codexis, Inc. (the “Company”) are currently parties to an Employment Agreement, dated as of May 28, 2012, as amended on April 21, 2016 and November 16, 2017 (the “Employment Agreement”), which sets forth the terms of your employment with the Company and provides, among other things, that you will be entitled to receive certain severance payments and benefits upon certain qualifying terminations of employment with the Company.  Effective as of the date of this amendment (this “Amendment”), you and the Company hereby agree to amend the Employment Agreement as set forth herein.
Section 5(d) of the Employment Agreement is deleted and replaced in its entirety by the following:
“(d)    Termination in Contemplation of Change in Control or Within 90 Days Prior to a Change in Control. Notwithstanding anything to the contrary in Section 5(b) or 5(c), in the event Executive is terminated by the Company without Cause or resigns for Good Reason and (i) the event giving rise to such termination or resignation occurs at the direction of a person or entity that has entered into an agreement with the Company that contemplates a transaction that, if consummated, would constitute a Change in Control or (ii) such termination or resignation occurs within ninety (90) days prior to a Change in Control, then for all purposes hereunder, including Section 5(b) and 5(c), such termination or resignation shall be deemed to have occurred within the twelve (12) month period immediately following a Change in Control and Executive shall be entitled to the benefits set forth in Section 5(c) with such benefits to be paid, or commence being paid, upon the Date of Termination in the case of a termination or resignation under subclause (i) or the latest of the date the Release becomes effective and irrevocable, the date of the Change in Control or as otherwise provided in Section 13(d) hereof in the case of a termination or resignation under subclause (ii), but otherwise subject to the terms and conditions of Section 5(c).”    
All terms and provisions of the Employment Agreement not amended hereby, either expressly or by necessary implication, shall remain in full force and effect.  From and after the date of this Amendment, all references to the term “Employment Agreement” in this Amendment or the original Employment Agreement shall include the terms contained in this Amendment.

US-DOCS\107373471.1

Please indicate your acceptance of and agreement to the terms and conditions set forth in this Amendment by signing in the space below and returning the executed Amendment to the Company.  
Sincerely,

Codexis, Inc.

By:    /s/ Richard A. Sabalot        

Name:    Richard A. Sabalot

Title:    Senior Corporate Counsel

Accepted by:

/s/ John Nicols                
John Nicols

June 28, 2019                
Date

US-DOCS\107373471.1Exhibit

Exhibit 10.1A

SIXTH AMENDMENT TO LOAN AND SECURITY AGREEMENT
THIS SIXTH AMENDMENT to Loan and Security Agreement (this “Amendment”) is made effective as of July 11, 2019 (the “Amendment Date”) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and CODEXIS, INC., a Delaware corporation (“Borrower”).
WHEREAS, Bank and Borrower have entered into that certain Loan and Security Agreement, dated as of June 30, 2017 (as amended, supplemented, restated or otherwise modified from time to time, the “Loan Agreement”); and
WHEREAS, Bank and Borrower desire to amend certain provisions of the Loan Agreement as provided herein and subject to the terms and conditions set forth herein;
NOW, THEREFORE, in consideration of the promises, covenants and agreements contained herein, and other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, Bank and Borrower hereby agree as follows:
		
	1.
	Capitalized terms used herein but not otherwise defined shall have the respective meanings given to them in the Loan Agreement.

		
	2.
	Section 1.1 of the Loan Agreement is hereby amended by amending and restating clause (j) of the definition of “Permitted Indebtedness” therein as follows:

(j)    Indebtedness (in the aggregate outstanding amount of not greater than Six Hundred Fifty Thousand Dollars ($650,000) at any given time) consisting of the financing of insurance premiums in the ordinary course of business;
		
	3.
	Limitation of Amendment.

		
	a.
	The amendment set forth above is effective for the purposes set forth herein and shall be limited precisely as written and shall not be deemed to (a) be a consent to any amendment, waiver or modification of any other term or condition of any Loan Document, or (b) otherwise prejudice any right, remedy or obligation which the Bank or Borrower may now have or may have in the future under or in connection with any Loan Document, as amended hereby.

		
	b.
	This Amendment shall be construed in connection with and as part of the Loan Documents and all terms, conditions, representations, warranties, covenants and agreements set forth in the Loan Documents, except as herein amended, are hereby ratified and confirmed and shall remain in full force and effect.

		
	4.
	To induce the Bank to enter into this Amendment, Borrower hereby represents and warrants to the Bank as follows: 

		
	a.
	Immediately after giving effect to this Amendment (a) the representations and warranties contained in Article 5 of the Loan Agreement are true, accurate and complete in all material respects as of the date hereof (except to the extent such representations and warranties relate to an earlier date, in which case they are true and correct in all material respects as of such date), and (b) no Event of Default has occurred and is continuing;

BOS 48677184v2

		
	b.
	Borrower has the power and due authority to execute and deliver this Amendment and to perform its obligations under the Loan Agreement, as amended by this Amendment; 

		
	c.
	The organizational documents of Borrower delivered to the Bank on the Closing Date, and updated pursuant to subsequent deliveries by the Borrower to the Bank, if any, remain true, accurate and complete and have not been amended, supplemented or restated and are and continue to be in full force and effect;

		
	d.
	The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not and will not contravene (i) any law or regulation binding on or affecting Borrower, (ii) any contractual restriction with a Person binding on Borrower, (iii) any order, judgment or decree of any court or other governmental or public body or authority, or subdivision thereof, binding on Borrower, or (iv) the organizational documents of Borrower;

		
	e.
	The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not require any order, consent, approval, license, authorization or validation of, or filing, recording or registration by Borrower with, or exemption by any governmental or public body or authority, or subdivision thereof, binding on Borrower, except as already has been obtained or made; and

		
	f.
	This Amendment has been duly executed and delivered by Borrower and is the binding obligation of Borrower, enforceable against Borrower in accordance with its terms, except as such enforceability may be limited by bankruptcy, insolvency, reorganization, liquidation, moratorium or other similar laws of general application and by general equitable principles. 

		
	5.
	Except as expressly set forth herein, the Loan Agreement shall continue in full force and effect without alteration or amendment.  This Amendment and the Loan Documents represent the entire agreement about this subject matter and supersede prior negotiations or agreements.

		
	6.
	This Amendment shall be deemed effective as of the Amendment Date upon the due execution and delivery to the Bank of this Amendment by each party hereto.

		
	7.
	This Amendment may be executed in any number of counterparts, each of which shall be deemed an original, and all of which, taken together, shall constitute one and the same instrument.

		
	8.
	This Amendment and the rights and obligations of the parties hereto shall be governed by and construed in accordance with the laws of the State of California.

[Balance of Page Intentionally Left Blank]

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BOS 48677184v2

IN WITNESS WHEREOF, the parties hereto have caused this Sixth Amendment to Loan and Security Agreement to be executed as of the date first set forth above.
	
			
	BORROWER:
	 
	 

	 
	 
	 

	CODEXIS, INC., A DELAWARE CORPORATION
	 
	 

	 
	 
	 

	 
	 
	 

	By /s/ Gordon Sangster
	 
	 

	Name: Gordon Sangster
	 
	 

	Title:   CFO
	 
	 

	 
	 
	 

	 
	 
	 

	BANK:
	 
	 

	 
	 
	 

	WESTERN ALLIANCE BANK, AN ARIZONA CORPORATION
	 
	 

	 
	 
	 

	 
	 
	 

	By /s/ Bill Wickline
	 
	 

	Name: Bill Wickline
	 
	 

	Title: SVP, Director of Portfolio Management
	 
	 

BOS 48677184v4Exhibit

Exhibit 10.1B
SEVENTH AMENDMENT TO LOAN AND SECURITY AGREEMENT
THIS SEVENTH AMENDMENT to Loan and Security Agreement (this “Amendment”) is made effective as of September 30, 2019 (the “Amendment Date”) and made by and among WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and CODEXIS, INC., a Delaware corporation (“Borrower”).
WHEREAS, Bank and Borrower have entered into that certain Loan and Security Agreement, dated as of June 30, 2017 (as amended, supplemented, restated or otherwise modified from time to time, the “Loan Agreement”); and
WHEREAS, Bank and Borrower desire to amend certain provisions of the Loan Agreement as provided herein and subject to the terms and conditions set forth herein;
NOW, THEREFORE, in consideration of the promises, covenants and agreements contained herein, and other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, Bank and Borrower hereby agree as follows:
		
	1.
	Capitalized terms used herein but not otherwise defined shall have the respective meanings given to them in the Loan Agreement.

		
	2.
	Section 1.1 of the Loan Agreement is hereby amended by adding the following definition thereto in alphabetical order:

“Seventh Amendment Date” is September 30, 2019.

		
	3.
	Section 1.1 of the Loan Agreement is hereby further amended by amending and restating the following definitions therein as follows:

“Amortization Date” is November 1, 2021.

“Draw Period” is the period commencing on the Closing Date and ending on the earlier of (i) September 30, 2020 and (ii) the occurrence of an Event of Default.

“Maturity Date” is October 1, 2023.

 “Revolving Facility Termination Fee” is an additional fee payable by Borrower to Bank, upon the election by Borrower to terminate the Revolving Facility, in amount equal to:
(i)    for a termination on or before the first anniversary of the Seventh Amendment Date, three percent (3.00%) of the Revolving Line;
(ii)    a termination after the first anniversary of the Seventh Amendment Date and on or before the second anniversary of the Seventh Amendment Date, two percent (2.00%) of the Revolving Line; and
(iii)    a termination after the second anniversary of the Seventh Amendment Date and on or before the third anniversary of the Seventh Amendment Date, one percent (1.00%) of the Revolving Line.
		
	4.
	Section 2.6 of the Loan Agreement is hereby further amended by replacing “.” at the end of Section 2.6(g) with “; and” and adding the following Section 2.6(h) thereto:

(h)    Seventh Amendment Fee.  On the Seventh Amendment Date, a fully earned and non-refundable fee in the amount of Twelve Thousand Five Hundred Dollars ($12,500.00).

BOS 48677184v2

		
	5.
	Section 5.16 of the Loan Agreement is hereby amended and restated in its entirety as follows:

5.16    Accounts.  All of Borrower’s or any Subsidiary’s operating, depository or investment accounts maintained or invested with a Person other than Bank are set forth on the Perfection Certificate, provided that such accounts disclosed on the Perfection Certificate are hereby deemed updated with the updated Perfection Certificate delivered to Bank as of the Fourth Amendment Date.  On and after (i) the 60th day following the Closing Date and prior to October 1, 2019, at any time that the aggregate balance of Borrower’s accounts held with Bank and Bank’s Affiliates is less than $15,000,000 for three (3) successive Business Days or less than $14,000,000 on any given day, and (ii) October 1, 2019, at any time that the aggregate balance of Borrower’s accounts held with Bank and Bank’s Affiliates is less than the sum of (A) $5,000,000 plus (B) the outstanding aggregate principal amount of the Term Loans, for three (3) successive Business Days, none of Borrower’s nor any domestic U.S. Subsidiary’s operating, depository or investment accounts are maintained or invested with a Person other than Bank.  Notwithstanding the foregoing, on and after the 60th day following the Closing Date, neither the Borrower nor any of its domestic Subsidiaries maintains any operating, depository or investment accounts maintained or invested with any Person other than the Bank unless such account (A) is subject to an account control agreement in favor of the Bank in such form and substance as is reasonably acceptable to the Bank, (B) is a deposit account exclusively used for payroll, payroll taxes and other employee wage and benefit payments to or for the benefit of Borrower’s or any domestic U.S. Subsidiary’s employees and identified to Bank by Borrower as such, or (C) is the Exempt Account (provided that such account and is maintained solely in connection with the Transfers of shares of CO2 Solutions, Inc. held by the Borrower on the Closing Date and any cash balance in such account in excess of Five Hundred Thousand Dollars ($500,000.00) is transferred to another account of Borrower that is maintained in accordance with Section 6.7 within five (5) Business Days). 

Furthermore, the aggregate amount of cash and cash equivalent assets held by direct and indirect Foreign Subsidiaries of Borrower in accounts not subject to a control agreement in favor of the Bank (and in such form and substance as is reasonably acceptable to the Bank) does not exceed One Million Two Hundred Thousand Dollars ($1,200,000.00) (of which no more than Four Hundred Thousand Dollars ($400,000.00) may be maintained in accounts other than the accounts for Codexis Laboratories India Pte., Ltd.).

		
	6.
	Limitation of Amendment.

		
	a.
	The amendments set forth above are effective for the purposes set forth herein and shall be limited precisely as written and shall not be deemed to (a) be a consent to any amendment, waiver or modification of any other term or condition of any Loan Document, or (b) otherwise prejudice any right, remedy or obligation which the Bank or Borrower may now have or may have in the future under or in connection with any Loan Document, as amended hereby.

		
	b.
	This Amendment shall be construed in connection with and as part of the Loan Documents and all terms, conditions, representations, warranties, covenants and agreements set forth in the Loan Documents, except as herein amended, are hereby ratified and confirmed and shall remain in full force and effect.

		
	7.
	To induce the Bank to enter into this Amendment, Borrower hereby represents and warrants to the Bank as follows: 

		
	a.
	Immediately after giving effect to this Amendment (a) the representations and warranties contained in Article 5 of the Loan Agreement are true, accurate and complete in all material respects as of the date hereof (except to the extent such representations and warranties relate to an earlier date, in which case they are true and correct in all material respects as of such date), and (b) no Event of Default has occurred and is continuing;

2
BOS 48677184v2

		
	b.
	Borrower has the power and due authority to execute and deliver this Amendment and to perform its obligations under the Loan Agreement, as amended by this Amendment; 

		
	c.
	The organizational documents of Borrower delivered to the Bank on the Closing Date, and updated pursuant to subsequent deliveries by the Borrower to the Bank, if any, remain true, accurate and complete and have not been amended, supplemented or restated and are and continue to be in full force and effect;

		
	d.
	The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not and will not contravene (i) any law or regulation binding on or affecting Borrower, (ii) any contractual restriction with a Person binding on Borrower, (iii) any order, judgment or decree of any court or other governmental or public body or authority, or subdivision thereof, binding on Borrower, or (iv) the organizational documents of Borrower;

		
	e.
	The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not require any order, consent, approval, license, authorization or validation of, or filing, recording or registration by Borrower with, or exemption by any governmental or public body or authority, or subdivision thereof, binding on Borrower, except as already has been obtained or made; and

		
	f.
	This Amendment has been duly executed and delivered by Borrower and is the binding obligation of Borrower, enforceable against Borrower in accordance with its terms, except as such enforceability may be limited by bankruptcy, insolvency, reorganization, liquidation, moratorium or other similar laws of general application and by general equitable principles. 

		
	8.
	Except as expressly set forth herein, the Loan Agreement shall continue in full force and effect without alteration or amendment.  This Amendment and the Loan Documents represent the entire agreement about this subject matter and supersede prior negotiations or agreements.

		
	9.
	This Amendment shall be deemed effective as of the Amendment Date upon the due execution and delivery to the Bank of this Amendment by each party hereto [and the payment by Borrower to the Bank of fee due under Section 2.6(g) of the Loan Agreement as amended hereby].

		
	10.
	This Amendment may be executed in any number of counterparts, each of which shall be deemed an original, and all of which, taken together, shall constitute one and the same instrument.

		
	11.
	This Amendment and the rights and obligations of the parties hereto shall be governed by and construed in accordance with the laws of the State of California.

[Balance of Page Intentionally Left Blank]

3
BOS 48677184v2

IN WITNESS WHEREOF, the parties hereto have caused this Seventh Amendment to Loan and Security Agreement to be executed as of the date first set forth above.
	
			
	BORROWER:
	 
	 

	 
	 
	 

	CODEXIS, INC., A DELAWARE CORPORATION
	 
	 

	 
	 
	 

	 
	 
	 

	By /s/ Ross Taylor
	 
	 

	Name: Ross Taylor
	 
	 

	Title:  Senior Vice President and CEO
	 
	 

	 
	 
	 

	 
	 
	 

	BANK:
	 
	 

	 
	 
	 

	WESTERN ALLIANCE BANK, AN ARIZONA CORPORATION
	 
	 

	 
	 
	 

	 
	 
	 

	By /s/ Lindsay Fouty
	 
	 

	Name: Lindsay Fouty
	 
	 

	Title: VP, Portfolio Management
	 
	 

BOS 48677184v4

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