Document:

Amendment to Lease Agreement - March 31, 2008

 Exhibit 10.8D 
 THIRD AMENDMENT TO LEASE 
 This Third Amendment to Lease
(“Amendment”) is entered into, and dated for reference purposes, as of March 31, 2008 (the “Execution Date”) by and between METROPOLITAN LIFE INSURANCE COMPANY, a New York corporation (“Metropolitan”), as Landlord
(“Landlord”), and Codexis, Inc. a Delaware corporation (“Codexis”), as Tenant (“Tenant”), with reference to the following facts (“Recitals”): 
 A. Landlord and Tenant are the parties to that certain written lease which is comprised of the following: that certain written Lease, dated
as of October, 2003, by and between Landlord and Tenant (the “Original Lease”) “) for certain premises described therein and commonly known as 501 Chesapeake Drive in Building 3 and all the rentable area of Building 4 (consisting of
200 and 220 Penobscot Drive (collectively, the “Original Premises”), all as more particularly described in the Original Lease, as amended by that certain First Amendment to Lease, dated as of June 1, 2004, by and between Landlord and
Tenant (the “First Amendment”), as amended by that certain Second Amendment to Lease, dated as of March 9, 2007, by and between Landlord and Tenant (the “Second Amendment”) for certain premises described therein and commonly
known as 640 Galveston Drive, which is part of Building 5 (the “640 Galveston Premises”), all as more particularly described in the Second Amendment. The Original Lease, as amended, is referred to as the “Existing Lease” and the
Original Premises plus the 640 Galveston Premises is collectively referred to as the “Existing Premises”. 
 B.
Landlord and Tenant desire to provide for (i) the lease to Tenant of the Building 2 Space (defined below) for a term longer than the term applicable respectively to each of the Original Premises and the 640 Galveston Premises; and
(ii) other amendments of the Existing Lease as more particularly set forth below. 
 NOW, THEREFORE, in consideration of
the foregoing, and of the mutual covenants set forth herein and of other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the parties hereto agree as follows: 
 Section 1. Scope of Amendment; Defined Terms. Except as expressly provided in this Amendment, the Existing Lease shall
remain in full force and effect. Should any inconsistency arise between this Amendment and the Existing Lease as to the specific matters which are the subject of this Amendment, the terms and conditions of this Amendment shall control. The term
“Lease” as used herein and in the Existing Lease shall refer to the Existing Lease as modified by this Amendment. All capitalized terms used in this Amendment and not defined herein shall have the meanings set forth in the Existing Lease
unless the context clearly requires otherwise. 
 Section 2. Confirmation of Term. Landlord and Tenant
acknowledge and agree that notwithstanding any provision of the Existing Lease to the contrary: (a) as contemplated by the Existing Lease, the Expiration Date of the Term of the Lease of the Original Premises is January 31, 2011;
(b) as contemplated by the Existing Lease, the 640 Galveston Expiration Date is April 30, 2012; and (c) the initial Term of the Lease of the Building 2 Space shall expire later as provided below. 
 Section 3. Lease of Building 2 Space. 
 (a) Landlord hereby leases to Tenant and Tenant hereby hires from Landlord the Building 2 Space (defined below) upon and subject to all of the terms, covenants and conditions of the Existing Lease except
as expressly provided herein. “Building 2 Space” is the entire rentable area of Building Number 2 located in Phase I of Seaport Centre at the street address of 400 Penobscot Drive, Redwood City, California 94063, as shown on
Exhibit A to this Amendment. Landlord and Tenant hereby agree that the Building 2 Space is conclusively presumed to be 37,856 rentable square feet. 
 (b) Delivery; Construction & Construction Period; Commencement Date; Term; Other Provisions. Notwithstanding any provision of the Existing Lease to the contrary, the following provisions
shall govern the Building 2 Space: 
 (1) Delivery; Construction; Construction Period; Commencement Date;
Term. Landlord shall tender to Tenant possession of the Building 2 Space in the condition specified in the Workletter (Exhibit B to this Amendment) no later than one (1) business day after execution of this Amendment by both
Tenant and Landlord (the “Projected Commencement Date”). The date on which Landlord actually tenders to Tenant possession of the Building 2 Space shall be the “Building 2 Commencement Date” on which the Term of this Lease of the
Building 2 Space commences, and on and after such date all the terms and conditions of the Lease shall apply, and Tenant shall observe and perform all terms and conditions of the Lease, except that until April 1, 2008 (the “Building 2
Rent Start Date”), Tenant shall not be obligated to pay Monthly Base Rent or Rent Adjustments. The Term of this Lease of the Building 2 Space (“Building 2 Term”) shall start on the Building 2 Commencement Date and end
March 31, 2013 (the “Building 2 Expiration Date”). 
  

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 (2) Tenant Additions/Tenant Improvements. Subject to Section 4
below, all improvements permanently affixed to or on Building Number 2 by Tenant under this Amendment or hereafter under this Lease, including, without limitation: (a) walls, ceilings, flooring, building fixtures (such as plumbing, power,
lighting and HVAC systems), including without limitation, all improvements made as part of the Special Tenant Work (described in Exhibit B-2 to the Workletter); (b) all lab benches and corresponding casework, lab sinks, lab or fume
hoods, supplemental or special ventilating and air conditioning equipment, and any and all lab installations and fixtures, shall, without compensation or credit to Tenant, become part of the Building 2 Space and the property of Landlord at
the time of their installation and shall remain in Building Number 2, unless pursuant to Subsection 4 below, other express provision of this Lease or a subsequent written agreement between the parties hereto, Tenant is permitted or
required to remove them. For the avoidance of doubt, the term “permanently affixed” shall not be construed to mean otherwise free-standing equipment that has been secured to the Premises for the primary purpose of seismic stability and/or
the prevention of theft. 
 (3) Confirmation of Commencement Date. Upon request by Landlord, Tenant and
Landlord shall enter into an agreement (the form of which is Exhibit C to this Amendment) confirming the Building 2 Commencement Date and the Building 2 Expiration Date. If within ten (10) business days after Landlord’s request
enclosing the proposed agreement, Tenant fails either (i) to enter into such agreement, or (ii) to give Landlord written notice of any item(s) therein which Tenant believes are incorrect, the corrections(s) proposed by Tenant and reasons
therefor, then the Building 2 Commencement Date and the Building 2 Expiration Date shall be the dates designated by Landlord in such agreement. 
 (4) Failure to Deliver Possession. If Landlord shall be unable to give possession of the Building 2 Space on the Projected Commencement Date by reason of the following: (i) the holding over or
retention of possession of any tenant, tenants or occupants, or (ii) for any other reason, then Landlord shall not be subject to any liability for the failure to give possession on said date. Under such circumstances, by operation of Subsection
(1) above, the Commencement Date is automatically adjusted and determined in relation to the date Landlord actually tenders possession of the Building 2 Space to Tenant. If Landlord tenders possession after March 31, 2008, the
Building 2 Rent Start Date shall be the date on which Landlord tenders possession. Failure to deliver possession on the originally scheduled Projected Commencement Date shall not affect the validity of this Lease or the obligations of the Tenant
hereunder. 
 (5) Premises. From and after the delivery of the Building 2 Space to Tenant, the term
“Premises” as used in the Lease shall mean the Existing Premises together with the Building 2 Space. 
 (c) Monthly
Base Rent for Building 2 Space. Notwithstanding any provision of the Existing Lease to the contrary, Monthly Base Rent for the Building 2 Space shall be payable on the Building 2 Rent Start Date and thereafter on the first day of each calendar
month of the Building 2 Term, in the manner

  

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required for Monthly Base Rent in the Existing Lease, but the amounts are additional to rent payable under the Existing Lease, and the amount of Monthly Base Rent due and payable by Tenant for
the Building 2 Space and monthly schedule therefor starting on the Building 2 Commencement Date shall be as set forth in the schedule below: 
  

								
	 Period from/to
	  	Monthly	  	Annual Rate/SF of Rentable Area	 
	 Commencement Date – 03/31/08
	  	*$	0.00	  	$	0.00	  
	 04/01/08 – 09/30/08
	  	$	32,400.00	  	 	(negotiated initial amount	) 
	 10/01/08 – 03/31/09
	  	$	68,140.80	  	$	21.60	  
	 04/01/09 – 03/31/10
	  	$	70,191.33	  	$	22.25	  
	 04/01/10 – 03/31/11
	  	$	72,304.96	  	$	22.92	  
	 04/01/11 – 03/31/12
	  	$	74,450.13	  	$	23.60	  
	 04/01/12 – 03/31/13
	  	$	76,689.95	  	$	24.31	  

  

	*	If, and only if, this Amendment is executed and the Premises delivered to Tenant before April 1, 2008, the early occupancy period before April 1, 2008 will be
free of Monthly Base Rent and Rent Adjustments. Tenant shall pay Landlord the initial installment of Monthly Base Rent (for April, 2008) concurrently with execution of this Amendment. 

 (d) Tenant’s Share of Operating Expenses. Notwithstanding any provision of the Existing Lease to the contrary, in addition to
Tenant’s payment of Rent Adjustment Deposits and Rent Adjustments with respect to the Existing Premises, Tenant shall pay Rent Adjustment Deposits and Rent Adjustments with respect to the Building 2 Space starting on the Building 2 Rent Start
Date and continuing during the Building 2 Term, which shall be payable as set forth in the Existing Lease, except that for such purposes Tenant’s Building 2 Share shall be as set forth below, and Tenant’s Phase Share and Tenant’s
Project Share shall be modified as set forth below: 
  

			
	 Tenant’s Building 2 Share:
	  	         100.0%

	 Tenant’s Phase 1 Share:
	  	 28.712%* (see provision below)

	 Tenant’s Project Share:
	  	 16.147%* (see provision below)

  

	*	If the Term of the Original Premises is not extended, then from the later of such expiration or the date Tenant vacates the Original Premises for the remaining Building
2 Term, Tenant’s Phase 1 Share shall be reduced by 13.05% and Tenant’s Project Share shall be reduced by 7.33%. If the Term of the 640 Galveston Space is not extended, then from the later of such expiration or the date Tenant vacates the
640 Galveston Space for the remaining Building 2 Term, Tenant’s Phase 1 Share shall be reduced by 3.112% and Tenant’s Project Share shall be reduced by 1.747%. 

 (e) Parking. Notwithstanding any provision of the Existing Lease to the contrary, on and after the Building 2 Commencement Date
during the Building 2 Term, Tenant shall have the right to use, on an unassigned basis, an additional one hundred twenty-five (125) Parking Spaces 
 (f) Signage. 
 (1) Grant of Right. Notwithstanding
any provision of the Existing Lease to the contrary, on and after the Building 2 Commencement Date for the Building 2 Term, Tenant shall have the right to (1) place its company name and logo on the door(s) at the main entry to Building
Number 2 (the “Entry Signage”); and (2) only for so long as Tenant leases, is continuously conducting regular, active, ongoing business in, and is in occupancy (and occupancy by a subtenant, licensee or other party permitted or
suffered by Tenant shall not satisfy such condition) of not less than fifty percent (50%) of the entire Building 2 Space, place its company name and logo on its pro-rata share of the signage area on the existing, exterior monument sign for
Building Number 2, subject to the terms and conditions set forth in this Section (“Monument Signage”)(collectively, the Entry Signage and Monument Signage are referred to as the “Exterior Sign Right”). 
  

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 (2) General Conditions & Requirements. The size, type,
style, materials, color, method of installation and exact location of the sign, and the contractor for and all work in connection with the sign, contemplated by this Section shall (i) be subject to Tenant’s compliance with all applicable
laws, regulations and ordinances and with any covenants, conditions and restrictions of record which affect the Property; (ii) be subject to Tenant’s compliance with all requirements of Landlord’s current Project signage criteria at
the time of installation; (iii) be consistent with the design of Building Number 2 and the Project; (iv) be further subject to Landlord’s prior written consent. Tenant shall, at its sole cost and expense, procure, install,
maintain in first class appearance and condition, and remove such sign. 
 (3) Removal &
Restoration. Upon the expiration or termination of the Exterior Sign Right, but in no event later than the expiration of the Building 2 Term or earlier termination of the Lease, Tenant shall, at its sole cost and expense, remove such sign and
shall repair and restore the area in which the sign was located to its condition prior to installation of such sign. 
 (4) Right Personal. The right to Monument Signage under this Section is personal to Codexis and may not be used by, and shall not be transferable or assignable (voluntarily or involuntarily) to, any person or entity. 
 Section 4. Certain Provisions Re Equipment & Trade Fixtures Entirely Paid for by Tenant; Lender Access
Rights. Notwithstanding any of the foregoing to the contrary, with respect to any part of the Premises (both the Building 2 Space and Existing Premises): 
 (a) if so requested by Tenant in writing (and prominently in all capital and bold lettering which also states that such request is pursuant to Section 4 of the Third Amendment) at the time Tenant
requests approval of any Tenant Work or Tenant Alterations, Landlord shall advise Tenant at the time of Landlord’s approval of such Tenant Work or Tenant Alterations as to whether Landlord will require that such Tenant Work or Tenant
Alterations be removed by Tenant; provided, however, regardless of the foregoing, in any event, Landlord may require removal of any Tenant Work or Tenant Alterations containing Hazardous Material, Tenant’s trade fixtures, and, subject to
Section 6.03 of the Original Lease, cabling and wiring installed for Tenant’s personal property or trade fixtures; 
 (b) with respect to equipment or trade fixtures (but not walls, ceilings, flooring or building fixtures, such as plumbing, power, lighting, HVAC systems) hereafter permanently affixed and paid for entirely by Tenant (without reimbursement
in full or part out of any funds provided by Landlord), which items are specifically identified in writing delivered by Tenant to Landlord, including the building address and location within the building where the items are located, with
substantiation by Tenant that such items have been paid for entirely by Tenant, then such equipment and trade fixtures shall become the property of Landlord upon the expiration or earlier termination of the Term of the Lease as to the part of the
Premises in which such item is located, and Landlord will not unreasonably withhold its consent to a written request by Tenant that such items be part of the Limited Collateral covered by a Landlord’s Consent to Encumbrance of Limited
Collateral (more particularly described in Section 4(c) below). 
 (c) in the event that Tenant borrows money and/or
obtains other financial accommodations up to an aggregate indebtedness or line of credit in the amount of Fifteen Million Dollars ($15,000,000.00) from General Electric Capital Corporation (“GECC”) (for its own account and/or as agent for
a group of lenders) or an institutional lender which is its successor or assign, or which provides substitute or replacement financing (“Lender”), and in connection therewith grants the Lender a security interest in “Limited
Collateral” (as defined in the form of “Landlord’s Consent to Encumbrance of Limited Collateral” which is set forth in Exhibit D to this Amendment) (and any agreement evidencing the foregoing loan and security
agreement is referred to as a “Loan Agreement”), provided that there shall be no more than one such Lender with a security interest in the Limited Collateral at any one time, then upon written request from Tenant, during the term of any
such Loan Agreement Landlord agrees that it will enter into an agreement providing Lender access to the Premises for the sole purpose of enforcing and perfecting the security interest of such Lender in the Limited Collateral, on those terms and
conditions contained in the form of “Landlord’s Consent to Encumbrance of Limited Collateral” which is set forth as Exhibit D to this Amendment. 
  

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 Section 5. Increase in the Security. Notwithstanding any provision
of the Existing Lease to the contrary: 
 (a) Tenant and Landlord acknowledge that pursuant to Section 5.02 of the Existing
Lease, Tenant elected to deliver the Letter of Credit in lieu of cash Security Deposit, and immediately prior to execution of this Amendment, the amount of the Letter of Credit required under the Existing Lease and held by Landlord is Four Hundred
Fifty-three Thousand Six Hundred Twenty-four Dollars ($453,624); 
 (b) The amount of Security Deposit and Letter of Credit
required as of the Execution Date of this Amendment is hereby increased by One Hundred Fifty-three Thousand Three Hundred Eighty Dollars ($153,380) and simultaneously with delivering to Landlord this Amendment signed by Tenant, Tenant shall deliver
to Landlord an amendment or replacement of the Letter of Credit which increases the amount of the Letter of Credit to Six Hundred Seven Thousand and Four Dollars ($607,004); 
 (c) The text of Section 5.02(c) of the Existing Lease (as amended by Section 4(c) of the Second Amendment) is deleted and the
following is inserted in its place: 
 “Notwithstanding anything to the contrary contained herein, after the Execution Date
of the Third Amendment to Lease, the following reduction provisions shall apply. If Tenant is not in Default under the Lease on February 1, 2008, an amendment or replacement of the Letter of Credit may be issued which decreases by Forty-five
Thousand Dollars ($45,000) the amount of the Letter of Credit to the revised total amount of Five Hundred Sixty-two Thousand and Four Dollars ($562,004). If Tenant is not in Default under the Lease on February 1, 2009, an amendment or
replacement of the Letter of Credit may be issued which decreases by Forty-five Thousand Dollars ($45,000) the amount of the Letter of Credit to the revised total amount of Five Hundred Seventeen Thousand and Four Dollars ($517,004). If Tenant is
not in Default under the Lease on February 1, 2010, an amendment or replacement of the Letter of Credit may be issued which decreases by Forty-five Thousand Dollars ($45,000) the amount of the Letter of Credit to the revised total amount of
Four Hundred Seventy-two Thousand and Four Dollars ($472,004).” 
 (d) The second sentence of Section 5.02(a) (as
amended by Section 4(d) of the Second Amendment) is deleted and the following is inserted in its place: “The Letter of Credit shall be maintained in effect until the “LOC Expiration Date”, which shall mean the date which is
ninety (90) days after the last to occur of the four events specified in Section 5.02(d) of the Existing Lease or the 640 Galveston Expiration Date or the Building 2 Expiration Date, and provided that on the LOC Expiration Date, Tenant
shall not be in Default, Landlord shall return to Tenant the Letter of Credit and any Letter of Credit Proceeds then held by Landlord (other than those held for application by Landlord on account of a Default as provided below)” 
 Section 6. Excess Rent. Notwithstanding anything to the contrary contained the Existing Lease, solely with respect
only to the Building 2 Space, in determining “Excess Rent” in conjunction with the sublease or assignment of any of the Building 2 Space, Section 10.03 of the Existing Lease is amended to add the following to the end of the first
sentence thereof: “; and (4) Excess Initial Improvements. For purposes of this Section 10.03, “Excess Initial Improvements” shall mean (w) the amount of actual out-of-pocket costs incurred by Tenant to build the Tenant
Work in or on Building Number 2 (excluding Tenant’s moveable personal property) in excess of the Allowance (in the aggregate, including the allowances provided for specific purposes), provided that Tenant has provided Landlord with a detailed
itemization of such costs and receipts therefor, (x) which sum shall be divided by the Rentable Area of the Building 2 Space, (y) which quotient shall be further divided by sixty (60), and (z) which quotient shall be multiplied by the
rentable area of the portion of the Building 2 Space being assigned or subleased.” 
  

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 Section 7. Negotiation Right. 
 (a) Landlord hereby grants Tenant a one-time right to negotiate the lease of the 600 Galveston Negotiation Space (defined below). if and to
the extent such space is Available (defined below) during the period beginning on the Execution Date of this Amendment and expiring twenty-four (24) months prior to the Expiration Date of the Building 2 Term (the “Negotiation
Period”), upon and subject to the terms and conditions of this Section (the “Negotiation Right”), and provided that at the time of exercise of such right: (i) Tenant must be conducting regular, active, ongoing business in, and be
in occupancy (and occupancy by a subtenant, licensee or other party permitted or suffered by Tenant shall not satisfy such condition) of the entire Building 2 Space; and (ii) there has been no material adverse change in Tenant’s
financial position from such position as of the date of execution of the Lease, as certified by Tenant’s independent certified public accountants, and as supported by Tenant’s certified financial statements, copies of which shall be
delivered to Landlord with Tenant’s written notice exercising its right hereunder. Without limiting the generality of the foregoing, Landlord may reasonably conclude there has been a material adverse change if Tenant’s independent
certified public accountants do not certify there has been no such change. 
 (b) The “600 Galveston Negotiation
Space” shall mean the leaseable space with a street address of 600 Galveston Drive and Rentable Area of approximately 25,438 square feet. For purposes of this Negotiation Right, the term “Available” shall mean that the space in
question is either: (1) vacant and free and clear of all “Prior Rights” (defined below); or (2) space as to which Landlord has received a proposal, or Landlord is making a proposal, for a lease or rights of any nature applicable
in the future when such space would be free and clear of all Prior Rights. For purposes of this Negotiation Right, the term “Prior Rights” shall mean rights of other parties, including without limitation, a lease, lease option, or option
or other right of extension, renewal, expansion, refusal, negotiation or other right, either: (i) pursuant to any lease or written agreement which is entered into on or before the Execution Date of this Amendment; or (ii) pursuant to any
extensions or renewal of any of the foregoing, whether or not set forth in such lease or written agreement, and Landlord shall be free at any time to enter such extension or renewal; or (iii) pursuant to any amendment or modification of any of
the foregoing, and Landlord shall be free at any time to enter such amendment or modification. 
 (c) Nothing herein shall be
deemed to limit or prevent Landlord from marketing, discussing or negotiating with any other party for a lease of, or rights of any nature as to, any part of the Negotiation Space, but during the Negotiation Period before Landlord makes any written
proposal to any other party (other than a party with Prior Rights) for any Negotiation Space which becomes Available (including giving a written response to any proposal or offer received from another party), or contemporaneously with making any
such proposal, and in any event within thirty (30) days after such space becomes vacant and free and clear of all Prior Rights, Landlord shall give Tenant written notice (“Landlord’s Notice”), which notice identifies the space
Available and Landlord’s estimate of the projected date such space will be vacant and deliverable to Tenant. Notwithstanding any of the foregoing to the contrary, Tenant acknowledges that: (i) Landlord has disclosed that as of the
Execution Date of this Amendment, the 600 Galveston Negotiation Space is vacant and free and clear of all Prior Rights, and that after the Execution Date of this Lease, Landlord has the right at any time to give Landlord’s Notice with respect
to such space. For a period of five (5) business days after Landlord gives Landlord’s Notice (the “Election Notice Period”), Tenant shall have the right to initiate negotiations in good faith for the lease of all (and not less
than all) the space identified in Landlord’s Notice by giving Landlord written notice (“Election Notice”) of Tenant’s election to exercise its Negotiation Right to lease such space. 
 (d) If Tenant timely and properly gives the Election Notice, Landlord and Tenant shall, during the five (5) business day period (the
“Second Period”) following Landlord’s receipt of the Election Notice, negotiate in good faith for the lease of the Negotiation Space which is the subject of the Landlord Notice as set forth below. Any lease by Tenant pursuant to this
Negotiation Right: (1) shall be for all (and not less than all) the Negotiation Space which is the subject of the Landlord Notice; (2) the subject Negotiation Space shall, upon delivery, be part of the Premises under the Lease, such that
the term “Premises” thereafter shall include the subject Negotiation Space; (3) starting on such delivery date, with respect to the subject Negotiation Space Tenant shall additionally pay Tenant’s Share of Operating Expenses,
with

  

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Tenant’s Share recalculated to reflect addition of the Negotiation Space; (4) the number of parking spaces applicable to the subject Negotiation Space shall be calculated at the rate of
3.3 spaces per 1000 square feet of Rentable Area of the subject Negotiation Space, and the type of, location of and charge for such spaces shall be as otherwise provided in the Lease; and (5) such lease shall be upon and subject to all the
other terms, covenants and conditions provided in the Lease, except that the following terms shall be subject to such negotiation and agreement of the parties: (aa) the amount of the Monthly Base Rent with respect to the Negotiation Space; (bb) the
term of the lease of the Negotiation Space shall be subject to negotiation, but shall not be less than the Term of the Lease of the Building 2 Space (including any extension pursuant to the Option to Extend); (cc) any improvements or alterations to
be done, or allowance therefor, if any, specifically agreed upon, and absent such agreement, Tenant shall accept the Negotiation Space in its then AS IS condition without any obligation of Landlord to repaint, remodel, improve or alter the subject
Negotiation Space for Tenant’s occupancy or to provide Tenant any allowance therefor, but such space shall be delivered broom clean and free of all tenants or occupants (and their personal property); (dd) increase in the Security; and (ee)
Landlord shall deliver the subject Negotiation Space to Tenant in such AS IS condition no later than thirty (30) days after Landlord regains possession of such space, but in no event shall Landlord have any liability for failure to deliver the
subject Negotiation Space to Tenant on any projected delivery date due to the failure of any occupant to timely vacate and surrender such space or due to Force Majeure, and such failure shall not be a default under the Lease or impair its validity.
The foregoing obligation of Landlord to negotiate is non-exclusive and nothing herein shall be deemed to prevent Landlord from negotiating with any other party for the Negotiation Space, whether or not Landlord and Tenant are negotiating for the
same, but any other such negotiation shall be subject to the aforesaid obligation to negotiate with Tenant in good faith. 
 (e)
If Tenant either fails or elects not to exercise its Negotiation Right as to the Negotiation Space covered by Landlord’s Notice by not giving its Election Notice within the Election Notice Period, or if Tenant gives Tenant’s Election
Notice but Tenant and Landlord do not execute (1) a written letter of intent reflecting the significant business terms for the lease of the Negotiation Space within five (5) business days after delivery of the Election Notice, and
(2) a corresponding amendment prepared by Landlord within five (5) days after Landlord gives Tenant such proposed amendment, then in any such event Tenant’s Negotiation Right shall terminate, and be null and void, as to the subject
space identified in the applicable Landlord’s Notice (but not as to any Negotiation Space subject to this Negotiation Right which has not become Available and been included in a Landlord’s Notice), and at any time thereafter Landlord shall
be free to lease and/or otherwise grant options or rights to the subject space on any terms and conditions whatsoever free and clear of the Negotiation Right. 
 (f) During any period that Tenant does not occupy the entire Premises or that there is an uncured default by Tenant under the Lease, or any state of facts which with the passage of time or the giving of
notice, or both, would constitute such a default, the Negotiation Right shall not apply and shall be ineffective and suspended, and Landlord shall not be obligated to give a Landlord’s Notice as to any space which becomes Available during such
suspension period, and Landlord shall not be obligated to negotiate (or enter into any amendment) with respect to any Negotiation Space which was the subject of a pending Landlord’s Notice for which an amendment has not been fully executed, and
during such suspension period Landlord shall be free to lease and/or otherwise grant options or rights to such space on any terms and conditions whatsoever free and clear of the Negotiation Right. The Negotiation Right shall terminate upon any of
the following: (1) the termination of the Lease, whether by Landlord upon the occurrence of a Tenant default or otherwise; or (2) the failure of Tenant timely to exercise, give any notices, perform or agree, within any applicable time
period specified above, with respect to any Negotiation Space which was the subject of any Landlord’s Notice. 
 (g) The
Negotiation Right is personal to Codexis and may not be used by, and shall not be transferable or assignable (voluntarily or involuntarily) to any person or entity. 
 Section 8. Option to Extend. The Option to Extend set forth in Section 26.21 of the Existing Lease shall apply to the Building 2 Space as part of the Premises, but as to only
the Building 2 Space the Option to Extend shall be modified as follows (such Option, as modified, may be referred to as the “Building 2 Option to Extend”): (a) there shall be a separate and distinct Option Term with respect to the

  

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Building 2 Space which shall commence immediately after the Building 2 Expiration Date and shall expire five years thereafter (the “Building 2 Option Term”), and Tenant and Landlord
acknowledge and agree that the Building 2 Option Term shall expire later than the expiration of the Option Terms respectively for each of the Original Premises and the 640 Galveston Space; (b) the Prevailing Market Rent for the Building 2
Option Term shall be determined for the Building 2 Space and the type and quality of tenant improvements for it, but the monthly rate of the Option Term Rent for the Building 2 Space shall be not less than the monthly rate of the Preceding Rent for
the last month of the initial Building 2 Term; and (c) the period within which the Building 2 Option to Extend may be exercised shall be calculated in reference to the Building 2 Expiration Date. 
 Section 9. Brokers. Notwithstanding any other provision of the Existing Lease to the contrary, Tenant represents
that in connection with this Amendment it is represented by CB Richard Ellis (“Tenant’s Broker”) and, except for Tenant’s Broker and Cornish and Carey Commercial (“Landlord’s Broker”) identified below, Tenant has
not dealt with any real estate broker, sales person, or finder in connection with this Amendment, and no such person initiated or participated in the negotiation of this Amendment. Tenant hereby indemnifies and agrees to protect, defend and hold
Landlord and Landlord’s Broker harmless from and against all claims, losses, damages, liability, costs and expenses (including, without limitation, attorneys’ fees and expenses) by virtue of any broker, agent or other person claiming a
commission or other form of compensation by virtue of alleged representation of, or dealings or discussions with, Tenant with respect to the subject matter of this Amendment, except for Landlord’s Broker and except for a commission payable to
Tenant’s Broker to the extent provided for in a separate written agreement between Tenant’s Broker and Landlord’s Broker. Tenant is not obligated to pay or fund any amount to Landlord’s Broker, and Landlord hereby agrees to pay
such commission, if any, to which Landlord’s Broker is entitled in connection with the subject matter of this Amendment pursuant to Landlord’s separate written agreement with Landlord’s Broker. Such commission shall include an amount
to be shared by Landlord’s Broker with Tenant’s Broker as agreed to by Tenant’s Broker and Landlord’s Broker in a separate agreement between themselves to share the commission paid to Landlord’s Broker by Landlord such that
Tenant’s Broker will receive a commission equal to one dollar ($1.00) per rentable square foot per year of the Building 2 Term. The provisions of this Section shall survive the expiration or earlier termination of the Lease. 
 Section 10. Attorneys’ Fees. Each party to this Amendment shall bear its own attorneys’ fees and costs
incurred in connection with the discussions preceding, negotiations for and documentation of this Amendment. In the event that either party brings any suit or other proceeding with respect to the subject matter or enforcement of this Amendment or
the Lease, the parties acknowledge and agree that the provisions of Section 11.03 of the Existing Lease shall apply. 
 Section 11. Effect of Headings; Recitals: Exhibits. The titles or headings of the various parts or sections hereof are intended solely for convenience and are not intended and shall not be deemed to or in any way be
used to modify, explain or place any construction upon any of the provisions of this Amendment. Any and all Recitals set forth at the beginning of this Amendment are true and correct and constitute a part of this Amendment as if they had been set
forth as covenants herein. Exhibits, schedules, plats and riders hereto which are referred to herein are a part of this Amendment. 
 Section 12. Entire Agreement; Amendment. is Amendment taken together with the Existing Lease, together with all exhibits, schedules, riders and addenda to each, constitutes the full and complete agreement and
understanding between the parties hereto and shall supersede all prior communications, representations, understandings or agreements, if any, whether oral or written, concerning the subject matter contained in this Amendment and the Existing Lease,
as so amended, and no provision of the Lease as so amended may be modified, amended, waived or discharged, in whole or in part, except by a written instrument executed by all of the parties hereto. 
 Section 13. Authority. Each person executing this Amendment represents and warrants that he or she is duly
authorized and empowered to execute it, and does so as the act of and on behalf of the party indicated below. Each party represents and warrants to the other that it has full authority and power to enter into and perform its obligations under this
Amendment, that the person executing this Amendment

  

 Page 8 

 
is fully empowered to do so, and that no consent or authorization is necessary from any third party. Landlord may request that Tenant provide Landlord evidence of due authorization and execution
of this Amendment. 
 Section 14. Counterparts. This Amendment may be executed in duplicates or counterparts,
or both, and such duplicates or counterparts together shall constitute but one original of the Amendment. Each duplicate and counterpart shall be equally admissible in evidence, and each original shall fully bind each party who has executed it.

 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first set forth above. 
  

							
	TENANT:	 		 	CODEXIS, INC.,
		 		 	a Delaware corporation
				
		 		 	By:	 	 /s/ Alan Shaw

		 		 	Print Name:	 	Alan Shaw
		 		 	Title:	 	 President & CEO
 (Chairman of Board, President or Vice President)

				
		 		 	By:	 	 /s/ Robert S. Breuil

		 		 	Print Name:	 	Robert S. Breuil
		 		 	Title:	 	 CFO & SVP
 (Secretary,
Assistant Secretary, CFO or Assistant Treasurer)

			
	LANDLORD:	 		 	METROPOLITAN LIFE INSURANCE COMPANY,
		 		 	a New York corporation
				
		 		 	By:	 	 /s/ Joel R. Redmon

		 		 	Print Name:	 	Joel R. Redmon
		 		 	Title:	 	Director

  

 Page 9 

 Exhibit A 
 Site Plan Showing Building 2 Space & Project 
 The Building 2 Space
is generally shown as the Building labeled Building 2 below. Phase III, 
 its Buildings, land and improvements are not a part of
the Project as defined in this Lease, & 
 are shown in this Exhibit for illustration only. 
  

 Exhibit A - Page 1 

 EXHIBIT B 
 WORKLETTER AGREEMENT 
 (TENANT BUILD WITH ALLOWANCE) 
 This Workletter Agreement (“Workletter”) is attached to and a part of a certain Third Amendment to Lease by and between
Metropolitan Life Insurance Company, a New York corporation, as Landlord, and Codexis, Inc., a Delaware corporation, as Tenant, for the Building 2 Space (the “Amendment” and the original lease, as amended shall be referred to as the
“Lease”). All references below to the Premises shall instead be deemed to mean the Building 2 Space and all references to the Building shall instead be deemed to mean Building Number 2. Terms used herein but not defined herein shall have
the meaning of such terms as defined elsewhere in the Lease. For purposes of this Workletter, references to “State” and “City” shall mean the State and City in which the Building is located. 
  

	1.	AS IS Condition; Delivery. 

 Landlord shall deliver the Premises broom clean in its current “as built” configuration with existing build-out of the tenant space, with the Premises and the Building (including the “Base Building”, as defined below) in
their AS IS condition, without any express or implied representations or warranties of any kind by Landlord, its brokers, manager or agents, or the employees of any of them; and Landlord shall not have any obligation to construct or install any
tenant improvements or alterations or to pay for any such construction or installation except to the extent expressly provided in the Amendment and all exhibits thereto. For purposes hereof, the “Base Building” (sometimes also referred to
as the “Base Building Work”) shall mean the improvements made and work performed during the Building’s initial course of construction and modifications thereto, excluding all original and modified build-outs of any tenant spaces.
Notwithstanding any provision of this Workletter or the Lease to the contrary, to the extent that within three (3) days after the Commencement Date (i) the roof and roof membrane above the Premises, (ii) foundation and structural
components of the Base Building, (iii) Landlord’s fire sprinkler and life-safety systems, if any, of the Base Building, and (iv) the electrical, water, sewer and plumbing systems of the Base Building serving the Premises (but only
from the local utility’s systems to the point of entry into the Premises or to the meter or other point after which such system serves exclusively the Premises) are not in good working condition, except to the extent any of the foregoing are to
be removed, demolished or altered by Tenant, and within three (3) days after the Commencement Date Tenant gives Landlord written notice specifying what is not in good working condition, Landlord shall make necessary repairs to put such item or
items in good working condition at Landlord’s sole cost and expense. Further, Tenant acknowledges and agrees that Tenant has been afforded ample opportunity to inspect the Premises, the Building and the Project, and has investigated their
condition to the extent Tenant desires to do so. 
  

	2.	Landlord Work. 

 2.1.
Notwithstanding any of the foregoing to the contrary, subject to delays caused by Force Majeure or Tenant Delay (defined below), Landlord, at Landlord’s sole cost and expense, shall perform the work set forth on Exhibit B-1 hereto
(“Landlord Work”), and within ninety (90) days after the Commencement Date shall Substantially Complete (defined below) the Landlord Work and leave the affected area in broom-clean condition with respect to Landlord Work (but Landlord
shall not be obligated to do any clean-up or refuse removal related to construction of Tenant Work). 
 2.2. Tenant acknowledges
and agrees that in order to deliver the Premises to Tenant on the schedule contemplated by this Lease, preparation for and performance of the Landlord Work will require access, work and construction within the Premises after delivery of possession
to Tenant, and that

  

 Exhibit B - Page 1 

 
Landlord and Landlord’s representatives and contractors shall have the right to enter the Premises at all times to perform such work until the Landlord Work is completed, and that such entry
and work shall not constitute an eviction of Tenant in whole or in part and shall in no way excuse Tenant from performance of its obligations under the Lease. Tenant and Landlord acknowledge and agree that the Landlord Work and necessary
coordination and cooperation to accomplish it will cause certain unavoidable level of disturbance, inconvenience, annoyance to Tenant’s use and enjoyment of the Premises, and that in performing such Landlord Work Landlord shall use commercially
reasonable efforts not to unreasonably and materially interfere with Tenant’s construction, installations and business operations. Tenant shall cooperate with Landlord and Landlord’s contractors(s) to allow the Landlord Work and shall move
Tenant’s trade fixtures, furnishings and equipment as reasonably requested by Landlord or Landlord’s contractor(s). The costs of such cooperation and moving, and any related disconnections and installations of Tenant’s trade fixtures,
equipment, phones, furnishings and other personal property, shall be at Tenant’s sole cost and expense. To the extent that Tenant, its contractors or subcontractors delay the Substantial Completion of the Landlord Work, such delay shall be a
“Tenant Delay” and the Landlord Work shall be deemed Substantially Complete on the date such Landlord Work would have been completed but for the delay caused by Tenant, its contractors or subcontractors. 
 2.3. For purposes of this Workletter, “Substantially Complete” and “Substantial Completion” of the Landlord Work shall
mean the completion of the Landlord Work, except for minor insubstantial details of construction, decoration or mechanical adjustments which remain to be done and which shall not unreasonably and materially interfere with Tenant’s regular
business operations in the Premises. Substantial Completion shall be deemed to have occurred notwithstanding a requirement to complete “punchlist” or similar minor corrective work. Contemporaneously with or promptly after Substantial
Completion of the Landlord Work, Tenant shall have the right to submit a written “punch list” to Landlord, setting forth any incomplete or defective item of construction. Landlord shall complete with reasonable diligence “punch
list” items mutually agreed upon by Landlord and Tenant with respect to the Landlord Work. In addition, Landlord shall repair all latent defects in workmanship and materials of the Landlord Work, provided that Tenant gives Landlord written
notice of any such latent defects within six (6) months after the date of Substantial Completion of the Landlord Work. For purposes of this Section, the term “latent defects” shall mean defects which were not readily apparent at the
time the “punchlist” was formulated. All construction and installation resulting from the Landlord Work shall immediately become and remain the property of Landlord. 
  

	3.	Tenant’s Plans. 

 3.1. Description. At its expense, Tenant shall employ: 
 (i) one or more architects reasonably
satisfactory to Landlord and licensed by the State (“Tenant’s Architect”) to prepare architectural drawings and specifications for all layout and Premises improvements not included in, or requiring any change or addition to, the AS IS
condition and Landlord Work, if any. 
 (ii) one or more engineers reasonably satisfactory to Landlord and
licensed by the State (“Tenant’s Engineers”) to prepare structural, mechanical and electrical working drawings and specifications for all Premises improvements not included in, or requiring any change or addition to, the AS IS
condition and Landlord Work, if any. 
 All such drawings and specifications are referred to herein as “Tenant’s Plans”.
Tenant’s Plans shall be in form and detail sufficient to secure all applicable governmental approvals. Tenant’s Architect shall be responsible for coordination of all engineering work for Tenant’s Plans and shall coordinate with any
consultants of Tenant (the use of which is subject to Landlord’s consent), and Landlord’s space planner or architect to assure the consistency of Tenant’s Plans with the Base Building Work and Landlord Work (if any). 
  

 Exhibit B - Page 2 

 Tenant shall pay Landlord, within forty-five (45) days of receipt of each invoice from Landlord, the
cost incurred by Landlord for Landlord’s architects and engineers to review Tenant’s Plans for consistency of same with the Base Building Work and Landlord Work, if any. Tenant’s Plans shall also include the following: 
 (a) Final Space Plan: The “Final Space Plan” for the Premises shall include a full and accurate description of room
titles, floor loads, alterations to the Base Building or Landlord Work (if any) or requiring any change or addition to the AS IS condition, and the dimensions and location of all partitions, doors, aisles, plumbing (and furniture and equipment to
the extent same affect floor loading). The Final Space Plan shall (i) be compatible with the design, construction, systems and equipment of the Base Building and Landlord Work, if any; (ii) specify only materials, equipment and
installations which are new and of a grade and quality no less than existing components of the Building when they were originally installed (collectively, (i) and (ii) may be referred to as “Building Standard” or “Building
Standards”); (iii) comply with Laws, (iv) be capable of logical measurement and construction, and (v) contain all such information as may be required for the preparation of the Mechanical and Electrical Working Drawings and
Specifications (including, without limitation, a capacity and usage report, from engineers designated by Landlord pursuant to Section 3.1(b). below, for all mechanical and electrical systems in the Premises). 
 (b) Mechanical and Electrical Working Drawings and Specifications: Tenant shall employ engineers approved by Landlord to
prepare Mechanical and Electrical Working Drawings and Specifications showing complete plans for electrical, life safety, automation, plumbing, water, and air cooling, ventilating, heating and temperature control (collectively, the “Mechanical
and Electrical Working Drawings and Specifications”) and shall employ engineers designated by Landlord to prepare for Landlord a capacity and usage report (“Capacity Report”) for all mechanical and electrical systems in the Premises.

 (c) Issued for Construction Documents: The “Issued for Construction Documents”
shall consist of all drawings ( 1/8” scale) and
specifications necessary to construct all Premises improvements including, without limitation, architectural and structural working drawings and specifications and Mechanical and Electrical Working Drawings and Specifications and all applicable
governmental authorities plan check corrections. 
 3.2. Approval by Landlord. Tenant’s Plans and any
revisions thereof shall be subject to Landlord’s approval, which approval or disapproval: 
 (i) shall not
be unreasonably withheld, provided however, that Landlord may disapprove Tenant’s Plans in its sole and absolute discretion if they (a) adversely affect the structural integrity of the Base Building, including applicable floor loading
capacity; (b) adversely affect any of the Building Systems (as defined below), the Common Areas or any other tenant space (whether or not currently occupied); (c) fail to fully comply with Laws, (d) affect the exterior appearance of
the Building; (e) provide for improvements which do not meet or exceed the Building Standards; or (f) involve any installation on the roof, or otherwise affect the roof, roof membrane or any warranties regarding either. Building Systems
collectively shall mean the structural, electrical, mechanical (including, without limitation, heating, ventilating and air conditioning), plumbing, fire and life-safety (including, without limitation, fire protection system and any fire alarm),
communication, utility, gas (if any), and security (if any) systems in the Building. 
  

 Exhibit B - Page 3 

 (ii) shall not be delayed beyond ten (10) business days with respect to
initial submissions and major change orders (those which impact Building Systems or any other item listed in subpart (i) of Section 3.2 above) and beyond five (5) business days with respect to required revisions and any other change
orders. 
 If Landlord disapproves of any of Tenant’s Plans, Landlord shall advise Tenant of what Landlord disapproves in reasonable
detail. After being so advised by Landlord, Tenant shall submit a redesign, incorporating the revisions required by Landlord, for Landlord’s approval. The approval procedure shall be repeated as necessary until Tenant’s Plans are
ultimately approved. Approval by Landlord shall not be deemed to be a representation or warranty by Landlord with respect to the safety, adequacy, correctness, efficiency or compliance with Laws of Tenant’s Plans. Tenant shall be fully and
solely responsible for the safety, adequacy, correctness and efficiency of Tenant’s Plans and for the compliance of Tenant’s Plans with any and all Laws. 
 3.3. Landlord Cooperation. Landlord shall cooperate with Tenant and make good faith efforts to coordinate Landlord’s construction review procedures to expedite the planning, commencement,
progress and completion of Tenant Work. Landlord shall complete its review of each stage of Tenant’s Plans and any revisions thereof and communicate the results of such review within the time periods set forth in Section 3.2 above.

 3.4. City Requirements. Any changes in Tenant’s Plans which are made in response to requirements of the
applicable governmental authorities and/or changes which affect the Base Building Work shall be immediately submitted to Landlord for Landlord’s review and approval. 
 3.5. “As-Built” Drawings and Specifications. A CADD-DXF file on CD-ROM, pdf versions of the drawings on CD-ROM, and a set of “Xerox” type blackline on bond prints of all
“as-built” drawings and specifications of the Premises (reflecting all field changes and including, without limitation, architectural, structural, mechanical and electrical drawings and specifications) prepared by Tenant’s Architect
and Engineers or by Contractors (defined below) shall be delivered by Tenant at Tenant’s expense to the Landlord within thirty (30) days after completion of the Tenant Work. If Landlord has not received such drawings and CD-ROM(s) within
thirty (30) days, Landlord may give Tenant written notice of such failure. If Tenant does not produce such drawings and CD-ROM(s) within ten (10) days after Landlord’s written notice, Landlord may, at Tenant’s sole cost which may
be deducted from the Allowance, produce such drawings and CD-ROM(s) using Landlord’s personnel, managers, and outside consultants and contractors. Landlord shall receive an hourly rate reasonable for such production. 
  

	4.	Tenant Work. 

 4.1.
Tenant Work Defined. 
 (a) All tenant improvement work required by the Issued for Construction Documents (including,
without limitation, any approved changes, additions or alterations pursuant to Section 7 below) is referred to in this Workletter as “Tenant Work.” 
 (b) As part of the Tenant Work Tenant shall perform the work set forth on Exhibit B-2 hereto. 
 4.2. Tenant to Construct. Tenant shall construct all Tenant Work pursuant to this Workletter, and except to the extent modified by or inconsistent with express provisions of this Workletter,
pursuant with the provisions of the terms and conditions of Article Nine of the Lease, governing Tenant Alterations (except to the extent modified by this Workletter) and all such Tenant Work shall be considered “Tenant Alterations” for
purposes of the Lease. 
  

 Exhibit B - Page 4 

 4.3. Construction Contract. All contracts and subcontracts for Tenant Work shall
include any commercially reasonable terms and conditions required by Landlord. 
 4.4. Contractor. Tenant shall select
one or more contractors to perform the Tenant Work (“Contractor”) subject to Landlord’s prior written approval, which shall not unreasonably be withheld. 
 4.5. Division of Landlord Work and Tenant Work. Tenant Work is defined in Section 4.1. above and Landlord Work, if any, is defined in Section 2. 
  

	5.	Tenant’s Expense; Allowance; Special Allowances. 

 5.1. Tenant agrees to pay for all Tenant Work, including, without limitation, the costs of design thereof, whether or not all such costs are included in the “Permanent Improvement Costs”
(defined below). Subject to the terms and conditions of this Workletter, Tenant shall apply the “Allowance” (defined below) to payment of the Permanent Improvement Costs. The term “Permanent Improvement Costs” shall mean the
actual and reasonable costs of construction of that Tenant Work which constitutes permanent improvements to the Premises, actual and reasonable costs of design thereof and governmental permits therefor, costs incurred by Landlord for Landlord’s
architects and engineers pursuant to Section 3.1, and Landlord’s construction administration fee (defined in Section 8.10 below). Provided, however, Permanent Improvement Costs shall exclude costs of “Tenant’s FF&
E” (defined below). For purposes of this Workletter, “Tenant’s FF& E” shall mean furniture, furnishings, telephone systems, computer systems, equipment, any other personal property or fixtures, and installation thereof.
Landlord shall provide Tenant a tenant improvement allowance (“Allowance”) in the amount equal to Ten Dollars ($10.00) per square foot of the Rentable Area of the Premises (a total of Three Hundred Seventy-eight Thousand Five Hundred Sixty
Dollars [$378,560.00]). The Allowance shall be used solely to reimburse Tenant for the Permanent Improvement Costs. 
 5.2. In
addition to the Allowance set forth above, Landlord shall provide Tenant those certain allowances to be used solely to reimburse Tenant for the actual and reasonable costs incurred by Tenant for the Tenant Work specified on Exhibit B-2
hereto, which allowances consist of the following: the Special AC Allowance, Special Chiller/Boiler/Air Handler Allowance, Special Energy Management Allowance and Special Compressor and Vacuum Pump Allowance (collectively, the “Special
Allowances”). 
 5.3 If Tenant does not utilize one hundred percent (100%) of the Allowance for Permanent Improvement
Costs and one hundred percent (100%) of the Special Chiller/Boiler/Air Handler Allowance, Special Energy Management Allowance and Special Compressor and Vacuum Pump Allowance for the purposes for which each is permitted within one (1) year
after the Commencement Date of the Premises, Tenant shall have no right to the unused portion of the respective Allowance. If Tenant does not utilize one hundred percent (100%) of the Special AC Allowance for the purposes for which it is
permitted within two (2) years after the Commencement Date of the Premises, Tenant shall have no right to the unused portion of the Special AC Allowance. 
  

	6.	Application and Disbursement of the Allowance. 

 6.1. Landlord acknowledges that Tenant will perform the Tenant Work in phases, and that for each phase, Tenant may apply a portion of the Allowance and a portion of one or more of the Special Allowances
until either such Allowance or Special Allowance is exhausted or the time period

  

 Exhibit B - Page 5 

 
during which such Allowance or Special Allowance may be used has expired. Tenant shall prepare a budget for each phase of the Tenant Work, including the Permanent Improvement Costs and all other
costs of the Tenant Work (a “Budget”) prior to the commencement of such phase, which Budget shall be subject to the reasonable approval of Landlord. Each such Budget shall be supported by such documentation as Landlord reasonably may
require to evidence the total costs for such phase (Landlord and Tenant hereby acknowledge and agree that Tenant will not be required to deliver guaranteed maximum price construction contracts in support of the Budgets, but instead will deliver a
Budget for each phase with built-in contingencies to address potential cost overruns). To the extent the Budget for a phase requires funds in excess of the available Allowance and available Special Allowances that are applicable to such phase (such
excess, an “Excess Cost”), Tenant shall be solely responsible for payment of such Excess Cost. Further, prior to any disbursement of the Allowance by Landlord with respect to a phase, Tenant shall pay and disburse its own funds for all
that portion of the Permanent Improvement Costs included in such phase equal to the sum of (a) such Permanent Improvement Costs in excess of the then-available Allowance allocated to such phase, to the extent that there is any such excess; plus
(b) the amount of “Landlord’s Retention” (defined below). “Landlord’s Retention” shall mean an amount equal to fifteen percent (15%) of the portion of the Allowance allocated to the phase in question, which
Landlord shall retain out of the Allowance and shall not be obligated to disburse unless and until after Tenant has completed the applicable phase of the Tenant Work and complied with Section 6.4 below. Further, with respect to each phase,
Landlord shall not be obligated to make any disbursement of the Allowance unless and until Tenant has provided Landlord with (a) bills and invoices covering all labor and material expended and used, (b) an affidavit from Tenant stating
that all of such bills and invoices have either been paid in full by Tenant or are due and owing, and all such costs qualify as Permanent Improvement Costs, (c) contractors affidavit covering all labor and materials expended and used,
(d) Tenant, contractors and architectural completion affidavits (as applicable), and (e) valid mechanics’ lien releases and waivers pertaining to any completed portion of the Tenant Work which shall be conditional or unconditional, as
applicable, all as provided pursuant to Section 6.2 and 6.4 below. 
 6.2. With respect to each phase of the Tenant Work
and upon Tenant’s full compliance with the provisions of Section 6 for such phase, and if Landlord determines that there are no applicable or claimed stop notices (or any other statutory or equitable liens of anyone performing any of the
Tenant Work for such phase or providing materials for such phase of the Tenant Work) or actions thereon, Landlord shall disburse the applicable portion of the Allowance and/or the Special Allowances, as applicable, as follows: 
 (a) In the event of conditional releases, to the respective contractor, subcontractor, vendor, or other person who has
provided labor and/or services in connection with such phase of the Tenant Work, upon the following terms and conditions: (i) such costs are included in the Budget for such phase, are Permanent Improvement Costs, are covered by the Allowance or
Special Allowances, as applicable, and Tenant has completed and delivered to Landlord a written request for payment, in form reasonably acceptable to Landlord, setting forth the exact name of the contractor, subcontractor or vendor to whom payment
is to be made and the date and amount of the bill or invoice, (ii) the request for payment is accompanied by the documentation set forth in Section 6.1; and (iii) Landlord, or Landlord’s appointed representative, has inspected
and approved the work for which Tenant seeks payment; or 
 (b) In the event of unconditional releases, directly
to Tenant upon the following terms and conditions: (i) Tenant seeks reimbursement for costs of Tenant Work which have been paid by Tenant, are included in the Budget for such phase, are Permanent Improvement Costs, and are covered by the
Allowance or Special Allowances, as applicable; (ii) Tenant has completed and delivered to Landlord a request for payment, in form reasonably acceptable to Landlord, setting

  

 Exhibit B - Page 6 

 
forth the name of the contractor, subcontractor or vendor paid and the date of payment, (iii) the request for payment is accompanied by the documentation set forth in Section 6.1; and
(iv) Landlord, or Landlord’s appointed representative, has inspected and approved the work for which Tenant seeks reimbursement. 
 6.3. Provided that Tenant provides Landlord with the aforementioned documents by the 15th of any month, payment shall be made by Landlord by the 30th day of the month following the month in which such
documentation is provided. Notwithstanding any provision of this Workletter to the contrary, Tenant shall make requests for disbursement of the Allowance or Special Allowances, as applicable, and Landlord shall be obligated to pay to Tenant such
amounts as are payable, no more often than once per calendar month and only if the disbursement is for $100,000.00 or more, and otherwise such requests and payments shall be as set forth above. 
 6.4. Prior to Landlord disbursing the Landlord’s Retention to Tenant for a particular phase of the Tenant Work, Tenant shall submit to
Landlord the following items within sixty (60) days after completion of such phase of the Tenant Work: (i) “As Built” drawings and specifications pursuant to Section 3.5 above, (ii) all unconditional lien releases for
all work performed for such phase by all general contractor(s) and subcontractor(s) performing work for such phase, (iii) a “Certificate of Completion” for such phase prepared by Tenant’s Architect, and (iv) a final report
for such phase with supporting documentation detailing all actual costs associated with the Permanent Improvement Costs incurred for such phase. 
  

	7.	Changes, Additions or Alterations. 

 If Tenant desires to make any non-de minimis change, addition or alteration or desires to make any change, addition or alteration to any of the Building Systems after approval of the Issued for
Construction Documents, Tenant shall prepare and submit to Landlord plans and specifications with respect to such change, addition or alteration. Any such change, addition or alteration shall be subject to Landlord’s approval in accordance with
the provisions of Section 3.2 of this Workletter. Tenant shall be responsible for any submission to and plan check and permit requirements of the applicable governmental authorities. Tenant shall be responsible for payment of the cost of any
such change, addition or alteration if it would increase the Budget and Excess Cost previously submitted and approved pursuant to Section 6 above. 
  

	8.	Miscellaneous. 

 8.1.
Scope. Except as otherwise set forth in the Lease, this Workletter shall not apply to any space added to the Premises by Lease option or otherwise. 
 8.2. Tenant Work shall include (at Tenant’s expense) for all of the Premises: 
 (a) Landlord approved lighting sensor controls as necessary to meet applicable Laws; 
 (b) Building Standard
fluorescent fixtures in all Premises office areas; 
 (c) Building Standard meters for each of electricity and chilled water used
by Tenant shall be connected to the Building’s system and shall be tested and certified prior to Tenant’s occupancy of the Premises by a State certified testing company; 
 (d) Building Standard ceiling systems (including tile and grid) and; 
  

 Exhibit B - Page 7 

 (e) Building Standard air conditioning distribution and Building Standard air terminal
units. 
 8.3. Sprinklers. Subject to any terms, conditions and limitations set forth herein, Landlord shall provide an
operative sprinkler system consisting of mains, laterals, and heads “AS IS” on the date of delivery of the Premises to Tenant. Tenant shall pay for piping distribution, drops and relocation of, or additional, sprinkler system heads and
Premises firehose or firehose valve cabinets, if Tenant’s Plans and/or any applicable Laws necessitate such. 
 8.4.
Floor Loading. Floor loading capacity shall be within building design capacity. Tenant may exceed floor loading capacity with Landlord’s consent, at Landlord’s sole discretion and must, at Tenant’s sole cost and expense,
reinforce the floor as required for such excess loading. 
 8.5. Work Stoppages. If any work on the Real Property
other than Tenant Work is delayed, stopped or otherwise affected by construction of Tenant Work, Tenant shall immediately take those actions necessary or desirable to eliminate such delay, stoppage or effect on work on the Real Property other than
Tenant Work. 
 8.6. Life Safety. Tenant (or Contractor) shall employ the services of a fire and life-safety
subcontractor reasonably satisfactory to Landlord for all fire and life-safety work at the Building. 
 8.7. Locks.
Tenant agrees to purchase from Landlord or its representative all cylinders and keys used in locks used in the Premises. 
 8.8.
Authorized Representatives. Tenant has designated Loren Barrett to act as Tenant’s representative with respect to the matters set forth in this Workletter. Such representative(s) shall have full authority and responsibility to act on
behalf of Tenant as required in this Workletter. Tenant may add or delete authorized representatives upon five (5) business days notice to Landlord. 
 8.9. Access to Premises. Promptly after execution of this Amendment, Tenant and its architects, engineers, consultants, and contractors shall have access at reasonable times and upon advance notice
and coordination with the Building management, to the Premises for the purpose of planning and conducting Tenant Work. Such access shall not in any manner interfere with Landlord Work, if any. Such access, and all acts and omissions in connection
with it, shall be subject to and governed by all other provisions of the Lease, including, without limitation, Tenant’s indemnification obligations, insurance obligations, etc, except for the payment of Base Rent and Additional Rent. To the
extent that such access by Tenant delays the Substantial Completion of the Landlord Work (if any), such delay shall be a Tenant Delay and the Landlord Work shall be deemed Substantially Complete on the date such Landlord Work would have been
completed but for such access. 
 8.10. Fee. Landlord shall receive a construction administration fee equal to one
percent (1.0%) of the Allowance in connection with the construction of the Tenant Work. Such fee is in addition to Tenant’s reimbursement of costs incurred by Landlord pursuant to other provisions hereof, including, without limitation, for
Landlord’s architects and engineers to review Tenant’s Plans. 
  

	9.	Force and Effect. 

 The
terms and conditions of this Workletter shall be construed to be a part of the Lease and shall be deemed incorporated in the Lease by this reference. Should any inconsistency arise between this Workletter and the Lease as to the specific matters
which are the subject of this Workletter, the terms and conditions of this Workletter shall control. 
  

 Exhibit B - Page 8 

 EXHIBIT B-1 
 TO WORKLETTER AGREEMENT 
 LANDLORD WORK 
 Landlord Work shall mean the following work, to be performed by Landlord’s contractor(s): 
 1. Landlord shall make necessary repairs and/or replacements to put in good working condition the existing Building lighting and existing exit signs (on emergency battery power, and add such emergency
battery power for exit signs to the extent it does not exist as of the Commencement Date). 
 2. Landlord shall make necessary repairs and/or
replacements to put in good working condition the power to operate Landlord’s existing fire sprinkler system and sprinkler heads, including repair of any sagging ceilings and insulation obstructing operation of sprinkler heads; and Landlord
shall provide a copy of an updated 5-year certificate of the fire sprinkler system. 
 3. Landlord shall make necessary repairs and/or
replacements of: (a) copper condensate drain lines that have been removed (prior to the Commencement Date) from the Building; (b) copper cabling from the main power supply to the chiller that has been removed (prior to the Commencement
Date) from the Building. 
 4. If and to the extent that the City of Redwood City requires, as a condition of approval of Tenant Plans or Tenant
Work, installation of additional building exit ramp(s) to comply with Title III of the ADA, Landlord shall build such required ramp(s). If the City does not require installation of such additional ramp(s), Landlord shall install a new step at one
exit door location to be specified by Tenant. Notwithstanding any other provision of this Workletter to the contrary, such work shall be performed within a reasonable time after the City orders such additional ramp(s) or in the event the step is to
be installed, after the time has passed within which the City can order such additional ramp(s) and Tenant has specified the exit door location. 
 5. Notwithstanding any of the foregoing to the contrary, the Landlord Work described above shall be reduced to the extent any of the foregoing items described in Sections 1 – 3 above (for example only and without limitation, lighting,
power cabling, ceiling or insulation components) are to be removed, demolished or altered by Tenant in connection with anticipated Tenant Work. 
  

 Exhibit B-1 - Page 1 

 EXHIBIT B-2 
 TO WORKLETTER AGREEMENT 
 SPECIAL TENANT WORK 
 SPECIAL ALLOWANCES FOR SUCH WORK ONLY 
 Special Tenant Work shall mean the work set forth below, , subject to reimbursement by Landlord to the extent of the Special Allowances as specified below. All such work, including the design thereof, plans and specifications, contractors,
work and procedure for reimbursement to Tenant of costs of such work, shall be subject to and governed by the provisions of the Workletter applicable to Tenant Work and the Allowance, except that the amounts of the Special Allowances, time such
allowances shall be available and purposes for which each such allowance may be used, shall be as specified below. Upon installation, all such Special Tenant Work shall be deemed to be part of the Building and owned by Landlord. 
 1. Replacement of 13 Package AC Units on the Building’s Roof. Within 2 years after the Commencement Date, Tenant shall, subject to
reimbursement by Landlord to the extent of the “Special AC Allowance” specified below, replace the existing thirteen (13) rooftop air conditioning (“AC”) units serving the Building with new equipment of good quality (which
includes rooftop AC units, certain associated controls and ductwork, and related materials and expenses) (“AC Units”), sufficient to provide AC cooling capacity for the entire Building (no less than eighty-two [82] tons of AC cooling
capacity in the aggregate). The vendors, contractors and contracts for such AC Unit replacement shall be subject to Landlord’s prior written approval, including among other things, providing for warranties acceptable to Landlord and that such
warranties shall name Landlord and be issued directly for the benefit of and enforceable by Landlord. Tenant shall provide a replacement schedule to Landlord. Landlord shall provide the amount of One Hundred Fifty-three Thousand Six Hundred Dollars
($153,600) solely to reimburse Tenant’s actual and reasonable costs of such AC replacement, and only for such purpose (“Special AC Allowance”). If Tenant does not utilize one hundred percent (100%) of the Special AC Allowance for
the specified purpose within two (2) years after the Commencement Date, Tenant shall have no right to the unused portion of the Special AC Allowance. The Special AC Allowance shall be in addition to, and shall not diminish the Tenant’s
Allowance. 
 2. Chillers, Boilers, Boilers Exhaust Fans and Air Handlers on the Building’s Roof. Within one (1) year
after the Commencement Date, Tenant shall, subject to reimbursement by Landlord to the extent of the “Special Chiller/Boiler/Air Handler Allowance” specified below, repair and/or replace the existing chillers, boilers, exhaust fans and air
handlers on the roof of the Building in order to put such items in good working condition (the “Chiller/Boiler/Air Handler Work”). The vendors, contractors and contracts for such Chiller/Boiler/Air Handler Work shall be subject to
Landlord’s prior written approval, including among other things, providing for warranties acceptable to Landlord and that such warranties shall name Landlord and be issued directly for the benefit of and enforceable by Landlord. Landlord shall
provide the amount of Forty-nine Thousand Seven Hundred Forty-four Dollars ($49,744) solely to reimburse Tenant’s actual and reasonable costs of such Chiller/Boiler/Air Handler Work, and only for such purpose (“Special Chiller/Boiler/Air
Handler Allowance”). If Tenant does not utilize one hundred percent (100%) of the Special Chiller/Boiler/Air Handler Allowance for the specified purpose within one (1) year after the Commencement Date, Tenant shall have no right to
the unused portion of the Special Chiller/Boiler/Air Handler Allowance. The Special Chiller/Boiler/Air Handler Allowance shall be in addition to, and shall not diminish the Tenant’s Allowance. 
 3. Building Energy Management System. Within one (1) year after the Commencement Date, Tenant shall, subject to reimbursement by Landlord
to the extent of the “Special Energy Management Allowance” specified below, repair and/or replace the existing Building Energy Management System in

  

 Exhibit B-2 - Page 1 

 
order to put such items in good working condition (the “Energy Management Work”). The vendors, contractors and contracts for such Energy Management Work shall be subject to
Landlord’s prior written approval, including among other things, providing for warranties acceptable to Landlord and that such warranties shall name Landlord and be issued directly for the benefit of and enforceable by Landlord. Landlord shall
provide the amount of Twelve Thousand Four Hundred Ninety-three Dollars ($12,493) solely to reimburse Tenant’s actual and reasonable costs of such Energy Management Work, and only for such purpose (“Special Energy Management
Allowance”). If Tenant does not utilize one hundred percent (100%) of the Special Energy Management Allowance for the specified purpose within one (1) year after the Commencement Date, Tenant shall have no right to the unused portion
of the Special Energy Management Allowance. The Special Energy Management Allowance shall be in addition to, and shall not diminish the Tenant’s Allowance. 
 4. Air Compressor and Vacuum Pump on the Building’s Roof. Within one (1) year after the Commencement Date, Tenant shall, subject to reimbursement by Landlord to the extent of the
“Special Compressor and Vacuum Pump Allowance” specified below, inspect, repair and/or replace the existing air compressor and vacuum pump on the roof of the Building in order to put such items in good working condition (the
“Compressor and Vacuum Pump Work”). The vendors, contractors and contracts for such Compressor and Vacuum Pump Work shall be subject to Landlord’s prior written approval, including among other things, providing for warranties
acceptable to Landlord and that such warranties shall name Landlord and be issued directly for the benefit of and enforceable by Landlord. Landlord shall provide the amount of Seven Thousand Five Hundred Dollars ($7,500) solely to reimburse
Tenant’s actual and reasonable costs of such Compressor and Vacuum Pump Work, and only for such purpose (“Special Compressor and Vacuum Pump Allowance”). If Tenant does not utilize one hundred percent (100%) of the Special
Compressor and Vacuum Pump Allowance for the specified purpose within one (1) year after the Commencement Date, Tenant shall have no right to the unused portion of the Special Compressor and Vacuum Pump Allowance. The Special Compressor and
Vacuum Pump Allowance shall be in addition to, and shall not diminish the Tenant’s Allowance. 
  

 Exhibit B-2 - Page 2 

 EXHIBIT C 
 COMMENCEMENT DATE AGREEMENT 
 METROPOLITAN LIFE INSURANCE COMPANY, a New York corporation
(“Landlord”), and CODEXIS, INC., a Delaware corporation (“Tenant”), have entered into a certain Third Amendment to Lease, which Amendment is dated as of ________, 2008 (the “Amendment”). The original Lease, as amended
by the Amendment, may be referred to as the “Lease”. 
 WHEREAS, Landlord and Tenant wish to confirm and memorialize the Building 2
Commencement Date and Building 2 Expiration Date; 
 NOW, THEREFORE, in consideration of the foregoing and the mutual covenants contained herein
and in the Amendment, Landlord and Tenant agree as follows: 
 1. Unless otherwise defined herein, all capitalized terms shall
have the same meaning ascribed to them in the Amendment and the Lease. 
 2. The Building 2 Commencement Date is
                        . 
 3. The Building 2 Expiration Date is                     . 
 4. Tenant hereby confirms that: (a) it has accepted possession of the Building 2 Space pursuant to the terms of the Amendment; and
(b) the Lease is in full force and effect. 
 5. Except as expressly modified hereby, all terms and provisions of the Lease
are hereby ratified and confirmed and shall remain in full force and effect and binding on the parties hereto. 
 6. The Lease
and this Building 2 Commencement Date Agreement contain all of the terms, covenants, conditions and agreements between the Landlord and the Tenant relating to the subject matter herein. No prior other agreements or understandings pertaining to such
matters are valid or of any force and effect. 
  

					
	TENANT:	 	 CODEXIS, INC.,
 a Delaware corporation

		 
			
		 	By:	 	  

		 	Print Name:	 	  

		 	Title:	 	  

		
	LANDLORD:	 	METROPOLITAN LIFE INSURANCE COMPANY,
		 	a New York corporation
			
		 	By:	 	  

		 	Print Name:	 	  

		 	Title:	 	  

  

 Exhibit C - Page 1 

 EXHIBIT D 
 FORM OF LANDLORD’S CONSENT TO ENCUMBRANCE OF LIMITED COLLATERAL 
 THIS
LANDLORD’S CONSENT TO ENCUMBRANCE OF LIMITED COLLATERAL (the “Consent”) is made as of
                        , 2008 by and between Metropolitan Life Insurance Company, a New York corporation (“Met”
or “Landlord”), having an address at 425 Market Street, Suite 1050, San Francisco, CA 94105, and General Electric Capital Corporation, a Delaware corporation (“Agent”), having an address at 83 Wooster Heights Road, Fifth Floor,
Danbury, CT 06810, with reference to the following: 
 A. Met is the Landlord and Codexis, Inc., a Delaware corporation
(“Codexis” or “Tenant”) is the Tenant under that certain lease dated as of October     , 2003[sic], entered into by and between Landlord and Tenant, as amended by that certain First Amendment to Lease
by and between Landlord and Tenant dated June 1, 2004 and by that certain Second Amendment to Lease dated as of March 9, 2007 (as amended to date and hereafter, the “Lease”). As of the date hereof, the Lease is of the premises
particularly described in the Lease (the “Premises”), commonly known as 200 and 220 Penobscot Drive, 501 Chesapeake Drive and 640 Galveston Drive, in the buildings (the “Building”) located in Redwood City, California. As of the
date hereof, a draft of a possible Third Amendment to Lease to add to the Premises additional space commonly known as 400 Penobscot Drive has been exchanged between Landlord and Tenant, and hereafter Landlord and Tenant may enter into that or other
amendments of the Lease. References to the Lease, Premises and Building herein shall be deemed modified to have the same meaning as such terms have under the Lease, as amended from time to time. 
 B. Tenant and Agent represent to Landlord that Agent and certain other lenders (together with Agent, collectively, “Lenders”) and
Tenant have entered into, or are about to enter into, a Loan and Security Agreement, dated on or about September     , 2007, pursuant to which Tenant has or will borrow, or obtain a line of credit, up to a maximum
principal amount of Fifteen Million Dollars ($15,000,000.00) to be used by Tenant for working capital purposes (as amended, restated, supplemented or otherwise modified from time to time, the “Loan Agreement”, provided however, this
Consent shall have no force or effect if and to the extent that Lenders permit or suffer the maximum principal amount to increase above the amount stated above) and pursuant to which Tenant has granted or will grant to Agent, on behalf of Agent and
the other Lenders, a security interest in certain assets owned by Tenant described on Exhibit A hereto, all or part of which is from time to time installed or located at the Premises (the “Collateral”). 
 C. Tenant has requested that Landlord consent to the encumbrance of the Collateral. Landlord is not willing to consent to encumbrance of the
Collateral, but subject to and with certain clarifications and limitations set forth in Exhibit A hereto defining and describing the “Limited Collateral”, Landlord is willing to consent to encumbrance of the Limited Collateral upon
and subject to the following terms and conditions: 
 NOW, THEREFORE, in consideration of the covenants and conditions contained
herein, and for other good and valuable consideration, receipt of which is hereby acknowledged, Landlord and Agent agree as follows: 
 1 During the term of the Loan Agreement, Landlord hereby consents to the encumbrance of the Limited Collateral and agrees to subordinate to the interest of Agent in the Limited Collateral any Landlord’s lien in or to the Limited
Collateral existing by reason of the Lease and the location of the Limited Collateral in the Premises; provided, however, that said consent and subordination shall be ineffective to the extent that Agent has released its security interest in the
Limited Collateral. 
  

 Exhibit D - Page 1 

 2 Subject to Agent’s obligations pursuant to Sections 4 and 5 hereof, Landlord agrees
that the Limited Collateral is and shall remain personal property. 
 3 Subject to the rights of Tenant under the Lease,
Landlord will permit Agent reasonable access onto the Premises for the purpose of exercising any right it may have under the terms of the Loan Agreement, including, without limitation, the right to remove the Limited Collateral, subject to all the
terms and conditions hereof. 
 4 To the extent that Tenant or Agent do not remove Limited Collateral which is located in the
Premises prior to the expiration or earlier termination of the Lease, after such expiration or termination Landlord may deem such Limited Collateral abandoned property, except if and to the extent that Agent has obtained additional time to remove
the Limited Collateral pursuant to Section 5 below. Subject to Landlord’s obligations under Section 6 below, Agent understands that Tenant is to bear the obligation of notifying Agent of Tenant’s default under the Lease or of the
expiration or earlier termination of the Lease, and that Landlord has no obligation to notify Agent or Lenders. 
 5
Agent’s right to enter the Premises is further subject to the following terms and conditions: 
 5.1 Subject to the rights
of Tenant under the Lease, Agent shall have the right to enter onto the Premises and take possession of the Limited Collateral provided that Agent (i) gives Landlord written notice that it seeks to enter and take possession of the Limited
Collateral, which notice shall include a representation by Agent that it is entitled to take possession of the Limited Collateral, and (ii) coordinates the date and time of possession with Landlord or Landlord’s managers prior thereto, and
such date may be no earlier than one (1) day after Landlord’s receipt of such notice and no later than eighteen (18) days after Landlord’s receipt of such notice, unless Landlord, in Landlord’s sole discretion, in writing
allows entry earlier or later. Tenant agrees that Landlord may rely on such representation by Agent without further inquiry or any obligation to verify same. Tenant hereby waives any claims it may have against Landlord which arise out of or are
connected with Landlord’s actions in compliance with such notice from Agent. 
 5.2 Except as provided below, in no event
shall Agent have the right to enter the Premises during any period for which the rent is unpaid by Tenant before or after termination of the Lease. Agent shall have a right of entry for eighteen (18) days after the earlier of the date Agent
gives notice to Landlord pursuant to Section 5.1 or Landlord gives notice to Agent pursuant to Section 6, provided that Agent pays Landlord rent for the number of days Agent requires entry to the Premises at the daily rental rate
calculated by dividing by thirty (30) the sum of the monthly base rent plus rent equal to the expenses and taxes payable by Tenant for the same period under the Lease (as such amounts are more particularly described in the Lease). The payment
of daily rental for the number of days Agent requires entry to the Premises is a condition precedent prior to any such entry. In the event that Agent removes all (and not less than all) the Limited Collateral and in fact uses a shorter period for
its entry than the number of days entry for which it paid in advance on an estimated basis, then Landlord shall reimburse Agent for any excess rental paid at the daily rate. Agent shall not have any rights whatsoever for its right of entry to be
longer than eighteen (18) days after the date of the applicable notice, and in the event that both parties have given notice, after the earliest notice given. Notwithstanding any of the foregoing to the contrary, Agent (a) shall not be
required to pay any rent if, within the initial seven days after the date the earliest such notice was given, Agent removes all (and not less than all) the Limited Collateral, or (b) shall not be required to pay rent for the initial seven days
after the date the earliest such notice was given unless Agent fails to remove all (and not less than all) the Limited Collateral within the eighteen (18) day period after the date the earliest such notice was given. 
  

 Exhibit D - Page 2 

 5.3 Agent shall not have the right to conduct or cause to be conducted any auction at the
Premises. 
 5.4 If Agent, in removing the Limited Collateral, damages any improvements at the Premises or the building of which
the Premises is a part, Agent, at its sole expense, shall cause the same to be repaired and restored to a condition at least equal to the condition existing immediately prior to the installation of the Limited Collateral. 
 6 So long as the Loan Agreement is in effect, Landlord agrees to subordinate to the interest of Agent in the Limited Collateral any
Landlord’s lien in or to the Limited Collateral existing by reason of the Lease and the location of the Limited Collateral in the Premises; provided, however, that said consent and subordination shall be ineffective to the extent that Agent has
released its security interest in the Limited Collateral. In the event that Landlord has not received notice from Agent given pursuant to Section 5.1 and Landlord finds it necessary to remove all or part of the Limited Collateral in the
exercise of any right under the Lease, then Landlord shall notify Agent of such necessity and Agent shall be given the right to enter the Premises for no more than eighteen (18) days after such notice, for the purpose of removing all of the
Limited Collateral from the Premises. Agent’s right to enter the Premises is subject to Agent’s obligation to pay rent as set forth in Section 5.2. Landlord is under no obligation to store the Limited Collateral for the benefit of
Agent beyond eighteen (18) days after the earlier of the date Agent gave notice pursuant to Section 5.1 or the date Landlord gave notice to Agent under this Section. Accordingly, upon the expiration of such eighteen (18) day notice
period, if Agent has not removed the Limited Collateral from the Premises then Agent’s lien and all right, title and interest of Agent in the Limited Collateral shall be deemed to be abandoned and all Limited Collateral located in the Premises
may be removed, sold and/or disposed of as Landlord may elect in its sole discretion. Further, if Agent seeks to remove the Limited Collateral (to the extent not sold or otherwise disposed of by Landlord) after such eighteen (18) day period,
and Landlord, in its sole discretion consents to such removal, Agent shall be liable for all of Landlord’s costs incurred in connection with storage at the Premises, removal and storage elsewhere, and with any aborted sale and notices and
advertising therefor. Further, within ninety (90) days after expiration of such eighteen (18) day period, with respect to all such Limited Collateral deemed abandoned, Agent shall file and/or record, in the formal record system for
perfection of security interests of applicable jurisdictions, appropriate documentation evidencing the abandonment, release and termination of Agent’s security interest in such Limited Collateral and Agent shall deliver to Landlord a copy of
such documents filed and/or recorded. 
 7 To the extent permitted by law, Agent shall protect, defend, indemnify and hold
harmless Landlord and its agents and managers from and against any and all actions, causes of action, claims, losses, costs, expenses, damages and liabilities, including without limitation reasonable attorneys’ fees, arising out of or in any
way connected with the acts or negligence of Agent in connection with any entry to the Premises or the project in which the Premises is located. 
 8 All representations, warranties and indemnifications made or given by Agent herein, together with any causes of action, rights and remedies which Landlord has or may have as a result of a breach of any
term of this Consent, shall survive any expiration or termination of this Consent. 
 9 Intentionally omitted. 
 10 This Consent is only a subordination of lien rights with express terms and conditions of a right of entry; and shall not be deemed or
construed to be a consent to anything else including, but not limited to, alterations on the Premises. 
  

 Exhibit D - Page 3 

 11 Landlord makes no representation or warranty as to the ownership of the Limited
Collateral or the priority of the security interest of the Agent. Agent acknowledges that Landlord, at the request of Tenant, has previously been asked may in the future be asked to execute one or more such consents in favor of other personal
property lenders and/or personal property lessors. Landlord is under no duty whatsoever to advise Agent in the event the Limited Collateral described herein shall be scheduled or claimed by any other such lender or personal property lessor. Tenant
and Agent hereby agree that Landlord shall have no liability arising out of or relating to the entry by Agent upon the Premises for the purpose of removal of the Limited Collateral. 
 12 At all times during any entry by Agent for the purpose of removal of any of the Limited Collateral from the Premises under this consent,
Agent shall maintain comprehensive general liability insurance, on an occurrence basis, in the amount of at least Five Million dollars ($5,000,000.00), covering the acts and omissions of Agent, its agents and contractors, issued by reputable
companies licensed to do business in California, and naming Landlord as an additional insured. Prior to any such entry Agent shall provide Landlord with a certificate of such insurance reasonably satisfactory to Landlord. So long as General Electric
Capital Corporation, a Delaware corporation, is the Agent acting on behalf of Lenders and personally holds the security interest in the Limited Collateral as such Agent, then its insurance shall not be required to name Landlord as additional insured
and a certificate of insurance shall not be required. 
 13 This Consent may not be modified or amended except by written
agreement of the parties hereto. 
 14 This Agreement may not be recorded. 
 15 All notices required to be given hereunder shall be in writing, and shall be mailed by certified mail, return receipt requested, or by
nationally recognized overnight courier service that provides proof of delivery. Notices shall be deemed effective upon the date actually received, date receipt is refused or date of inability to deliver due to change of address without notice.

 Notices to Landlord shall be addressed: 
 Metropolitan Life Insurance Company 
 425 Market Street, Suite 1050 
 San Francisco, California 94105 
 Attention: Director, EIM 
 with copies to the following: 
 Metropolitan Life Insurance Company 
 425 Market Street, Suite 1050 
 San Francisco, California 94105 
 Attention: Associate General Counsel 
  

 Exhibit D - Page 4 

 Notices to Agent shall be addressed: 
 General Electric Capital Corporation 
 c/o GE Healthcare Financial Services, Inc., LSF 
 83 Wooster Heights Road, Fifth
Floor 
 Danbury, CT 06810 
 Attention: Senior Vice President of Risk 
 Phone: (203) 205-5200 

Facsimile: (203) 205-2192 
 with a copy to: 
 General Electric Capital Corporation 
 c/o GE Healthcare Financial Services, Inc. 
 Two Bethesda Metro Center, Suite 600 
 Bethesda, MD 20814 
 Attention: General Counsel 
 Phone: (301) 961-1640 
 Facsimile: (301) 664-9866 
 Notices to Tenant shall be addressed: 
 Codexis, Inc. 
 200 Penobscot Drive 
 Redwood City, California 94063 
 Attention: Director of Finance 
 16 In the event either party shall bring any
action against the other for any matter arising out of or relating to this Consent, the prevailing party shall be entitled to recover reasonable attorney’s fees and costs. 
 17 This Consent shall be binding upon and inure to the benefit of the respective heirs, administrators, successors and assigns to the
parties hereto. 
 18 Each of Agent, Landlord and Tenant separately and for itself warrants and represents that the person or
persons signing below is or are duly authorized to execute this Consent on its behalf. 
  

 Exhibit D - Page 5 

 IN WITNESS WHEREOF, the undersigned have duly executed this Landlord’s Consent to
Encumbrance of Limited Collateral as of the day and year first above written. 
  

									
	LANDLORD:	 	 	 	AGENT:	 	 
			
	METROPOLITAN LIFE INSURANCE
 COMPANY, a New York corporation

	 		 	GENERAL ELECTRIC CAPITAL
 CORPORATION, a Delaware
corporation

					
	By:	 	  
	 		 	By:	 	  

	Name:	 	  
	 		 	Name:	 	  

	Its:	 	  
	 		 	Its:	 	  

 AGREED, as of the day and year first above written, for the purposes of the Recitals, Section 5,
Section 11 and Sections 13 through 18 hereof. 
  

			
	
	TENANT:
	CODEXIS, INC., a Delaware corporation
		
	By	 	  

	Name:	 	  

	Its	 	  

  

 Exhibit D - Page 6 

 EXHIBIT A 
 TO LANDLORD’S CONSENT TO ENCUMBRANCE OF LIMITED COLLATERAL 
 DESCRIPTION OF
COLLATERAL 
 Certain assets of Tenant, including, without limitation, all of Tenant’s cash, cash equivalents, accounts, books and
records, goods, inventory, machinery, equipment, furniture and trade fixtures (such as equipment bolted to floors), together with all addition, substitutions, replacements and improvements to, and proceeds, including, insurance proceeds, of the
foregoing, but excluding building fixtures (such as plumbing, lighting and HVAC systems) (collectively, the “Collateral”) 
 DESCRIPTION OF LIMITED COLLATERAL 
 The “Limited Collateral” shall mean the following personal property owned by
Tenant: all of Tenant’s cash, cash equivalents, accounts, books and records, goods, inventory, machinery not permanently affixed to the Premises, equipment not permanently affixed to the Premises, furniture and trade fixtures not permanently
affixed to the Premises, together with all addition, substitutions, replacements and improvements to, and proceeds, including, insurance proceeds, of the foregoing, and for avoidance of doubt the following shall not be part of the “Limited
Collateral”: (a) walls, ceilings, flooring, building fixtures (such as plumbing, power, lighting and HVAC systems), including without limitation all improvements made as part of the Special Tenant Work (as defined in the Third Amendment to
Lease dated as of                 , 2008); (b) all improvements installed in the 640 Galveston Space (as defined in the Second Amendment to Lease dated as of
March 9, 2007) by Landlord prior to March 9, 2007 or thereafter permanently affixed to the 640 Galveston Space, including, without limitation, all lab benches and corresponding casework, lab sinks, lab hoods, supplemental or special
ventilating and air conditioning equipment, and any and all lab installations and fixtures, unless pursuant to express provision of the Lease or a written agreement between Landlord and Tenant, Tenant is permitted or required to remove a
specified item or items and such item or items is listed below; and (c) insurance proceeds to which Landlord is entitled pursuant to the Lease, including without limitation, insurance proceeds of any tangible property, machinery, equipment or
trade fixtures which is permanently affixed to the Premises. For the avoidance of doubt, the term “permanently affixed” in the preceding sentence shall not be construed to mean otherwise free-standing equipment that has been secured to the
Premises for the primary purpose of seismic stability and/or the prevention of theft. If pursuant to Section 4 of the Third Amendment, Landlord has agreed in writing, in response to written request made by Tenant, that specified equipment or
trade fixtures paid for entirely by Tenant (without reimbursement in full or part out of any funds provided by Landlord) be included as part of the Limited Collateral, which items shall be specifically identified in writing delivered by Tenant to
Landlord, including the building address and location within the building where the items are located, such items shall be listed below and thereby be part of the Limited Collateral. 
 [IF APPLICABLE, SPECIFICALLY LIST ITEM OF EQUIPMENT AND LOCATION BY BUILDING ADDRESS & LOCATION WITHIN THE BUILDING.] 
  

 Exhibit D - Page 7Master Security Agreement

 Exhibit 10.9 
 Master Security Agreement No. 5081102 
 MASTER SECURITY
AGREEMENT 
 No. 5081102 
 Dated as of October 25, 2005 (“Agreement”) 
 THIS
AGREEMENT is between Oxford Finance Corporation (together with its successors and assigns, if any, “Secured Party”) and Codexis, Inc. (“Debtor”). Secured Party has an office at 133 N.
Fairfax Street, Alexandria, VA 22314. Debtor is a corporation organized and existing under the laws of the state of Delaware. Debtor’s mailing address and chief place of business is 200 Penobscot Drive, Redwood City, CA 94063. 
  

	1.	CREATION OF SECURITY INTEREST. 

 Debtor grants to Secured Party, its successors and assigns, a security interest in and against all property listed on any collateral schedule now or in the future annexed to or made a part of this Agreement (“Collateral
Schedule”), and in and against all additions, attachments, accessories and accessions to such property, all substitutions, replacements or exchanges therefor, and all insurance and/or other proceeds thereof (all such property is
individually and collectively called the “Collateral”). This security interest is given to secure the payment and performance of all debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now
existing or arising in the future, including but not limited to the payment and performance of certain Promissory Notes from time to time identified on any Collateral Schedule (collectively “Notes” and each a
“Note”), and any renewals, extensions and modifications of such debts, obligations and liabilities (such Notes, debts, obligations and liabilities are called the “Indebtedness”). Debtor acknowledges
that, notwithstanding that the Note(s) may be paid in full, this Security Agreement shall continue to secure the payment and performance of all other debts, obligations and liabilities of any kind whatsoever of Debtor to Secured Party, now existing
or arising in the future, and that Secured Party shall be under no obligation to release the Collateral unless and until all Indebtedness of Debtor to Secured Party has been paid and satisfied; provided, however, Secured Party, in its sole and
exclusive discretion, may elect to release some of the Collateral without prejudice to Secured Party’s security interest in the remaining Collateral. 
  

	2.	REPRESENTATIONS, WARRANTIES AND COVENANTS OF DEBTOR. 

 Debtor represents, warrants and covenants as of the data of this Agreement and as of the date of each Collateral Schedule that: 
  

	 	(a)	Due Organization. Debtor’s exact legal name is as set forth in the preamble of this Agreement and Debtor is, and will remain, duly organized, existing and
in good standing under the laws of the State set forth in the preamble of this Agreement, has its chief executive offices at the location specified in the preamble, and is, and will remain duly qualified and licensed in every jurisdiction wherever
necessary to carry on its business and operations; 

  

	 	(b)	Power and Capacity to Enter Into and Perform Obligations. Debtor has adequate power and capacity to enter into, and to perform its obligations under this
Agreement, each Collateral Schedule, each Note and any other documents evidencing, or given in connection with, any of the Indebtedness (all of the foregoing are called the “Debt Documents”); 

  

					
		  	Page 1 of 26	  	Codexis Initial Here:                     
		  		  	Oxford Initial Here:                     

 Master Security Agreement No. 5081102 
  

	 	(c)	Due Authorization. This Agreement and the other Debt Documents have been duly authorized, executed and delivered by Debtor and constitute legal, valid and
binding agreements enforceable in accordance with their terms, except to the extent that the enforcement of remedies may be limited under applicable bankruptcy and insolvency laws; 

  

	 	(d)	Approvals and Consents. No approval, consent or withholding of objections is required from any governmental authority or instrumentality with respect to the
entry into, or performance by Debtor of any of the Debt Documents, except any already obtained; 

  

	 	(e)	No Violations or Defaults. The entry into, and performance by, Debtor of the Debt Documents will not (i) violate any of the organizational documents of
Debtor or any judgment, order, law or regulation applicable to Debtor, or (ii) result in any breach of or constitute a default under any contract to which Debtor is a party, or result in the creation of any lien, claim or encumbrance on any of
Debtor’s property (except for liens in favor of Secured Party) pursuant to any indenture, mortgage, deed of trust, bank loan, credit agreement, or other agreement or instrument to which Debtor is a party; 

  

	 	(f)	Litigation. There are no suits or proceedings pending in court or before any commission, board or other administrative agency against or affecting Debtor which
could, in the aggregate, have a material adverse effect on Debtor, its business or operations, or its ability to perform its obligations under the Debt Documents, nor does Debtor have reason to believe that any such suits or proceedings are
threatened; 

  

	 	(g)	Solvency. The fair salable value of Debtor’s assets (including goodwill minus disposition costs) exceeds the fair value of its liabilities; the Debtor is
not left with unreasonably small capital after the transactions in this Agreement or any Collateral Schedule and Debtor is able to pay its debts (including trade debts) as they mature; 

  

	 	(h)	Financial Statements. All financial statements relating to Debtor that have been or may hereafter be delivered by Debtor to Secured Party present fairly in all
material respects Debtor’s financial condition as of the date thereof and Debtor’s results of operations for the period then ended, and since the date of the most recent financial statement, there has been no material adverse change in
Debtor’s financial condition; 

  

	 	(i)	Use of Collateral. The Collateral is not, and will not be, used by Debtor for personal, family or household purposes; 

  

					
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	 	(j)	Collateral in Good Condition and Repair. The Collateral is, and will remain, in good condition and repair and Debtor will not be negligent in its care and use;

  

	 	(k)	Location of Collateral. All of the tangible Collateral is located at the locations set forth on each Collateral Schedule. Debtor shall give the Secured Party 30
days prior written notice of any relocation of any Collateral; 

  

	 	(l)	Ownership of Collateral. Debtor 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; 

  

	 	(m)	Encumbrances. The Collateral is, and will remain, free and clear of all liens, claims and encumbrances of any kind whatsoever, except for Permitted Liens;

  

	 	(n)	Intellectual Property Rights. Debtor will (i) protect, defend and maintain the validity and enforceability of the Intellectual Property and promptly advise
Secured Party in writing of material infringements and (ii) not allow any Intellectual Property material to Debtor’s business, as determined by Debtor in its good faith and reasonable discretion, to be abandoned, forfeited or dedicated to
the public without Secured Party’s written consent; 

  

	 	(o)	Taxes. All federal, state and local tax returns required to be filed by Debtor have been filed with the appropriate governmental agencies by the date due
(including any extensions) and all taxes due and payable by Debtor have been timely paid. Debtor will pay when due all taxes, assessments and other liabilities except as contested in good faith and by appropriate proceedings and for which adequate
reserves have been established; 

  

	 	(p)	No Defaults. No event or condition exists under any material agreement, instrument or document to which Debtor is a party or may be subject, or by which Debtor
or any of its properties are bound, which constitutes a default or an event of default thereunder, or will, with the giving of notice, passage of time, or both, would constitute a default or event of default thereunder; 

  

	 	(q)	Certification of Financial Information. All reports, certificates, schedules, notices and financial information submitted by Debtor to the Secured Party pursuant
to this Agreement shall be certified as true and correct by the president or chief financial officer of Debtor; 

  

	 	(r)	Notice of Material Adverse Change. Debtor shall give the Secured Party prompt written notice of any event, occurrence or other matter which (a) has resulted
or may result in a material adverse change in its financial condition or business operations of Debtor, or (b) which would impair the ability of Debtor to perform its obligations hereunder or under any of the other financing agreements to which
it is a party, or (c) which would impair the ability of Secured Party to enforce the Indebtedness or realize upon the Collateral; 

  

					
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	 	(s)	Change in Management. Debtor shall not, without giving prior written notice to Secured Party, change the persons holding the offices of Chief Executive Officer
or Chief Financial Officer; 

  

	 	(t)	Transactions with Affiliates. Debtor shall not, without the prior written consent of Secured Party, directly or indirectly enter into or permit to exist any
material transaction with any Affiliate of Debtor except for transactions that are in the ordinary course of Debtor’s business, upon fair and reasonable terms that are no less favorable to Debtor than would be obtained in an arm’s length
transaction with a nonaffiliated Person; 

  

	 	(u)	[intentionally omitted] 

  

	 	(v)	Perfection Certificate. Debtor has previously delivered to the Secured Party a certificate signed by the Debtor and entitled “Perfection Certificate”
(the “Perfection Certificate”). The Debtor represents and warrants to the Secured Party as follows: (a) the Debtor’s exact legal name is that indicated on the Perfection Certificate and on the signature page hereof,
(b) the Debtor is an organization of the type, and is organized in the jurisdiction set forth in the Perfection Certificate, (c) the Perfection Certificate accurately sets forth the Debtor’s organizational identification number or
accurately states that the Debtor has none, (d) the Perfection Certificate accurately sets forth the Debtor’s place of business or, if more than one, its chief executive office, as well as the Debtor’s mailing address, if different,
(e) all other information set forth on the Perfection Certificate pertaining to the Debtor is accurate and complete, and (f) that there has been no change in any information provided in the Perfection Certificate since the date on which it
was executed by the Debtor; 

  

	 	(w)	Primary Account and Wire Transfer Instructions. Debtor maintains its Primary Account (the “Primary Operating Account”) and the Wire
Transfer Instructions for the Primary Operating Account are as follows: 

 Wells Fargo Bank

 P.O. Box 150, 400 Hamilton Ave. 
 Palo Alto, CA 94301 
 ABA No.: 121000248 
 Account No.: 403-0003362 
 Account Name: Codexis, Inc. 
 Debtor hereby agrees that Loans will be advanced to the account specified above and regularly scheduled payments will be automatically debited from the same account; 
  

	 	(x)	[intentionally omitted] 

  

	 	(y)	 Notice of Investor Abandonment. Debtor shall give the Secured Party prompt written notice if (a) it is the clear intention of Debtor’s
investors to not continue to

  

					
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fund the Debtor in the amounts and timeframe necessary to enable Debtor to satisfy the Indebtedness as it becomes due and payable or (b) there is a material impairment in the perfection or
priority of the Secured Party’s security interest in the Collateral; and 

  

	 	(z)	Indebtedness to Maxygen. Without the prior written consent of Secured Party, which consent shall not be unreasonably withheld or delayed, Debtor shall not
create, incur, assume or permit to exist any Indebtedness to Maxygen, Inc. (“Maxygen”) in excess of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000) in aggregate in any fiscal year, nor shall Debtor make any payments to
Maxygen in any fiscal year in excess of the lower of: (i) the aggregate of the fair market value of services provided by Maxygen to Debtor during such fiscal year, or (ii) the aggregate of One Million, Two Hundred Twenty-Five Thousand
Dollars ($1,225,000). Notwithstanding the foregoing, Debtor shall be permitted to pay the balance of previously incurred, existing and anticipated Indebtedness to Maxygen up to a total amount of One Million, Five Hundred Thousand Dollars
($1,500,000) for the period January 1, 2005 to December 31, 2005. 

  

	3.	COLLATERAL. 

 The Debtor
covenants and agrees that, so long as any of the Debt Documents shall remain in effect, or unless the Secured Party shall otherwise consent in writing: 
  

	 	(a)	Possession of Collateral; Inspection of Collateral. Until the declaration of any default, Debtor shall remain in possession of the Collateral, except as
necessary for maintenance and repair, except as specified in Section 3(c), and except that Secured Party shall have the right to possess (i) any chattel paper or instrument that constitutes a part of the Collateral, and (ii) any other
Collateral in which Secured Party’s security interest may be perfected only by possession. Secured Party may inspect any of the Collateral during normal business hours after giving Debtor reasonable prior notice. 

  

	 	(b)	Maintenance of Collateral. Debtor shall (i) use the Collateral only in its trade or business, (ii) maintain all of the Collateral in good operating
order and repair, normal wear and tear excepted, (iii) use and maintain the Collateral only in compliance with manufacturers recommendations and all applicable laws, and (iv) keep all of the Collateral free and clear of all liens, claims
and encumbrances (except for Permitted Liens). 

  

	 	(c)	 Disposition of Collateral. Secured Party does not authorize and Debtor agrees it shall not (i) part with possession of any of the
Collateral (except to Secured Party or for maintenance and repair), (ii) locate any of the Collateral outside the continental United States, other than any Collateral necessary for the operation of Debtor’s subsidiary location in Germany
in an aggregate value not exceeding $300,000.00, with all of any such Collateral located at Debtor’s subsidiary location in Germany to be financed by Secured Party as soft costs, and with

  

					
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ownership to all of such Collateral located at Debtor’s subsidiary location in Germany to be retained by Debtor and not passed to its subsidiary; or (iii) sell, rent, lease, mortgage,
license, grant a security interest in or otherwise transfer or encumber (except for Permitted Liens) any of the Collateral. 

  

	 	(d)	Taxes. Debtor shall pay promptly when due all taxes, license fees, assessments and public and private charges levied or assessed on any of the Collateral, on its
use, or on this Agreement or any of the other Debt Documents. At its option, Secured Party may discharge taxes, liens, security interests or other encumbrances at any time levied or placed on the Collateral and may pay for the maintenance, insurance
and preservation of the Collateral and effect compliance with the terms of this Agreement or any of the other Debt Documents. Debtor agrees to reimburse Secured Party, on demand, all costs and expenses incurred by Secured Party in connection with
such payment or performance and agrees that such reimbursement obligation shall constitute Indebtedness. 

  

	 	(e)	Books and Records. Debtor shall, at all times, keep accurate and complete records of the Collateral, and Secured Party shall have the right to inspect and make
copies of all of Debtor’s books and records relating to the Collateral during normal business hours, after giving Debtor reasonable prior notice. 

  

	 	(f)	Third Party Possession of Collateral. Debtor agrees and acknowledges that any third person who may at any time possess all or any portion of the Collateral shall
be deemed to hold, and shall hold, the Collateral as the agent of, and as pledge holder for, Secured Party. Secured Party may at any time give notice to any third person described in the preceding sentence that such third person is holding the
Collateral as the agent of, and as pledge holder for, the Secured Party. 

  

	 	(g)	Change of Address, Name or Jurisdiction. The Debtor has not at any time within the past four (4) months either changed its name or changed the state of
jurisdiction in which it is organized and existing, nor has it maintained its chief executive office or any of the Collateral at any other location, except as set forth above, and shall not do so hereafter except upon prior written notice to the
Secured Party. The Secured Party shall be entitled to rely upon the foregoing unless it receives 14 days’ advance written notice of a change in the Debtor’s name, state of jurisdiction, address of the Debtor’s chief executive offices
or location of the Collateral. 

  

	 	(h)	Fixtures. Not permit any item of the Collateral to become a fixture to real estate or an accession to other property without the prior written consent of the
Secured Party, and the Collateral is now and shall at all times remain personal property except with the Secured Party’s prior written consent. If any of the Collateral is or will be attached to real estate in such a manner as to become a
fixture under applicable state law and if such real estate is encumbered, the Debtor will obtain from the holder of each Lien or encumbrance a written consent and subordination to the security interest hereby granted, or a written disclaimer of any
interest in the Collateral, in a form acceptable to the Secured Party. 

  

					
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	 	(i)	Distributions. Debtor shall not (i) pay any dividends or make any distributions on its equity securities; (ii) purchase, redeem, retire, defease or
otherwise acquire for value any of its equity securities, other than repurchases pursuant to the terms of employee stock purchase plans, employee restricted stock agreements or similar arrangements in an aggregate amount not to exceed One Hundred
Thousand Dollars ($100,000); (iii) return any capital to any holder of its equity securities as such; (iv) make any distribution of assets, equity securities, obligations or securities to any holder of its equity securities as such; or
(v) set apart any sum for any such purpose; provided, however, Debtor may pay dividends payable solely in common stock. 

  

	 	(j)	Indebtedness Payments. Debtor shall not (i) prepay, redeem, purchase, defease or otherwise satisfy in any manner prior to the scheduled repayment thereof
any Additional Indebtedness for borrowed money or lease obligations, (ii) amend, modify or otherwise change the terms of any Additional Indebtedness for borrowed money or lease obligations so as to accelerate the scheduled repayment thereof or
(iii) repay any notes to officers, directors or shareholders except as expressly provided for in a duly executed subordination agreement in favor of, and approved by Secured Party. 

  

	 	(k)	Bridge Loans. Debtor shall not incur any indebtedness for borrowed money or lease obligations (collectively, “Bridge Loans”) from any of
its officers, directors or shareholders (collectively, “Bridge Loan Lenders”) unless each of the Bridge Loan Lenders have executed and delivered subordination agreements in favor of Secured Party, in form satisfactory to
Secured Party, which subordinate all of the Bridge Loans to the Indebtedness, and which permit repayment of the Bridge Loans from the proceeds of new equity investments and loans. 

  

	4.	INSURANCE. 

  

	 	(a)	Risk of Loss. Debtor shall at all times bear the entire risk of any loss, theft, damage to, or destruction of, any of the Collateral from any cause whatsoever.

  

	 	(b)	 Insurance Requirements. Debtor agrees to keep the Collateral insured against loss or damage by fire and extended coverage perils, theft,
burglary, and for any or all Collateral, which are vehicles, for risk of loss by collision, and if requested by Secured Party, against such other risks as Secured Party may reasonably require. The insurance coverage shall be in an amount no less
than the full replacement value of the Collateral, and deductible amounts, insurers and policies shall be acceptable to Secured Party. Debtor shall deliver to Secured Party policies or certificates of insurance evidencing such coverage. Each policy
shall name Secured Party as a loss payee, shall provide for coverage to Secured Party regardless of the breach by Debtor of any warranty or representation made therein, shall not be subject to co-insurance, and shall provide that coverage may not be
canceled or altered by the insurer without a good faith endeavor by insurer to provide thirty (30) days prior written notice to Secured Party. Debtor appoints Secured Party as its attorney-in-fact to make proof of loss, claim for insurance and

  

					
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adjustments with insurers, and to receive payment of and execute or endorse all documents, checks or drafts in connection with insurance payments. Secured Party shall not act as Debtor’s
attorney-in-fact unless Debtor is in default. Proceeds of insurance shall be applied, at the option of Debtor if there is no default as set forth in Section 7, or at the option of Secured Party if there is a default as set forth in
Section 7, to repair or replace the Collateral or to reduce any of the Indebtedness. 

  

	5.	REPORTS. 

  

	 	(a)	Notice of Events. Debtor shall promptly notify Secured Party of (i) any change in the name of Debtor, (ii) any change in the state of its incorporation
or registration, (iii) any relocation of its chief executive offices, (iv) any of the Collateral being lost, stolen, missing, destroyed, materially damaged or worn out, (v) any lien, claim or encumbrance other than Permitted Liens
attaching to or being made against any of the Collateral, or (vi) any occurrence of any default pursuant to Section 7 herein. 

  

	 	(b)	Financial Statements, Reports and Certificates. Debtor will deliver to Secured Party within 120 days of the close of each fiscal year of Debtor, Debtor’s
complete financial statements including a balance sheet, income statement, statement of shareholders’ equity and statement of cash flows, each prepared in accordance with Generally Accepted Accounting Principles consistently applied, certified
by a recognized firm of certified public accountants satisfactory to Secured Party. Debtor will deliver to Secured Party copies of Debtor’s quarterly financial statements including a balance sheet, income statement, and statement of cash flows,
each of which present fairly in all material respects Debtor’s financial condition as of the date thereof, and which are certified by Debtor’s chief financial officer or president, within forty-five (45) days after the close of each
of Debtor’s fiscal quarter. Debtor will deliver to Secured Party copies of all Forms 10-K and 10-Q, if any, within 30 days after the dates on which they are filed with the Securities and Exchange Commission. Debtor will deliver to Secured Party
copies of Debtor’s monthly financial statements including a balance sheet and income statement, and statement of cash flows, each of which present fairly in all material respects Debtor’s financial condition as of the date thereof, and
which are certified by Debtor’s chief financial officer or president, within thirty (30) days after the close of each month. With quarterly and monthly financial statements, Debtor shall also provide to Secured Party a copy of its bank
statement(s) for all accounts reflected in such quarterly and monthly financial statements. Concurrently with delivery of the foregoing information, and from time to time promptly upon request of Secured Party, Debtor will deliver to Secured Party a
Compliance Certificate substantially consistent with the form of the document attached hereto as Schedule A. Debtor will deliver to Secured Party promptly upon request of Secured Party, in form satisfactory to Secured Party, such other and
additional information as Secured Party may reasonably request from time to time. 

  

					
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	6.	FURTHER ASSURANCES. 

  

	 	(a)	Further Assurances Regarding Security Interests. Debtor shall, upon request of Secured Party, furnish to Secured Party such further information, execute and
deliver to Secured Party such documents and instruments (including, without limitation, Uniform Commercial Code financing statements) and shall do such other acts and things as Secured Party may at any time reasonably request relating to the
perfection or protection of the security interest created by this Agreement or for the purpose of carrying out the intent of this Agreement. Without limiting the foregoing, Debtor shall cooperate and do all acts deemed necessary or advisable by
Secured Party to continue in Secured Party a perfected first security interest in the Collateral, and shall obtain and finish to Secured Party any subordinations, releases, landlord waivers, lessor waivers, mortgagee waivers, or control agreements,
and similar documents as may be from time to time requested by, and in form and substance satisfactory to, Secured Party. 

  

	 	(b)	Authorization To File Financing Statements. Debtor shall perform any and all acts requested by the Secured Party to establish, maintain and continue the Secured
Party’s security interest and liens in the Collateral, including but not limited to, executing or authenticating financing statements and such other instruments and documents when and as reasonably requested by the Secured Party. Debtor hereby
authorizes Secured Party through any of Secured Party’s employees, agents or attorneys to file any and all financing statements, including, without limitation, any original filings, continuations, transfers or amendments thereof required to
perfect Secured Party’s security interest and liens in the Collateral under the UCC without authentication or execution by Debtor. Debtor hereby irrevocably authorizes the Secured Party at any time and from time to time to file in any filing
office in any Uniform Commercial Code jurisdiction any initial financing statements) and amendments thereto that (a) indicate the Collateral (i) is subject to Secured Party’s security interest, regardless of whether any particular
asset comprised in the Collateral falls within the scope of Article 9 of the Uniform Commercial Code of the State or such jurisdiction, or (ii) as being of an equal or lesser scope or with greater detail, and (b) provide any other
information required by part 5 of Article 9 of the Uniform Commercial Code of the State or such other jurisdiction for the sufficiency or filing office acceptance of any financing statement or amendment, including (i) whether the Debtor is an
organization, the type of organization and any organization identification number issued to the Debtor, and (ii) in the case of a financing statement filed as a fixture filing, a sufficient description of real property to which the Collateral
relates. The Debtor agrees to furnish any such information to the Secured Party promptly upon the Secured Party’s request. 

  

	 	(c)	Indemnification. Debtor shall indemnify and defend the Secured Party, its successors and assigns, and their respective directors, officers and employees, from
and against all claims, actions and suits (including, without limitation, related attorneys’ fees) of any kind whatsoever arising, directly or indirectly, in connection with any of the Collateral or the Debt Documents except to the extent
resulting from the gross negligence or willful misconduct of the persons so indemnified. 

  

					
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	7.	DEFAULT AND REMEDIES. 

  

	 	(a)	Defaults. Debtor shall be in default under this Agreement and each of the other Debt Documents if any one of the following should occur:

  

	 	(i)	Debtor breaches its obligation to pay within three (3) business days following the due date thereof any installment or other amount due or coming due under any of
the Debt Documents, other than by Secured Party’s failure to process a deduction from Debtor’s Primary Operating Account pursuant to Section 2(w); 

  

	 	(ii)	Debtor, without the prior written consent of Secured Party, attempts to or does sell, rent, lease, license, mortgage, grant a security interest in, or otherwise
transfer or encumber, or allow Liens (except for Permitted Liens) upon, any of the Collateral; 

  

	 	(iii)	Debtor breaches any of its insurance obligations under Section 4; 

  

	 	(iv)	Debtor breaches any of its obligations under Sections 2(m) or 2(y) or Sections 3(i), (j), or (k); 

  

	 	(v)	Debtor breaches any of its other non-payment obligations under any of the Debt Documents and fails to cure that breach within thirty (30) days after it has
occurred; 

  

	 	(vi)	Any warranty, representation or statement made by Debtor in any of the Debt Documents or otherwise in connection with any of the Indebtedness shall be false or
misleading in any material respect; 

  

	 	(vii)	Any of the Collateral is subjected to attachment, execution, levy, seizure or confiscation in any legal proceeding or otherwise, or if any legal or administrative
proceeding is commenced against Debtor or any of the Collateral, which in the good faith judgment of Secured Party subjects any of the Collateral to a material risk of attachment, execution, levy, seizure or confiscation and no bond is posted or
protective order obtained to negate such risk; 

  

	 	(viii)	Debtor breaches or is in default under any other agreement between Debtor and Secured Party; 

  

	 	(ix)	Debtor or any guarantor or other obligor for any of the Indebtedness (collectively “Guarantor”) dissolves, terminates its existence, becomes
insolvent or ceases to do business as a going concern; 

  

					
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	 	(x)	If Debtor or any Guarantor is a natural person, and Debtor or any such Guarantor dies or becomes incompetent; 

  

	 	(xi)	A receiver is appointed for all or of any part of the property of Debtor or any Guarantor, or Debtor or any Guarantor makes any assignment for the benefit of creditors;

  

	 	(xii)	Debtor or any Guarantor files a petition under any bankruptcy, insolvency or similar law, or any such petition is filed against Debtor or any Guarantor and is not
dismissed within forty-five (45) days; 

  

	 	(xiii)	Debtor’s improper filing of an amendment or termination statement relating to a filed financing statement describing the Collateral; 

  

	 	(xiv)	Debtor shall merge with or consolidate into any other entity or sell all or substantially all of its assets or in any manner terminate its existence;

  

	 	(xv)	If Debtor is a privately held corporation, more than 50% of Debtor’s voting capital stock, or effective control of Debtor’s voting capital stock, issued and
outstanding from time to time, is not retained by the holders of such stock on the date the Agreement is executed; 

  

	 	(xvi)	If Debtor is a publicly held corporation, there shall be a change in the ownership of Debtor’s stock such that Debtor is no longer subject to the reporting
requirements of the Securities Exchange Act of 1934 or no longer has a class of equity securities registered under Section 12 of the Securities Act of 1933; 

  

	 	(xvii)	Debtor defaults under any agreement to pay Additional Indebtedness or any other financing arrangement between Debtor and a third party in an amount exceeding $100,000;

  

	 	(xviii)	Secured Party shall have determined in its sole and good faith judgment that (a) it is the clear intention of Debtor’s investors to not continue to fund the
Debtor in the amounts and timeframe necessary to enable Debtor to satisfy the Indebtedness as it becomes due and payable or (b) there is a material impairment in the perfection or priority of the Secured Party’s security interest in the
Collateral; or 

  

	 	(xix)	[intentionally omitted] 

  

	 	(xx)	 Without the prior written consent of Secured Party, which consent shall not be unreasonably withheld or delayed, Debtor creates, incurs, assumes or
permits to exist any Indebtedness to Maxygen, Inc. (“Maxygen”) in excess of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000) in aggregate in any fiscal year, or Debtor makes any payments to Maxygen in any fiscal year in
excess of the lower of: (i) the aggregate of the fair market value of services provided by Maxygen to

  

					
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Debtor during such fiscal year, or (ii) the aggregate of One Million, Two Hundred Twenty-Five Thousand Dollars ($1,225,000). Notwithstanding the foregoing, Debtor shall be permitted to pay
the balance of previously incurred, existing and anticipated Indebtedness to Maxygen up to a total amount of One Million, Five Hundred Thousand Dollars ($1,500,000) for the period January 1, 2005 to December 31, 2005.

  

	 	(b)	Acceleration. If Debtor is in default, the Secured Party, at its option, may declare any or all of the Indebtedness to be immediately due and payable, without
demand or notice to Debtor or any Guarantor (provided that if there is a default as a result of a bankruptcy or insolvency all Indebtedness shall become immediately due and payable without any action by Secured Party). The accelerated obligations
and liabilities shall bear interest (both before and after any judgment) until paid in full at the Default Rate. 

  

	 	(c)	Rights and Remedies. Secured Party shall have all of the rights and remedies of a Secured Party under the Uniform Commercial Code, and under any other applicable
law. Without limiting the foregoing, if an event of default exists, Secured Party shall have the right to (i) notify any account debtor of Debtor or any obligor on any instrument which constitutes part of the Collateral to make payment to the
Secured Party, (ii) with or without legal process, enter any premises where the Collateral may be and take possession of and remove the Collateral from the premises or store it on the premises, (iii) sell the Collateral at public or
private sale, in whole or in part, and have the right to bid and purchase at said sale, or (iv) lease or otherwise dispose of all or part of the Collateral, applying proceeds from such disposition to the obligations then in default. If
requested by Secured Party, Debtor shall promptly assemble the Collateral and make it available to Secured Party at a place to be designated by Secured Party, which is reasonably convenient to both parties. Secured Party may also render any or all
of the Collateral unusable at the Debtor’s premises and may dispose of such Collateral on such premises without liability for rent or costs. Any notice that Secured Party is required to give to Debtor under the Uniform Commercial Code of the
time and place of any public sale or the time after which any private sale or other intended disposition of the Collateral is to be made shall be deemed to constitute reasonable notice if such notice is given to the last known address of Debtor at
least five (5) days prior to such action. Upon the occurrence and during the continuation of a default, Debtor hereby appoints Secured Party as Debtor’s attorney-in-fact, with full authority in Debtor’s place and stead and in
Debtor’s name or otherwise, from time to time in Secured Party’s sole and arbitrary discretion, to take any action and to execute any instrument which Secured Party may deem necessary or advisable to accomplish the purpose of this
Agreement. If an event of Default exists and is continuing, Secured Party is granted a non-exclusive royalty free license to use Debtor’s Intellectual Property in connection with Secured Party’s disposition of Collateral in the exercise of
Secured Party’s rights or remedies hereunder. 

  

					
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	 	(d)	Application of Proceeds. The proceeds and/or avails of the Collateral, or any part thereof, and the proceeds and the avails of any remedy hereunder (as well as
any other amounts of any kind held by Secured Party, at the time of or received by Secured Party after the occurrence of a default hereunder) shall be paid to and applied as follows: 

  

	 	a.	First, to the payment of out-of-pocket costs and expenses, including all amounts expended to preserve the value of the Collateral, all costs of repossession,
storage, and disposition including without limitation attorneys’, appraisers’, and auctioneers’ fees, of foreclosure or suit, if any, and of such sale and the exercise of any other rights or remedies, and of all proper fees, expenses,
liability and advances, including reasonable legal expenses and attorneys’ fees, incurred or made hereunder by Secured Party, including without limitation, Secured Party’s Expenses; 

  

	 	b.	Second, to the payment to Secured Party of the amount then owing or unpaid on the Loans for scheduled payments, any accrued and unpaid interest, and all other
Indebtedness (provided, however, if such proceeds shall be insufficient to pay in full the whole amount so due, owing or unpaid upon the Loans, then to the unpaid interest thereon, then to the outstanding principal amount of the Loans,
and then to the payment of other amounts then payable to Secured Party under any of the Debt Documents or otherwise); and 

  

	 	c.	Third, to the payment of the surplus, if any, to Debtor, its successors and assigns, or to whomsoever may be lawfully entitled to receive the same.

  

	 	(e)	Fees and Costs. Debtor agrees to pay all reasonable attorneys’ fees and other costs incurred by Secured Party in connection with the enforcement, assertion,
defense or preservation of Secured Party’s rights and remedies under this Agreement, or if prohibited by law, such lesser sum as may be permitted. Debtor further agrees that such fees and costs shall constitute Indebtedness.

  

	 	(f)	Remedies Cumulative. Secured Party’s rights and remedies under this Agreement or otherwise arising are cumulative and may be exercised singularly or
concurrently. Neither the failure nor any delay on the part of the Secured Party to exercise any right, power or privilege under this Agreement shall operate as a waiver, nor shall any single or partial exercise of any right, power or privilege
preclude any other or further exercise of that or any other right, power or privilege. SECURED PARTY SHALL NOT BE DEEMED TO HAVE WAIVED ANY OF ITS RIGHTS UNDER THIS AGREEMENT OR UNDER ANY OTHER AGREEMENT, INSTRUMENT OR PAPER SIGNED BY DEBTOR UNLESS
SUCH WAIVER IS EXPRESSED IN WRITING AND SIGNED BY SECURED PARTY. A waiver on any one occasion shall not be construed as a bar to or waiver of any right or remedy on any future occasion. 

  

					
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 Master Security Agreement No. 5081102 
  

	 	(g)	WAIVER OF JURY TRIAL. DEBTOR AND SECURED PARTY UNCONDITIONALLY WAIVE THEIR RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF
THIS AGREEMENT, ANY OF THE OTHER DEBT DOCUMENTS, ANY OF THE INDEBTEDNESS SECURED HEREBY, ANY DEALINGS BETWEEN DEBTOR AND SECURED PARTY RELATING TO THE SUBJECT MATTER OF THIS TRANSACTION OR ANY RELATED TRANSACTIONS, AND/OR THE RELATIONSHIP THAT IS
BEING ESTABLISHED BETWEEN DEBTOR AND SECURED PARTY. THE SCOPE OF THIS WAIVER IS INTENDED TO BE ALL ENCOMPASSING OF ANY AND ALL DISPUTES THAT MAY BE FILED IN ANY COURT. THIS WAIVER IS IRREVOCABLE. THIS WAIVER MAY NOT BE MODIFIED EITHER ORALLY OR IN
WRITING. THE WAIVER ALSO SHALL APPLY TO ANY SUBSEQUENT AMENDMENTS, RENEWALS, SUPPLEMENTS OR MODIFICATIONS TO THIS AGREEMENT, ANY OTHER DEBT DOCUMENTS, OR TO ANY OTHER DOCUMENTS OR AGREEMENTS RELATING TO THIS TRANSACTION OR ANY RELATED TRANSACTION.
THIS AGREEMENT MAY BE FILED AS A WRITTEN CONSENT TO A TRIAL BY THE COURT. 

  

	8.	MISCELLANEOUS. 

  

	 	(a)	Assignment. This Agreement and/or any of the other Debt Documents may be assigned, in whole or in part, by Secured Party without notice to Debtor, and Debtor
agrees not to assert against any such assignee, or assignee’s assigns, any defense, set-off, recoupment claim or counterclaim which Debtor has or may at any time have against Secured Party for any reason whatsoever. Debtor agrees that if Debtor
receives written notice of an assignment from Secured Party, Debtor will pay all amounts payable under any assigned Debt Documents to such assignee or as instructed by Secured Party. Debtor also agrees to confirm in writing receipt of the notice of
assignment as may be reasonably requested by Secured Party or assignee. 

  

	 	(b)	Notices. All notices to be given in connection with this Agreement shall be in writing, shall be addressed to the parties at their respective addresses set forth
in this Agreement (unless and until a different address may be specified in a written notice to the other party), and shall be deemed given (i) on the date of receipt if delivered in hand or by facsimile transmission, (ii) on the next
business day after being sent by express mail, and (iii) on the fourth business day after being sent by regular, registered or certified mail. As used herein, the term “business day” shall mean and include any day other than
Saturdays, Sundays, or other days on which commercial banks in California or Virginia are required or authorized to be closed. 

  

	 	(c)	Correction of Errors. Secured Party may correct patent errors and fill in all blanks in this Agreement, any Collateral Schedule or in any Note consistent with
the agreement of the parties. 

  

					
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 Master Security Agreement No. 5081102 
  

	 	(d)	Time is of the Essence. Time is of the essence of this Agreement. This Agreement shall be binding, jointly and severally, upon all parties described as the
“Debtor” and their respective heirs, executors, representatives, successors and assigns, and shall inure to the benefit of Secured Party, its successors and assigns. 

  

	 	(e)	Entire Agreement. This Agreement and the Debt Documents constitute the entire agreement between the parties with respect to the subject matter of this Agreement
and supersede all prior understandings (whether written, verbal or implied) with respect to such subject matter. NEITHER THIS AGREEMENT NOR ANY OF THE DEBT DOCUMENTS SHALL BE CHANGED OR TERMINATED ORALLY OR BY COURSE OF CONDUCT, BUT ONLY BY A
WRITING SIGNED BY BOTH PARTIES. Section headings contained in this Agreement have been included for convenience only, and shall not affect the construction or interpretation of this Agreement. This Agreement is the result of negotiations between and
has been reviewed by each of Debtor and Secured Party executing this Agreement as of the date hereof and their respective counsel; accordingly, this Agreement shall be deemed to be the product of the parties hereto, and no ambiguity shall be
construed in favor of or against Debtor or Secured Party. 

  

	 	(f)	Termination of Agreement. This Agreement shall continue in full force and effect until all of the Indebtedness has been indefeasibly paid in full to Secured
Party or its assignee; provided, that Debtor’s indemnity obligations set forth in Section 6(c) shall survive until all applicable statute of limitations periods with respect to actions that may be brought against
Secured Party have run. The surrender, upon payment or otherwise, of any Note or any of the other documents evidencing any of the Indebtedness shall not affect the right of Secured Party to retain the Collateral for such other Indebtedness as may
then exist or as it may be reasonably contemplated will exist in the future. This Agreement shall automatically be reinstated if Secured Party is ever required to return or restore the payment of all or any portion of the Indebtedness (all as though
such payment had never been made). Secured Party shall, at Debtor’s sole cost and expense, execute such further documents and take such further actions as may be reasonably necessary to effect the release of its security interests contemplated
by this paragraph, including duly executing and delivering termination statements for filing in all relevant jurisdictions under the Code. 

  

	 	(g)	 CHOICE OF LAW. DEBTOR AGREES THAT SECURED PARTY AND/OR ITS SUCCESSORS AND ASSIGNS SHALL HAVE THE OPTION BY WHICH STATE LAWS THIS AGREEMENT SHALL
BE GOVERNED AND CONSTRUED: (A) THE LAWS OF THE COMMONWEALTH OF VIRGINIA; OR (B) IF COLLATERAL HAS BEEN PLEDGED TO SECURE THE LIABILITIES, THEN BY THE LAWS OF THE STATE OR STATES WHERE THE COLLATERAL IS LOCATED, AT SECURED PARTY’S
OPTION. THIS CHOICE OF STATE LAWS IS EXCLUSIVE TO THE SECURED PARTY. DEBTOR SHALL NOT HAVE ANY OPTION TO CHOOSE THE LAWS BY WHICH THIS AGREEMENT SHALL BE GOVERNED. DEBTOR

  

					
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 Master Security Agreement No. 5081102 
  

	 	 
ACKNOWLEDGES THAT THIS AGREEMENT IS BEING SIGNED BY THE SECURED PARTY IN PARTIAL CONSIDERATION OF SECURED PARTY’S RIGHT TO ENFORCE IN THE JURISDICTION STATED ABOVE. DEBTOR CONSENTS TO
JURISDICTION IN THE COMMONWEALTH OF VIRGINIA OR THE STATE IN WHICH ANY COLLATERAL IS LOCATED AND VENUE IN ANY FEDERAL OR STATE COURT IN THE COMMONWEALTH OF VIRGINIA OR THE STATE IN WHICH COLLATERAL IS LOCATED FOR SUCH PURPOSES AND WAIVES ANY AND ALL
RIGHTS TO CONTEST SAID JURISDICTION AND VENUE AND ANY OBJECTION THAT SAID COUNTY IS NOT CONVENIENT. DEBTOR WAIVES ANY RIGHTS TO COMMENCE ANY ACTION AGAINST SECURED PARTY IN ANY JURISDICTION EXCEPT VIRGINIA, OR IF SECURED PARTY CHOOSES TO LITIGATE IN
A STATE WHERE COLLATERAL IS LOCATED THEN IN SUCH COUNTY AND STATE. 

  

	 	(h)	Power of Attorney. To facilitate direct collection, the Debtor hereby appoints the Secured Party and any officer or employee of the Secured Party, as the Secured
Party may from time to time designate, as attorney-in-fact for the Debtor to (a) endorse the name of the Debtor in favor of the Secured Party upon any and all checks, drafts, money orders, notes, acceptances or other evidences of payment or
Collateral that may come into the Secured Party’s possession; (b) do all acts and things necessary to carry out this Agreement and the transactions contemplated hereby, including signing the name of the Debtor on any instruments required
by law in connection with the transactions contemplated hereby and on financing statements as permitted by the Virginia Uniform Commercial Code. The Debtor hereby ratifies and approves all acts of such attorneys-in-fact, and neither the Secured
Party nor any other such attorney-in-fact shall be liable for any acts of commission or omission, or for any error of judgment or mistake of fact or law of any such attorney-in-fact. This power, being coupled with an interest, is irrevocable so long
as the Loan remains unsatisfied, or any Debt Document remains effective, as solely determined by the Secured Party. Secured Party agrees to exercise this power of attorney only during the existence of an event of default. 

 

	 	(i)	Loss, Depreciation or Other Damage. The Secured Party shall not be liable for or prejudiced by any loss, depreciation or other damage to Collateral unless caused
by the Secured Party’s willful and malicious act, and the Secured Party shall have no duty to take any action to preserve or collect any Collateral. 

  

	 	(j)	Demand; Protest. Debtor waives demand, protest, notice of protest, notice of default or dishonor, notice of payment and nonpayment, notice of any default,
nonpayment at maturity, release, compromise, settlement, extension, or renewal of accounts, documents, instruments, chattel paper, and guarantees at any time held by Secured Party on which Debtor may in any way be liable. 

 

					
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 Master Security Agreement No. 5081102 
  

	9.	DEFINITIONS. 

 As used
herein, the following terms, when initial capital letters are used, shall have the respective meanings set forth below. In addition, all terms defined in the Code shall have the meanings given therein unless otherwise defined herein. 
 Defined Terms. As used in this Agreement, the following terms shall have the following meanings, unless the context otherwise requires: 

“Additional Indebtedness” means, with respect to Debtor or any of its subsidiaries, the aggregate amount of,
without duplication, (a) all obligations of such Person for borrowed money, (b) all obligations of such Person evidenced by bonds, debentures, notes or other similar instruments, (c) all obligations of such Person to pay the deferred
purchase price of property or services (excluding trade payables aged less than one hundred eighty (180) days), (d) all capital lease obligations of such Person, (e) all obligations or liabilities of others secured by a Lien on any
asset of such Person, whether or not such obligation or liability is assumed, (f) all obligations or liabilities of others guaranteed by such Person, and (g) any other obligations or liabilities which are required by GAAP to be shown as
debt on the balance sheet of such Person. A listing of Additional Indebtedness existing on the date hereof is set forth in Schedule B. Unless otherwise indicated, the term “Additional Indebtedness” shall include all
Indebtedness of Debtor and all of its subsidiaries. 
 “Affiliate” of a Person is a Person that owns or
controls directly or indirectly the Person, any Person that controls or is controlled by or is under common control with the Person, and each of that Person’s senior executive officers, directors, partners and, for any Person that is a limited
liability company, that Person’s managers and members. 
 “Code” means the Virginia Uniform
Commercial Code (including revised Article 9 thereof). 
 “Collateral” has the meaning given such
capitalized term in Section 1. 
 “Collateral Schedule” has the meaning given such
capitalized term in Section 1. 
 “Debt Documents” has the meaning given such capitalized
term in Section 2(b). 
 “Default Rate” is the lower of thirteen percent (13%) per annum
or the maximum rate not prohibited by applicable law. 
 “Indebtedness” has the meaning given such
capitalized term in Section 1. 
 “Intellectual Property” shall mean (a) all of the
Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign copyrights, copyright registrations and copyright applications, whether or not registered or filed with any
governmental authority, together with (i) all renewals thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder,
(iii) all income,

  

					
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 Master Security Agreement No. 5081102 
  

 
royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or
future infringements thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world
(collectively “Copyright Rights”); (b) all of the Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all United States and foreign patents, and pending and
abandoned United States and foreign patent applications, including, without limitation, the inventions and improvements described or claimed therein, together with(i) any reissues, divisions, continuations, certificates of re-examination, extensions
and continuations-in-part thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor thereunder, (iii) all income, royalties,
damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iv) all of the Debtor’s
present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively “Patent Rights”); (c) all of the
Debtor’s right, title and interest, whether now owned or existing or hereafter acquired or arising, in and to all domestic and foreign trademarks, trademark registrations, trademark applications and trade names, whether or not registered or
filed with any governmental authority, together with (i) all renewals thereof, (ii) all present and future rights of the Debtor under all present and future license agreements relating thereto, whether the Debtor is licensee or licensor
thereunder, (iii) all income, royalties, damages and payments now or hereafter due and/or payable to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements
thereof, (iv) all of the Debtor’s present and future claims, causes of action and rights to sue for past, present or future infringements thereof, and (v) all rights corresponding thereto throughout the world (collectively
“Trademark Rights”); (d) all present and future licenses and license agreements of the Debtor, and all rights of the Debtor under or in connection therewith, whether the Debtor is licensee or licensor thereunder, including,
without limitation, any present or future franchise agreements under which the Debtor is franchisee or franchisor, together with (i) all renewals thereof, (ii) all income, royalties, damages and payments now or hereafter due and/or payable
to the Debtor thereunder or with respect thereto, including, without limitation, damages and payments for past, present or future infringements thereof, (iii) all claims, causes of action and rights to sue for past, present or future
infringements thereof, and (iv) all rights corresponding thereto throughout the world (collectively “License Rights”); (e) all present and future trade secrets of the Debtor; and (f) all other present and future
intellectual property of the Debtor.] 
 “Lien(s)” shall mean any voluntary or involuntary mortgage,
pledge, deed of trust, assignment, security interest, encumbrance, hypothecation, lien, or charge of any kind (including any conditional sale or other title retention agreement, any financing lease having substantially the same economic effect as
any of the foregoing, and the filing of, or agreement to give, any financing statement under the Uniform Commercial Code or comparable law of any jurisdiction). 
  

					
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 Master Security Agreement No. 5081102 
  

 “Loan” means an advance of credit by Secured Party to Debtor.

 “Note” has the meaning given such capitalized term in Section 1. 
 “Permitted Liens” means: (i) liens in favor of Secured Party, (ii) liens for taxes not yet due or for taxes
being contested in good faith and which do not involve, in the judgment of Secured Party, any risk of the sale, forfeiture or loss of any of the Collateral, and (iii) inchoate materialmen’s, mechanic’s, repairmen’s and similar
liens arising by operation of law in the normal course of business for amounts which are not delinquent. 
 “Person” is any individual, sole proprietorship, partnership, limited liability company, joint venture, company association, trust, unincorporated organization, association, corporation, institution, public benefit
corporation, firm, joint stock company, estate, entity or government agency. 
 “Primary Operating
Account” has the meaning given such capitalized term in Section 2(w). 
 “Secured
Party’s Expenses” means all reasonable costs or expenses (including reasonable attorneys’ fees and expenses) incurred in connection with the preparation, negotiation, documentation, administration and funding of the Debt
Documents; and Secured Party’s reasonable attorneys’ fees, costs and expenses incurred in amending. modifying, enforcing or defending the Debt Documents (including fees and expenses of appeal or review), including the exercise of any
rights or remedies afforded hereunder or under applicable law, whether or not suit is brought, whether before or after bankruptcy or insolvency, including without limitation all fees and costs incurred by Secured Party in connection with Secured
Party’s enforcement of its rights in a bankruptcy or insolvency proceeding filed by or against Debtor or its property. 
 “Subordinated Indebtedness” means Additional Indebtedness subordinated to the Indebtedness of Debtor to Secured Party on terms and conditions acceptable to Secured Party in its sole discretion. 
 IN WITNESS WHEREOF, Debtor and Secured Party, intending to be legally bound hereby, have duly executed this Agreement in one or more
counterparts, each of which shall be deemed to be an original, as of the day and year first aforesaid. 
  

							
	SECURED PARTY:	 	DEBTOR:
		
	Oxford Finance Corporation	 	Codexis, Inc.
				
	By:	 	 /s/ Michael J. Altenburger
	 	By:	 	 /s/ Tassos Gianakakos

	Name:	 	Michael J. Altenburger	 	Name:	 	Tassos Gianakakos
	Title:	 	Chief Financial Officer	 	Title:	 	Senior Vice President

  

					
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 Master Security Agreement No. 5081102 
  

 SCHEDULE A 
 FORM OF 
 COMPLIANCE CERTIFICATE 
  

									
	Oxford	 		 	Finance	 		 	Corporation
	133	 	N.	 		 	Fairfax	 	Street
	Alexandria, VA 22314	 		 		 		 	

  

			
	Re:	  	Codexis, Inc.

 Gentlemen: 
 Reference is made to the Master Security Agreement dated as of October 25, 2005, (as the same have been and may be amended from time to time in writing, the “Loan Agreement”, the
capitalized terms used herein as defined therein), between Oxford Finance Corporation and Codexis, Inc. (the “Company”). 
 The undersigned authorized representative of the Company hereby certifies that in accordance with the terms and conditions of the Loan Agreement, the Company is in complete compliance for the financial
reporting period ending                              with all required financial reporting under the
Loan Agreement, except as noted below. Attached herewith are the required documents supporting the foregoing certification. The undersigned further certifies that the accompanying financial statements present fairly in all material respects the
Debtor’s financial condition as of the date thereof, that annual audited financial statements have been prepared in accordance with Generally Accepted Accounting Principles, and all such financial statements are consistent from one period to
the next, except as explained below. 
 Indicate compliance status by circling Yes/No under “Complies”

  

					
	 REPORTING REQUIREMENT
	 	 REQUIRED
	 	 COMPLIES

	Interim Financial Statements	 	Quarterly within 45 days	 	YES / NO
			
	Monthly Financial Statements	 	Monthly within 30 days	 	
			
	Audited Financial Statements	 	FYE within 120 days	 	
			
	Date of most recent Board-approved budget/plan
                            	 		 	
	Summary submitted with Borrowing Request	 		 	YES / NO
			
	Any material change in budget/plan since prior Borrowing Request	 		 	YES / NO

  

					
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 Master Security Agreement No. 5081102 
  

 EXPLANATIONS 
  

			
	Very truly yours,
	
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	
	Title:*	 	

  
  

	*	 Must be executed by Debtor’s Chief Financial Officer or President. 

  

					
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 Master Security Agreement No. 5081102 
  

 SCHEDULE B 
 DEBTOR ADDITIONAL INDEBTEDNESS AS OF SEPTEMBER 30, 2005 
  

			
	 Current Liabilities
	  	
	 Accrued vacation
	  	438,019
	 Other accruals
	  	1,125,685
	 Equipment loan
	  	993,343
	 Lease Incentive
	  	62,531
	 Deferred Revenue
	  	3,618,030
		  	 
	 Subtotal
	  	6,237,608
	 Long Term Liabilities
	  	
	 Equipment Loan
	  	2,705,561
	 Lease Incentive
	  	270,966
	 Deferred Revenue
	  	1,956,092
		  	 
	 Subtotal
	  	4,932,619
		  	 
	 Total Liabilities
	  	11,170,227
		  	 

  

					
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 COLLATERAL MIX RIDER 
 TO 
 MASTER SECURITY AGREEMENT NO. 5081102 
 DATED OCTOBER 25, 2005 
 BETWEEN 
 OXFORD FINANCE CORPORATION (the “SECURED PARTY”) 
 AND 
 CODEXIS, INC.
(the “DEBTOR”) 
 Debtor shall cause the composition and mix of Collateral to conform to and meet the following concentration
requirements (hereinafter “Concentration Requirement”) for the class of Collateral (hereinafter “Collateral Class”) as identified and set forth below. Debtor herein represents and warrants that it shall maintain such Collateral
Class and its respective Concentration Requirement at all times from and after December 31, 2006. If on such date the Concentration Requirement is not in compliance (a “Concentration Variance”), Debtor will do one of the following (a
“Concentration Correction”): 
  

	1.	Grant to Secured Party a security interest in additional equipment satisfactory to Secured Party, not previously subject to Secured Party’s security interest
(collectively, the “Additional Equipment”), in sufficent type and amount so that the Concentration Requirement set forth below is met and the Concentration Variance is eliminated. The Additional Equipment shall be subject to all of the
terms and conditions of the Master Security Agreement, including without limitation, Debtor’s representations, warranties, and covenants, which shall be deemed remade by Debtor upon its grant of a security interest in the Additional Equipment.

  

	2.	Pay Secured Party cash in an amount equal to the Concentration Variance to hold as cash collateral until the Note is fully repaid. Debtor hereby grants Secured Party a
security interest in such cash collateral and all proceeds and products thereof. Debtor agrees that such cash collateral held by Secured Party: (a) shall not bear interest, (b) may be commingled with other funds of Secured Party, and
(c) may be applied by Secured Party to amounts owing by Debtor upon the occurrence and during the continuance of any Event of Default under the Master Security Agreement or the Note(s) thereunder. 

 The failure of Debtor to do a Concentration Correction by December 31, 2006, shall constitute a Default under the Master Security Agreement and the
Note(s) thereunder. 
  

			
	 Collateral Class
	 	 Concentration Requirement

	New Laboratory Equipment	 	Minimum of 60%
	New Computer and Furniture	 	Maximum of 10%
	Soft Costs	 	Maximum of 30% of the outstanding principal amount as initially represented by the Promissory Notes from time to time

  

					
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 Dated as of October 25, 2005 
  

							
	OXFORD FINANCE CORPORATION	 	CODEXIS, INC.
				
	By:	 	 /s/ Michael J. Altenburger
	 	By:	 	 /s/ Tassos Gianakakos

	Name:	 	Michael J. Altenburger	 	Name:	 	Tassos Gianakakos
	Title:	 	Chief Financial Officer	 	Title:	 	Senior Vice President

  

					
		  	Page 24 of 26	  	Codexis Initial Here:                     
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 SECRETARY’S CERTIFICATE 
 Codexis, Inc. 
  

			
	To:	  	 Oxford Finance Corporation
 133 North Fairfax Street
 Alexandria, Virginia 22314

 The undersigned hereby certifies as follows: 
  

	(i)	He is the duly appointed Secretary of Codexis, Inc., a Delaware corporation (the “Corporation”). 

 (ii) Each of the officers designated below is a duly appointed officer of the Corporation, and the signature appearing opposite his name below is his
genuine signature: 
  

					
	 NAME
	  	 OFFICE
	 	 SIGNATURE

	Alan Shaw	  	President and Chief Executive Officer	 	/s/ Alan Shaw
	Tassos Gianakakos	  	Senior Vice President	 	/s/ Tassos Gianakakos
	  
	  	  
	 	  

 (iii) Schedule A attached hereto is a true and correct copy of the Corporation’s Fourth
Amended and Restated Certificate of Incorporation, as filed with the Delaware Secretary of State on July 22, 2004, as amended on January 19, 2005, July 26, 2005 and October 20, 2005 (the “Certificate”). The
Certificate has not in any way been amended, annulled, rescinded, repealed, revoked or supplemented, and remains in full force and effect as of the date hereof. 
 (iv) Schedule B attached hereto is a true and correct copy of the Corporation’s bylaws as presently in effect. 
 (v) Schedule C attached hereto is a true and correct copy of resolutions adopted by the board of directors of the Corporation on August 11, 2005 related to Oxford Finance Corporation (the
“Resolutions”). Said Resolutions have not been revoked, modified, rescinded, or amended and are in full force and effect. 
 [Signature Page Follows] 
  

					
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 SECRETARY’S CERTIFICATE 
 IN WITNESS WHEREOF, I have hereunto set my hand, this 25th day of October, 2005. 
  

	
	 /s/ Alan C. Mendelson

	Alan Mendelson
	 Secretary
 Codexis,
Inc.

 ATTEST: 
 The undersigned does hereby certify that he is President and Chief Executive Officer of the Corporation and does hereby certify that Alan Mendelson was, at the time he executed the foregoing Certificate,
a duly elected, qualified and acting Secretary of the Corporation, and he was duly authorized and empowered to do so, and the signature thereon is genuine. 
  

	
	 /s/ Alan Shaw

	Signature of Corporate Officer
	Attesting to Secretary Signature

  

					
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