Exhibit 10.6

SIXTH AMENDMENT TO LEASE

This Sixth Amendment to Lease (“Amendment”) is entered into, and dated for
reference purposes, as of September 27, 2012 (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 [sic], by and between Landlord and Tenant (the “Original Lease”) for
certain premises described therein and commonly known as 501 Chesapeake Drive
which is a part of Building 3 (the “501 Chesapeake Space”) and all the rentable
area of Building 4 (consisting of 200 and 220 Penobscot Drive (collectively, the
“200 & 220 Penobscot Space”, and together with the 501 Chesapeake Space are
referred to collectively as 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”); as
amended by that certain Third Amendment to Lease, dated as of March 31, 2008, by
and between Landlord and Tenant (the “Third Amendment”) for certain premises
described therein and commonly known as 400 Penobscot Drive, which is the entire
Building 2 (the “Building 2 Space”), all as more particularly described in the
Third Amendment; as amended by that certain Fourth Amendment to Lease, dated as
of September 17, 2010, by and between Landlord and Tenant (the “Fourth
Amendment”); and as amended by that certain Fifth Amendment to Lease, dated as
of March 16, 2011, by and between Landlord and Tenant (the “Fifth Amendment”)
for certain premises described therein and commonly known as 101 Saginaw Drive,
which is part of Building 1 (the “101 Saginaw Space”); all as more particularly
described in the Fifth Amendment. The Original Lease, as amended, is referred to
for purposes of this Amendment as the “Existing Lease”.

B. Landlord and Tenant desire to provide for extension of the Term of the 501
Chesapeake Space and 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 “Existing Lease” defined
above shall refer to the Existing Lease as it existed before giving effect to
the modifications set forth in this Amendment and the term “Lease” as used
herein and in the Existing Lease shall refer to the Existing Lease as modified
by this Amendment, except as expressly provided in 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 501 Chesapeake Space Expiration Date is
January 31, 2013; (b) as contemplated by the Existing Lease, the Building 2
Expiration Date is January 31, 2020; (c) as contemplated by the Existing Lease,
the expiration date of the 101 Saginaw Space is January 31, 2020 (the “101
Saginaw Space Expiration Date”, inadvertently referred to as January 30, 2020 in
Section 6(c) of the Fifth Amendment); and (d) as contemplated by the Existing
Lease, the Expiration Date of the Term of the Lease of the 200 & 220 Penobscot
Space is January 31, 2020.

 

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Section 3. Extension of Term for 501 Chesapeake Space. Landlord and Tenant agree
that the Term for the 501 Chesapeake Space is hereby extended for the period of
forty-eight (48) months (the “501 Chesapeake Second Extended Term”) commencing
on February 1, 2013 (the “501 Chesapeake Second Extension Commencement Date”)
and expiring January 31, 2017 (hereafter, the “501 Chesapeake Expiration Date”),
unless sooner terminated pursuant to the terms of the Lease. Landlord and Tenant
acknowledge and agree that this Amendment provides all rights and obligations of
the parties with respect to extension of the current Term for the 501 Chesapeake
Space only, whether or not in accordance with any other provisions, if any, of
the Existing Lease regarding renewal or extension of such space.

Section 4. Amendment of Rent for 501 Chesapeake Second Extended Term.
Notwithstanding any provision of the Existing Lease to the contrary, commencing
on 501 Chesapeake Second Extension Commencement Date and continuing through the
501 Chesapeake Expiration Date, the amount of Monthly Base Rent due and payable
by Tenant for the 501 Chesapeake Space shall be as follows:

 

Period from/to

   Monthly Amount  

February 1, 2013 to January 31, 2014

   $ 18,968.60   

February 1, 2014 to January 31, 2015

   $ 19,537.66   

February 1, 2015 to January 31, 2016

   $ 20,123.79   

February 1, 2016 to January 31, 2017

   $ 20,727.50   

Section 5. “AS IS” Condition. Tenant acknowledges and agrees that Tenant
presently occupies and has occupied the 501 Chesapeake Space, and Tenant accepts
the 501 Chesapeake Space in its 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 regarding the Premises. Landlord shall
not have any obligation to construct or install any tenant improvements or
alterations or to pay for any such construction or installation in any portion
of the Premises.

Section 6. Negotiation Right.

(a) Landlord and Tenant confirms that the Negotiation Right with respect to 123
Saginaw Negotiation Space (as set forth in Section 11 of the Fifth Amendment)
continues to be in effect. The following Negotiation Rights have terminated:
(i) the Negotiation Right with respect to 525 Chesapeake Drive (as set forth in
Section 6 of the Second Amendment); and (ii) the Negotiation Right with respect
to the 600 Galveston Negotiation Space (as set forth in Section 7 of the Third
Amendment, as amended by Section 7(b)(ii) of the Fifth Amendment)).

(b) Landlord hereby grants Tenant a one-time right to negotiate the lease of the
525 Chesapeake 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 501
Chesapeake Expiration Date (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 501 Chesapeake 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.

 

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(c) The “525 Chesapeake Negotiation Space” shall mean the space with a street
address of 525 Chesapeake Drive and Rentable Area of approximately 15,393 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 within eighteen (18) months after the Execution
Date; 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.

(d) 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 525 Chesapeake 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 525 Chesapeake 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 Landlord has disclosed that as of the date of
execution of this Lease, Landlord is marketing the 525 Chesapeake Negotiation
Space, and as set forth more fully in Subsection (b) above, if Landlord entered
into a lease within eighteen (18) months after the Execution Date, Landlord
shall remain free at any time to enter into an extension or renewal of such
lease, whether or not any such right is set forth in such lease, and to enter
into any amendment or modification of such lease, all of which constitute Prior
Rights with respect to the 525 Chesapeake Negotiation 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.

(e) 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 525 Chesapeake 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 525 Chesapeake
Negotiation Space which is the subject of the Landlord Notice; (2) the subject
525 Chesapeake Negotiation Space shall, upon delivery, be part of the Premises
under this Lease, such that the term “Premises” thereafter shall include the
subject 525 Chesapeake Negotiation Space; (3) starting on such delivery date,
with respect to the subject 525 Chesapeake Negotiation Space Tenant shall
additionally pay Tenant’s Share of Operating Expenses, with Tenant’s Share
recalculated to reflect addition of the 525 Chesapeake Negotiation Space;
(4) the number of parking spaces applicable to the subject 525 Chesapeake
Negotiation Space shall be calculated at the rate of 3.3 spaces per 1000 square
feet of Rentable Area of the subject 525 Chesapeake 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 525 Chesapeake
Negotiation Space; (bb) the term of the lease of the 525 Chesapeake Negotiation
Space; (cc) any improvements or alterations to be done, or allowance therefor,
if any, specifically agreed upon, and absent such agreement, Tenant shall accept
the 525 Chesapeake Negotiation Space in its

 

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then AS IS condition without any obligation of Landlord to repaint, remodel,
improve or alter the subject 525 Chesapeake 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 525 Chesapeake 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
525 Chesapeake 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 525 Chesapeake 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.

(f) If Tenant either fails or elects not to exercise its Negotiation Right as to
the 525 Chesapeake 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
525 Chesapeake 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 525 Chesapeake 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.

(g) 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 525 Chesapeake 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
525 Chesapeake Negotiation Space which was the subject of any Landlord’s Notice.

(h) 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 7. Option to Extend.

(a) Landlord and Tenant confirms that the Option to Extend with respect to the
200 & 220 Penobscot Space, Building 2 Space and 101 Saginaw Space (as set forth
in Section 12 of the Fifth Amendment) continues to be in effect. Landlord and
Tenant hereby agree to delete the Option to Extend with respect to the 501
Chesapeake Space as set forth in Section 26.21 of the Original Lease, as amended
by Section 3 of the Fourth Amendment.

(b) Landlord hereby grants Tenant two (2) consecutive options to extend the Term
of the Lease with respect to the 501 Chesapeake Space for an additional term of
five (5) years per option pursuant to the

 

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same terms and conditions of Section 12 of the Fifth Amendment. Accordingly,
Section 12(b) of the Fifth Amendment is hereby amended by deleting and replacing
the phrase “as to the portion of the Premises consisting of the 200 & 220
Penobscot Space, Building 2 Space and 101 Saginaw Space (all references in this
Section 12 to the “Premises” shall instead be deemed to mean such space only)”
with the following phrase: “as to the portion of the Premises consisting of the
200 & 220 Penobscot Space, Building 2 Space, 101 Saginaw Space and 501
Chesapeake Space (all references in this Section 12 to the “Premises” shall
instead be deemed to mean such space only)”.

Section 8. Time of Essence. Without limiting the generality of any provision of
the Lease, time shall be of the essence with respect to all of the provisions of
this Amendment.

Section 9. Brokers. Notwithstanding any other provision of the Existing Lease to
the contrary, Tenant represents and warrants to Landlord that Cornish & Carey
Commercial Newmark Knight Frank is the sole broker who negotiated and brought
about the consummation of this Amendment and that no discussions or negotiations
were had with any other broker concerning this Amendment. Based on the foregoing
representation and warranty, Landlord has agreed to pay any commission or fee
owed to such broker pursuant to Landlord’s agreement between Landlord and such
broker, and Tenant is not obligated to pay or fund any amount to such broker.
Tenant hereby indemnifies and agrees to protect, defend and hold Landlord
harmless from and against any claims of brokerage commissions arising out of any
discussions or negotiations allegedly had by Tenant with any other broker in
connection with the Building and the Premises. The foregoing obligations of
Tenant shall survive the expiration or sooner 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. This 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. OFAC. Landlord advises Tenant hereby that the purpose of this
Section is to provide to the Landlord information and assurances to enable
Landlord to comply with the law relating to OFAC.

Tenant hereby represents, warrants and covenants to Landlord, either that
(i) Tenant is regulated by the SEC, FINRA or the Federal Reserve (a “Regulated
Entity”) or (ii) neither Tenant nor any person or entity that directly or
indirectly (a) controls Tenant or (b) has an ownership interest in Tenant of
twenty-five percent (25%) or more, appears on the list of Specially Designated
Nationals and Blocked Persons (“OFAC List”) published by the Office of Foreign
Assets Control (“OFAC”) of the U.S. Department of the Treasury.

 

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If, in connection with this Lease, there is one or more Guarantors of Tenant’s
obligations under this Lease, then Tenant further represents, warrants and
covenants either that (i) any such Guarantor is a Regulated Entity or
(ii) neither Guarantor nor any person or entity that directly or indirectly
(a) controls such Guarantor or (b) has an ownership interest in such Guarantor
of twenty-five percent (25%) or more, appears on the OFAC List.

Tenant covenants that during the term of this Lease to provide to Landlord
information reasonably requested by Landlord including without limitation,
organizational structural charts and organizational documents which Landlord may
deem to be necessary (“Tenant OFAC Information”) in order for Landlord to
confirm Tenant’s continuing compliance with the provisions of this Section.
Tenant represents and warrants that the Tenant OFAC Information it has provided
or to be provided to Landlord or Landlord’s Broker in connection with the
execution of this Lease is true and complete.

Section 14. Ratification. Tenant represents to Landlord, as of the Execution
Date, that: (a) the Existing Lease is in full force and effect and has not been
modified except as provided by this Amendment; (b) to Tenant’s actual knowledge,
there are no uncured defaults or unfulfilled obligations on the part of Landlord
or Tenant; and (c) Tenant is currently in possession of the entire Premises as
of the Execution Date, and neither the Premises, nor any part thereof, is
occupied by any subtenant or other party other than Tenant. Landlord represents
to Tenant, as of the Execution Date, that: (a) the Existing Lease is in full
force and effect and has not been modified except as provided by this Amendment,
and (b) to Landlord’s actual knowledge, there are no uncured monetary defaults
on the part of Tenant.

Section 15. 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 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.

 

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Section 16. Applicable Law. This Amendment shall be construed in accordance with
the Laws of the State of California

Section 17. 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/ John J. Nicols

    Print Name:   John J. Nicols     Title:   President and Chief Executive
Officer LANDLORD:     METROPOLITAN LIFE INSURANCE COMPANY,     a New York
corporation     By:  

/s/ JA Denning

    Print Name:   JA Denning     Title:   Director

 

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