Exhibit 10.11B

TRANSITION AND SEPARATION AGREEMENT

This Transition and Separation Agreement (the “Agreement”) by and between Alan
Shaw, Ph.D. (“Executive”) and Codexis, Inc., a Delaware corporation (the
“Company”), is made effective as of the date Executive signs this Agreement (the
“Effective Date”) with reference to the following facts:

A. Executive’s employment with the Company and status as an officer, director
and employee of the Company and each of its affiliates will end effective upon
the Termination Date (as defined below).

B. Executive and the Company want to end their relationship amicably and also to
establish the obligations of the parties including, without limitation, all
amounts due and owing to the Executive.

NOW, THEREFORE, in consideration of the mutual covenants and agreements
hereinafter set forth, the parties agree as follows:

1. Termination Date. Executive acknowledges and agrees that his status as an
officer, director and employee of the Company and as an officer and/or director
of the Company’s subsidiaries will end effective as of February 17, 2012 (the
“Termination Date”). Executive hereby agrees to execute such further document(s)
as shall be determined by the Company as necessary or desirable to give effect
to the termination of Executive’s status as an officer and, if applicable,
director of the Company and each of its subsidiaries; provided that such
documents shall not be inconsistent with any of the terms of this Agreement.

2. Transition Consulting Services.

(a) Consulting Period. During the period of time (the “Consulting Period”)
commencing on the Termination Date and ending on the six (6) month anniversary
of the Termination Date (the “Consulting Period End Date”), Executive shall be
available to provide services to the Company, on a non-exclusive basis, as a
consultant and shall provide such transition services (the “Transition
Services”) as necessary in Executive’s areas of expertise and work experience
and responsibility as may be requested by the Board of Directors of the Company
(the “Board”). Executive acknowledges and agrees that, during the Consulting
Period, Executive shall not, directly or indirectly, become employed by or
provide assistance to any competitor of the Company. During the Consulting
Period, Executive reaffirms his commitment to remain in compliance with that
certain Confidential Information, Secrecy, and Invention Agreement entered into
between Executive and Maxygen, the former parent corporation of the Company, as
of September 14, 2001 (the “Confidentiality Agreement”), it being understood
that the term “employment” as used in the Confidentiality Agreement shall
include the Transition Services during the Consulting Period.

(b) Consulting Fees. In exchange for the performance of the Transition Services,
for the Consulting Period, the Company shall pay to Executive monthly consulting
fees as an independent contractor (the “Consulting Fees”) in an amount equal to
$42,083.34 per month, which represents the monthly amount paid to Executive by
the Company as Executive’s base salary at the rate in effect immediately prior
to Termination Date. The Consulting Fees will be paid to Executive in accordance
with the Company’s standard payment procedures for consultants and independent
contractors.

 

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(c) Benefits. As an independent contractor, Executive understands and agrees
that, while performing any services for the Company after the Termination Date,
Executive shall not be eligible to participate in or accrue benefits under any
Company benefit plan for which status as an employee of the Company is a
condition of such participation or accrual. To the extent that Executive were
deemed eligible to participate, as an employee, in any Company benefit plan, he
hereby waives his participation.

(d) Stock Options. During the Consulting Period, Executive’s options to purchase
shares of Company common stock (collectively, “Options”) pursuant to the terms
of the Company’s 2002 Equity Incentive Plan, as amended, and 2010 Equity
Incentive Award Plan, as amended (the “2010 Plan”), and the option agreements
entered into to evidence such Options (each such agreement an “Option
Agreement”) shall continue to vest and become exercisable in accordance with
their original vesting schedules, subject to Executive continuing to provide the
Transition Services to the Company. In the event Executive ceases to provide the
Transition Services, Executive’s unvested equity awards shall be forfeited as of
the date of such complete cessation of services. Each of Executive’s equity
awards that is not vested as of the Consulting Period End Date shall terminate
for no consideration and be of no further effect.

Executive shall have until March 16, 2012 to elect in writing, on a
grant-by-grant basis, to amend each Option Agreement evidencing an Option held
by Executive that is vested as of the Consulting Period End Date to the extent
necessary to provide that such Option shall remain exercisable until the earlier
of (i) March 31, 2013, (ii) the original expiration date of the Option or
(iii) the closing of a Change in Control (as defined in the 2010 Plan) of the
Company. If Executive does not make such election before March 16, 2012, then
such Option(s) shall remain exercisable following the Termination Date as
provided in the applicable Option Agreement(s). Executive acknowledges that upon
making such an election, each unexercised “incentive stock option” within the
meaning of Section 422 of the Code shall be deemed modified for the purposes of
Section 424 of the Code and, to the extent the exercise price thereof is lower
than the fair market value of the Company’s common stock as of the date of the
election or to the extent the election is made after the Termination Date, such
Option shall no longer qualify as an incentive stock option and Executive will
lose the potentially favorable tax treatment associated with such option. If
Executive desires to exercise any vested Options, Executive must follow the
procedures set forth in Executive’s Option Agreements, including payment of the
exercise price and any withholding obligations. If by the earliest date
specified above in this Section 2(d) the Company has not received a duly
executed notice of exercise and remuneration in accordance with Executive’s
Option Agreements, Executive’s vested Options shall automatically terminate for
no consideration and be of no further effect.

(e) Independent Contractor Status. Executive and the Company acknowledge and
agree that, during the Consulting Period, Executive shall be an independent
contractor. During the Consulting Period and thereafter, Executive shall not be
an agent or employee of the Company and shall not be authorized to act on behalf
of the Company. The Company will not make deductions for taxes from any
Consulting Fees paid hereunder. Personal income and self-employment taxes for
Consulting Fees paid to Executive hereunder shall be the sole responsibility of
Executive. Executive agrees to indemnify and hold the Company and the other
entities released herein harmless for any tax claims or penalties resulting from
any failure by Executive to make required personal income and self-employment
tax payments with respect to the Consulting Fees.

 

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(f) Protection of Information. Executive agrees that, during the Consulting
Period and thereafter, Executive will not, except for the purposes of performing
the Transition Duties, seek to obtain any confidential or proprietary
information or materials of the Company.

3. Final Paycheck; Payment of Accrued Wages and Expenses.

(a) Final Paycheck. As soon as administratively practicable on or after the
Termination Date, the Company will pay Executive all accrued but unpaid base
salary and all accrued and unused vacation earned through the Termination Date,
subject to standard payroll deductions and withholdings. Executive is entitled
to these payments regardless of whether Executive executes this Agreement or a
Release of Claims (as defined below).

(b) Business Expenses. The Company shall reimburse Executive for all outstanding
expenses incurred prior to the Termination Date which are consistent with the
Company’s policies in effect from time to time with respect to travel,
entertainment and other business expenses, subject to the Company’s requirements
with respect to reporting and documenting such expenses, including, without
limitation, expenses incurred pursuant to Executive’s services as a director of
any of the Company’s subsidiaries.

4. Separation Payments and Benefits. Without admission of any liability, fact or
claim, the Company hereby agrees, subject to the execution of this Agreement
and, on or within thirty (30) days following the Consulting Period End Date, the
General Release of Claims attached hereto as Exhibit A (the “Release of Claims”)
and Executive’s performance of his continuing obligations pursuant to this
Agreement and the Confidentiality Agreement, to provide Executive the severance
benefits set forth below. Specifically, the Company and Executive agree as
follows:

(a) Severance. For the twelve (12)-month period commencing on the Consulting
Period End Date (the “Severance Period”), Executive shall be entitled to receive
the continued payment of his base salary (the aggregate amount for such twelve
(12)-month period, $505,000.00), subject to continuing compliance by Executive
with the terms hereof and the Release of Claims. Such payment shall be made in
substantially equal installments on a periodic basis in accordance with the
Company’s normal payroll practices.

(b) Bonus. The Company shall pay Executive an amount equal to $220,500.00, which
represents Executive’s bonus for fiscal year 2011, less required withholding
taxes, such payment to be made in a single cash lump sum no later than thirty
(30) days following the Termination Date.

(c) Healthcare Continuation Coverage. If Executive elects to receive continued
healthcare coverage pursuant to the provisions of the Consolidated Omnibus
Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall
directly pay, or reimburse Executive for, that portion of the premium for
Executive and Executive’s covered dependents necessary such that Executive
contributes the same amount to COBRA coverage as Executive contributed to
medical, dental and vision coverage prior to the date of this Agreement, such
payment or reimbursement to continue until the earlier of (i) the end of the
Severance Period or (ii) the date Executive becomes eligible for comparable
coverage under another employer’s plans, provided that Executive submits
documentation to the Company substantiating his payments for COBRA coverage. Any
such reimbursement payments, if applicable, shall be made to Executive no later
than twenty (20) days after

 

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Executive’s submission of documentation to the Company substantiating his
payments for COBRA coverage. After the Company ceases to pay premiums pursuant
to the preceding sentence, Executive may, if eligible, elect to continue
healthcare coverage at Executive’s expense in accordance with the provisions of
COBRA.

(d) Professional Advisor Fees. The Company shall reimburse Executive for the
reasonable attorneys’ and professional tax advisors’ fees and related expenses
and disbursements incurred by Executive in connection with Executive’s
separation of employment with the Company and the negotiation and preparation of
this Agreement, in an aggregate amount not to exceed $7,500.

(e) Taxes. Executive understands and agrees that all payments under this
Agreement will be subject to appropriate tax withholding and other deductions.
To the extent any taxes may be payable by Executive for the benefits provided to
him by this Agreement beyond those withheld by the Company, Executive agrees to
pay them himself and to indemnify and hold the Company and the other entities
released herein harmless for any tax claims or penalties, and associated
attorneys’ fees and costs, resulting from any failure by him to make required
payments. To the extent that any reimbursements payable pursuant to this
Agreement are subject to the provisions of Section 409A of the Code, such
reimbursements shall be paid to Executive no later than December 31 of the year
following the year in which the expense was incurred, the amount of expenses
reimbursed in one year shall not affect the amount eligible for reimbursement in
any subsequent year, and Executive’s right to reimbursement under this Agreement
will not be subject to liquidation or exchange for another benefit.

(f) SEC Reporting. Executive acknowledges that to the extent required by the
Securities Exchange Act of 1934, as amended (the “Exchange Act”), he or she will
have continuing obligations under Section 16(a) and 16(b) of the Exchange Act to
report his transactions in Company common stock for six (6) months following the
Termination Date. Executive hereby agrees not to undertake, directly or
indirectly, any reportable transactions which include, but are not limited to,
buying, selling or otherwise disposing of any common stock of the Company held
by Executive until the end of such six (6) month period.

(g) Sole Separation Benefit. Executive agrees that the payments provided by this
Section 4 are not required under the Company’s normal policies and procedures
and are provided as a severance solely in connection with this Agreement and the
Release of Claims. Executive acknowledges and agrees that the payments
referenced in this Section 4 constitute adequate and valuable consideration, in
and of themselves, for the promises contained in this Agreement and the Release
of Claims.

5. Full Payment. Executive acknowledges that the payment and arrangements herein
shall constitute full and complete satisfaction of any and all amounts properly
due and owing to Executive as a result of his employment with the Company and
the termination thereof. Executive further acknowledges that, other than the
Confidentiality Agreement and the Indemnification Agreement between Executive
and the Company dated April 27, 2010 (the “Indemnification Agreement”), this
Agreement shall supersede each agreement entered into between Executive and the
Company regarding Executive’s employment, including, without limitation, any
offer letter, employment agreement, severance and/or change in control
agreement, and each such agreement other than the Option Agreements shall be
deemed terminated and of no further effect as of the Termination Date.

 

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6. Executive’s Release of the Company. Executive understands that by agreeing to
the release provided by this Section 6, Executive is agreeing not to sue, or
otherwise file any claim against, the Company or any of its employees or other
agents for any reason whatsoever based on anything that has occurred as of the
date Executive signs this Agreement.

(a) On behalf of Executive and Executive’s heirs, assigns, executors,
administrators, trusts, spouse and estate, Executive hereby releases and forever
discharges the “Releasees” hereunder, consisting of the Company, and each of its
owners, affiliates, subsidiaries, predecessors, successors, assigns, agents,
directors, officers, partners, employees, and insurers, and all persons acting
by, through, under or in concert with them, or any of them, of and from any and
all manner of action or actions, cause or causes of action, in law or in equity,
suits, debts, liens, contracts, agreements, promises, liability, claims,
demands, damages, loss, cost or expense, of any nature whatsoever, known or
unknown, fixed or contingent (hereinafter called “Claims”), which Executive now
has or may hereafter have against the Releasees, or any of them, by reason of
any matter, cause, or thing whatsoever from the beginning of time to the date
hereof, including, without limiting the generality of the foregoing, any Claims
arising out of, based upon, or relating to Executive’s hire, employment,
remuneration or resignation by the Releasees, or any of them, Claims arising
under federal, state, or local laws relating to employment, Claims of any kind
that may be brought in any court or administrative agency, including any Claims
arising under Title VII of the Civil Rights Act of 1964, as amended by the Civil
Rights Act of 1991, 42 U.S.C. § 2000 et seq.; the Equal Pay Act, 29 U.S.C.
§ 206(d); the Civil Rights Act of 1866, 42 U.S.C. § 1981; the Family and Medical
Leave Act of 1993, 29 U.S.C. § 2601 et seq.; the Americans with Disabilities Act
of 1990, 42 U.S.C. § 12101 et seq.; the False Claims Act , 31 U.S.C. § 3729 et
seq.; the Employee Retirement Income Security Act, 29 U.S.C. § 1001 et seq.; the
Worker Adjustment and Retraining Notification Act, 29 U.S.C. § 2101 et seq. the
Fair Labor Standards Act, 29 U.S.C. § 215 et seq., the Sarbanes-Oxley Act of
2002; the California Labor Code; the employment and civil rights laws of
California; Claims for breach of contract; Claims arising in tort, including,
without limitation, Claims of wrongful dismissal or discharge, discrimination,
harassment, retaliation, fraud, misrepresentation, defamation, libel, infliction
of emotional distress, violation of public policy, and/or breach of the implied
covenant of good faith and fair dealing; and Claims for damages or other
remedies of any sort, including, without limitation, compensatory damages,
punitive damages, injunctive relief and attorney’s fees.

(b) Notwithstanding the generality of the foregoing, Executive does not release
the following claims:

(i) Claims for unemployment compensation or any state disability insurance
benefits pursuant to the terms of applicable state law;

(ii) Claims for workers’ compensation insurance benefits under the terms of any
worker’s compensation insurance policy or fund of the Company;

(iii) Claims to continued participation in certain of the Company’s group
benefit plans pursuant to the terms and conditions of COBRA;

(iv) Claims to any benefit entitlements vested as the date of Executive’s
employment termination, pursuant to written terms of any Company employee
benefit plan;

 

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(v) Claims for indemnification under the Indemnification Agreement, the
Company’s Bylaws, California Labor Code Section 2802 or any other applicable
law; and

(vi) Executive’s right to bring to the attention of the Equal Employment
Opportunity Commission claims of discrimination; provided, however, that
Executive does release Executive’s right to secure any damages for alleged
discriminatory treatment.

(c) EXECUTIVE ACKNOWLEDGES THAT EXECUTIVE HAS BEEN ADVISED OF AND IS FAMILIAR
WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES AS
FOLLOWS:

“A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR
SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE,
WHICH, IF KNOWN BY HIM OR HER, MUST HAVE MATERIALLY AFFECTED HIS OR HER
SETTLEMENT WITH THE DEBTOR.”

BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS
EXECUTIVE MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW
PRINCIPLES OF SIMILAR EFFECT.

7. Non-Disparagement, Transition, Transfer of Company Property and Limitations
on Service. Executive further agrees that:

(a) Non-Disparagement. Executive agrees that he shall not disparage, criticize
or defame the Company, its affiliates and their respective affiliates,
directors, officers, agents, partners, stockholders, employees, products,
services, technology or business, either publicly or privately. The Company
agrees that it shall not, and it shall instruct its officers and members of its
Board of Directors to not, disparage, criticize or defame Executive, either
publicly or privately. Nothing in this Section 7(a) shall have application to
any evidence or testimony required by any court, arbitrator or government
agency.

(b) Transition. Each of the Company and Executive shall use their respective
reasonable efforts to cooperate with each other in good faith to facilitate a
smooth transition of Executive’s duties to other executive(s) of the Company.

(c) Transfer of Company Property. On or before the Termination Date, Executive
shall turn over to the Company all files, memoranda, records, and other
documents, and any other physical or personal property which are the property of
the Company and which he had in his possession, custody or control at the time
he signed this Agreement.

8. Executive Representations. Executive warrants and represents that (a) he has
not filed or authorized the filing of any complaints, charges or lawsuits
against the Company or any affiliate of the Company with any governmental agency
or court, and that if, unbeknownst to Executive, such a complaint, charge or
lawsuit has been filed on his behalf, he will immediately cause it to be
withdrawn and dismissed, (b) he has reported all hours worked as of the date of
this

 

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Agreement and has been paid all compensation, wages, bonuses, commissions,
and/or benefits to which he may be entitled and no other compensation, wages,
bonuses, commissions and/or benefits are due to him, except as provided in this
Agreement, (c) he has no known workplace injuries or occupational diseases and
has been provided and/or has not been denied any leave requested under the
Family and Medical Leave Act or any similar state law, (d) the execution,
delivery and performance of this Agreement by Executive does not and will not
conflict with, breach, violate or cause a default under any agreement, contract
or instrument to which Executive is a party or any judgment, order or decree to
which Executive is subject, and (e) upon the execution and delivery of this
Agreement by the Company and Executive, this Agreement will be a valid and
binding obligation of Executive, enforceable in accordance with its terms.

9. No Assignment by Executive. Executive warrants and represents that no portion
of any of the matters released herein, and no portion of any recovery or
settlement to which Executive might be entitled, has been assigned or
transferred to any other person, firm or corporation not a party to this
Agreement, in any manner, including by way of subrogation or operation of law or
otherwise. If any claim, action, demand or suit should be made or instituted
against the Company or any other Releasee because of any actual assignment,
subrogation or transfer by Executive, Executive agrees to indemnify and hold
harmless the Company and all other Releasees against such claim, action, suit or
demand, including necessary expenses of investigation, attorneys’ fees and
costs. In the event of Executive’s death, this Agreement shall inure to the
benefit of Executive and Executive’s executors, administrators, heirs,
distributees, devisees, and legatees. None of Executive’s rights or obligations
may be assigned or transferred by Executive, other than Executive’s rights to
payments hereunder, which may be transferred only upon Executive’s death by will
or operation of law.

10. Non-Solicitation. Without limiting the Confidentiality Agreement, Executive
hereby agrees that Executive shall not, at any time during the Consulting Period
or within the one (1) year period immediately following the Termination Date,
directly or indirectly, either for himself or on behalf of any other person,
recruit or otherwise solicit or induce any employee or consultant of the Company
to terminate its employment or arrangement with the Company, or otherwise change
its relationship with the Company. Notwithstanding the foregoing, nothing herein
shall prevent Executive from directly or indirectly hiring any individual who
submits a resume or otherwise applies for a position in response to a publicly
posted job announcement or otherwise applies for employment with any person with
whom Executive may be associated absent any violation of Executive’s obligations
pursuant to the preceding sentence.

11. Governing Law. This Agreement shall be construed and enforced in accordance
with, and the rights of the parties shall be governed by, the laws of the State
of California or, where applicable, United States federal law, in each case,
without regard to any conflicts of laws provisions or those of any state other
than California.

12. Miscellaneous. This Agreement, collectively with the Confidentiality
Agreement, the Indemnification Agreement, the Option Agreements and the General
Release of Claims attached as Exhibit A hereto comprise the entire agreement
between the parties with regard to the subject matter hereof and supersedes, in
their entirety, any other agreements between Executive and the Company with
regard to the subject matter hereof. The Company and Executive acknowledge that
the termination of the Executive’s employment with the Company is intended to
constitute an involuntary separation from service for the purposes of
Section 409A of the Code, and the related Department of Treasury regulations.
Executive acknowledges that there are no other agreements, written, oral or
implied, and that he may not rely on any prior negotiations, discussions,
representations or agreements. This Agreement may be modified only in writing,
and

 

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such writing must be signed by both parties and recited that it is intended to
modify this Agreement. This Agreement may be executed in separate counterparts,
each of which is deemed to be an original and all of which taken together
constitute one and the same agreement.

13. Company Assignment and Successors. The Company shall assign its rights and
obligations under this Agreement to any successor to all or substantially all of
the business or the assets of the Company (by merger or otherwise). This
Agreement shall be binding upon and inure to the benefit of the Company and its
successors, assigns, personnel and legal representatives.

14. Maintaining Confidential Information. Executive reaffirms his obligations
under the Confidentiality Agreement. Executive acknowledges and agrees that the
payments provided in Section 4 above shall be subject to Executive’s continued
compliance with Executive’s obligations under the Confidentiality Agreement.

15. Executive’s Cooperation. After the Termination Date, Executive shall
cooperate with the Company and its affiliates, upon the Company’s reasonable
request, with respect to any internal investigation or administrative,
regulatory or judicial proceeding involving matters within the scope of
Executive’s duties and responsibilities to the Company or its affiliates during
his employment with the Company (including, without limitation, Executive being
available to the Company upon reasonable notice for interviews and factual
investigations, appearing at the Company’s reasonable request to give testimony
without requiring service of a subpoena or other legal process, and turning over
to the Company all relevant Company documents which are or may have come into
Executive’s possession during his employment); provided, however, that any such
request by the Company shall not be unduly burdensome or interfere with
Executive’s personal schedule or ability to engage in gainful employment.

(Signature page(s) follow)

 

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IN WITNESS WHEREOF, the undersigned have caused this Transition and Separation
Agreement to be duly executed and delivered as of the date indicated next to
their respective signatures below.

 

DATED: February 17, 2012            

/s/ Alan Shaw Ph.D.

      Alan Shaw, Ph.D.       CODEXIS, INC. DATED: February 17, 2012          
By:  

/s/ Doug Sheehy

      Doug Sheehy       Senior Vice President and General Counsel

 

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EXHIBIT A

GENERAL RELEASE OF CLAIMS

This General Release of Claims (“Release”) is entered into as of
                    , 2012, between Alan Shaw, Ph.D. (“Executive”) and Codexis,
Inc., a Delaware corporation (the “Company”) (collectively referred to herein as
the “Parties”), effective eight (8) days after Executive’s signature hereto (the
“Effective Date”), unless Executive revokes his acceptance of this Release as
provided in Paragraph 1(c), below.

1. Executive’s Release of the Company. Executive understands that by agreeing to
this Release, Executive is agreeing not to sue, or otherwise file any claim
against, the Company or any of its employees or other agents for any reason
whatsoever based on anything that has occurred as of the date Executive signs
this Release.

(a) On behalf of Executive and Executive’s heirs, assigns, executors,
administrators, trusts, spouse and estate, Executive hereby releases and forever
discharges the “Releasees” hereunder, consisting of the Company, and each of its
owners, affiliates, subsidiaries, predecessors, successors, assigns, agents,
directors, officers, partners, employees, and insurers, and all persons acting
by, through, under or in concert with them, or any of them, of and from any and
all manner of action or actions, cause or causes of action, in law or in equity,
suits, debts, liens, contracts, agreements, promises, liability, claims,
demands, damages, loss, cost or expense, of any nature whatsoever, known or
unknown, fixed or contingent (hereinafter called “Claims”), which Executive now
has or may hereafter have against the Releasees, or any of them, by reason of
any matter, cause, or thing whatsoever from the beginning of time to the date
hereof, including, without limiting the generality of the foregoing, any Claims
arising out of, based upon, or relating to Executive’s hire, employment,
remuneration or resignation by the Releasees, or any of them, including Claims
arising under federal, state, or local laws relating to employment, Claims of
any kind that may be brought in any court or administrative agency, any Claims
arising under the Age Discrimination in Employment Act (“ADEA”), 29 U.S.C.
§ 621, et seq.; Title VII of the Civil Rights Act of 1964, as amended by the
Civil Rights Act of 1991, 42 U.S.C. § 2000 et seq.; the Equal Pay Act, 29 U.S.C.
§ 206(d); the Civil Rights Act of 1866, 42 U.S.C. § 1981; the Family and Medical
Leave Act of 1993, 29 U.S.C. § 2601 et seq.; the Americans with Disabilities Act
of 1990, 42 U.S.C. § 12101 et seq.; the False Claims Act , 31 U.S.C. § 3729 et
seq.; the Employee Retirement Income Security Act, 29 U.S.C. § 1001 et seq.; the
Worker Adjustment and Retraining Notification Act, 29 U.S.C. § 2101 et seq. the
Fair Labor Standards Act, 29 U.S.C. § 215 et seq., the Sarbanes-Oxley Act of
2002; the California Labor Code; the employment and civil rights laws of
California; Claims for breach of contract; Claims arising in tort, including,
without limitation, Claims of wrongful dismissal or discharge, discrimination,
harassment, retaliation, fraud, misrepresentation, defamation, libel, infliction
of emotional distress, violation of public policy, and/or breach of the implied
covenant of good faith and fair dealing; and Claims for damages or other
remedies of any sort, including, without limitation, compensatory damages,
punitive damages, injunctive relief and attorney’s fees.

(b) Notwithstanding the generality of the foregoing, Executive does not release
the following claims:

(i) Claims for unemployment compensation or any state disability insurance
benefits pursuant to the terms of applicable state law;

 

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(ii) Claims for workers’ compensation insurance benefits under the terms of any
worker’s compensation insurance policy or fund of the Company;

(iii) Claims to continued participation in certain of the Company’s group
benefit plans pursuant to the terms and conditions of COBRA;

(iv) Claims to any benefit entitlements vested as the date of Executive’s
employment termination, pursuant to written terms of any Company employee
benefit plan;

(v) Claims for indemnification under the Indemnification Agreement between
Executive and the Company dated April 27, 2010, the Company’s Bylaws, California
Labor Code Section 2802 or any other applicable law; and

(vi) Executive’s right to bring to the attention of the Equal Employment
Opportunity Commission claims of discrimination; provided, however, that
Executive does release Executive’s right to secure any damages for alleged
discriminatory treatment.

(c) In accordance with the Older Workers Benefit Protection Act of 1990,
Executive has been advised of the following:

(i) Executive has the right to consult with an attorney before signing this
Release;

(ii) Executive has been given at least twenty-one (21) days to consider this
Release;

(iii) Executive has seven (7) days after signing this Release to revoke it, and
Executive will not receive the severance benefits provided by Section 4 of that
certain Transition and Separation Agreement entered into between the Parties as
of February 17, 2012 (the “Transition and Separation Agreement”) unless and
until such seven (7) day period has expired. If Executive wishes to revoke this
Release, Executive must deliver notice of Executive’s revocation in writing, no
later than 5:00 p.m. Pacific Time on the 7th day following Executive’s execution
of this Release to Doug Sheehy, SVP & General Counsel, 200 Penobscot Drive,
Redwood City, CA 94063, fax: (650) 421-8108.

(d) EXECUTIVE ACKNOWLEDGES THAT EXECUTIVE HAS BEEN ADVISED OF AND IS FAMILIAR
WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES AS
FOLLOWS:

“A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR
SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE,
WHICH, IF KNOWN BY HIM OR HER, MUST HAVE MATERIALLY AFFECTED HIS OR HER
SETTLEMENT WITH THE DEBTOR.”

BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS
EXECUTIVE MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW
PRINCIPLES OF SIMILAR EFFECT.

 

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2. Executive Representations. Executive represents and warrants that:

(a) Executive has returned to the Company all Company property in Executive’s
possession;

(b) Executive is not owed wages, commissions, bonuses or other compensation,
other than any payments that become due under Section 4 of the Transition and
Separation Agreement;

(c) During the course of Executive’s employment Executive did not sustain any
injuries for which Executive might be entitled to compensation pursuant to
worker’s compensation law or Executive has disclosed any injuries of which he is
currently, reasonably aware for which he might be entitled to compensation
pursuant to worker’s compensation law;

(d) From the date Executive executed the Transition and Separation Agreement
through the date Executive executes this Release, Executive has not made any
disparaging comments about the Company, nor will Executive do so in the future;
and

(e) Executive has not initiated any adversarial proceedings of any kind against
the Company or against any other person or entity released herein, nor will
Executive do so in the future, except as specifically allowed by this Release.

3. Maintaining Confidential Information. Executive reaffirms his obligations
under that certain Confidential Information, Secrecy, and Invention Agreement
entered into between Executive and Maxygen, the former parent corporation of the
Company, as of September 14, 2001 (the “Confidentiality Agreement”). Executive
acknowledges and agrees that the payments provided in Section 4 of the
Transition and Separation Agreement shall be subject to Executive’s continued
compliance with Executive’s obligations under the Confidentiality Agreement.

4. Non-Solicitation. Executive reaffirms his obligations pursuant to Section 10
of the Transition and Separation Agreement.

5. Cooperation with the Company. Executive reaffirms his obligations to
cooperate with the Company pursuant to Section 13 of the Transition and
Separation Agreement.

6. Severability. The provisions of this Release are severable. If any provision
is held to be invalid or unenforceable, it shall not affect the validity or
enforceability of any other provision.

7. Choice of Law. This Release shall in all respects be governed and construed
in accordance with the laws of the State of California, including all matters of
construction, validity and performance, without regard to conflicts of law
principles.

8. Integration Clause. This Release and the Transition and Separation Agreement
contain the Parties’ entire agreement with regard to the transition and
separation of Executive’s employment, and supersede and replace any prior
agreements as to those matters, whether oral or written. This Release may not be
changed or modified, in whole or in part, except by an instrument in writing
signed by Executive and the Chief Executive Officer of the Company.

 

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9. Execution in Counterparts. This Release may be executed in counterparts with
the same force and effectiveness as though executed in a single document.
Facsimile signatures shall have the same force and effectiveness as original
signatures.

10. Intent to be Bound. The Parties have carefully read this Release in its
entirety; fully understand and agree to its terms and provisions; and intend and
agree that it is final and binding on all Parties.

(Signature page(s) follow)

 

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IN WITNESS WHEREOF, and intending to be legally bound, the Parties have executed
the foregoing on the dates shown below.

 

EXECUTIVE      CODEXIS, INC.

 

    

 

Alan Shaw, Ph.D.      By:      Title: Date:      Date:

 

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