Document:

2002 Stock Plan, as amended, and Form of Stock Option Agreement

 Exhibit 10.10 
 CODEXIS, INC. 
 2002 STOCK PLAN 
 (as amended through August 28, 2007) 
 1. Purposes of the Plan. The purposes of this Plan are to attract and retain the best available personnel for positions of substantial responsibility, to provide additional incentive
to Employees, Directors and Consultants and to promote the success of the Company’s business. Options granted under the Plan may be Incentive Stock Options or Nonstatutory Stock Options, as determined by the Administrator at the time of grant.
Stock Purchase Rights may also be granted under the Plan. 
 2. Definitions. As used herein, the following definitions
shall apply: 
 (a) “Administrator” means the Board or any of its Committees as shall be administering the Plan
in accordance with Section 4 hereof. 
 (b) “Applicable Laws” means the requirements relating to the
administration of stock option plans under U.S. state corporate laws, U.S. federal and state securities laws, the Code, any stock exchange or quotation system on which the Common Stock is listed or quoted and the applicable laws of any other country
or jurisdiction where Options or Stock Purchase Rights are granted under the Plan. 
 (c) “Board” means the
Board of Directors of the Company. 
 (d) “Change in Control” means the occurrence of any of the following
events: 
 (i) Any “person” (as such term is used in Sections 13(d) and 14(d) of the Exchange Act) becomes the
“beneficial owner” (as defined in Rule 13d-3 of the Exchange Act), directly or indirectly, of securities of the Company representing fifty percent (50%) or more of the total voting power represented by the Company’s then
outstanding voting securities; or 
 (ii) The consummation of the sale or disposition by the Company of all or substantially
all of the Company’s assets; or 
 (iii) The consummation of a merger or consolidation of the Company with any other
corporation, other than a merger or consolidation which would result in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting securities
of the surviving entity or its parent) at least fifty percent (50%) of the total voting power represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately after such merger or consolidation.

 (e) “Code” means the Internal Revenue Code of 1986, as amended. 

 (f) “Committee” means a committee of Directors or of other individuals
satisfying Applicable Laws appointed by the Board in accordance with Section 4 hereof. 
 (g) “Common
Stock” means the Common Stock of the Company. 
 (h) “Company” means Codexis, Inc., a Delaware
corporation. 
 (i) “Consultant” means any person who is engaged by the Company or any Parent or Subsidiary to
render consulting or advisory services to such entity. 
 (j) “Director” means a member of the Board.

 (k) “Disability” means total and permanent disability as defined in Section 22(e)(3) of the Code.

 (l) “Employee” means any person, including officers and Directors, employed by the Company or any Parent or
Subsidiary of the Company. Neither service as a Director nor payment of a director’s fee by the Company shall be sufficient to constitute “employment” by the Company. 
 (m) “Exchange Act” means the Securities Exchange Act of 1934, as amended. 
 (n) “Fair Market Value” means, as of any date, the value of Common Stock determined as follows: 
 (i) If the Common Stock is listed on any established stock exchange or a national market system, including without limitation the Nasdaq
National Market or The Nasdaq SmallCap Market of The Nasdaq Stock Market, its Fair Market Value shall be the closing sales price for such stock (or the closing bid, if no sales were reported) as quoted on such exchange or system on the day of
determination, as reported in The Wall Street Journal or such other source as the Administrator deems reliable; 
 (ii)
If the Common Stock is regularly quoted by a recognized securities dealer but selling prices are not reported, its Fair Market Value shall be the mean between the high bid and low asked prices for the Common Stock on the day of determination; or

 (iii) In the absence of an established market for the Common Stock, the Fair Market Value thereof shall be determined in
good faith by the Administrator. 
 (o) “Incentive Stock Option” means an Option intended to qualify as an
incentive stock option within the meaning of Section 422 of the Code. 
 (p) “Nonstatutory Stock Option”
means an Option not intended to qualify as an Incentive Stock Option. 
 (q) “Option” means a stock option
granted pursuant to the Plan. 
  

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 (r) “Option Agreement” means a written or electronic agreement between the
Company and an Optionee evidencing the terms and conditions of an individual Option grant. The Option Agreement is subject to the terms and conditions of the Plan. 
 (s) “Optioned Stock” means the Common Stock subject to an Option or a Stock Purchase Right. 
 (t) “Optionee” means the holder of an outstanding Option or Stock Purchase Right granted under the Plan. 
 (u) “Parent” means a “parent corporation,” whether now or hereafter existing, as defined in Section 424(e) of the Code. 
 (v) “Plan” means this 2002 Stock Plan. 
 (w) “Restricted Stock” means Shares issued pursuant to a Stock Purchase Right or Shares of restricted stock issued pursuant to an Option. 
 (x) “Restricted Stock Purchase Agreement” means a written agreement between the Company and the Optionee evidencing the
terms and restrictions applying to Shares purchased under a Stock Purchase Right. The Restricted Stock Purchase Agreement is subject to the terms and conditions of the Plan and the notice of grant. 
 (y) “Securities Act means the Securities Act of 1933, as amended. 
 (z) “Service Provider” means an Employee, Director or Consultant. 
 (aa) “Share” means a share of the Common Stock, as adjusted in accordance with Section 13 below. 
 (bb) “Stock Purchase Right” means a right to purchase Common Stock pursuant to Section 11 below. 
 (cc) “Subsidiary” means a “subsidiary corporation,” whether now or hereafter existing, as defined in
Section 424(f) of the Code. 
 3. Stock Subject to the Plan. Subject to the provisions of
Section 13 of the Plan, the maximum aggregate number of Shares that may be subject to Options and sold under the Plan is 12,457,642 Shares. The Shares may be authorized but unissued, or reacquired Common Stock. 
 If an Option or Stock Purchase Right expires or becomes unexercisable without having been exercised in full, the unpurchased Shares that were
subject thereto shall become available for future grant or sale under the Plan (unless the Plan has terminated). However, Shares that have actually been issued under the Plan, upon exercise of either an Option or Stock Purchase Right, shall not be
returned to the Plan and shall not become available for future distribution under the Plan, except that if unvested Shares of Restricted Stock are repurchased by the Company at their original purchase price, such Shares shall become available for
future grant under the Plan. 
  

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 4. Administration of the Plan. 
 (a) Administrator. The Plan shall be administered by the Board or a Committee appointed by the Board, which Committee shall be
constituted to comply with Applicable Laws. 
 (b) Powers of the Administrator. Subject to the provisions
of the Plan and, in the case of a Committee, the specific duties delegated by the Board to such Committee, and subject to the approval of any relevant authorities, the Administrator shall have the authority in its discretion: 
 (i) to determine the Fair Market Value; 
 (ii) to select the Service Providers to whom Options and Stock Purchase Rights may from time to time be granted hereunder; 
 (iii) to determine the number of Shares to be covered by each such award granted hereunder; 
 (iv) to approve forms of agreement for use under the Plan; 
 (v) to determine the
terms and conditions of any Option or Stock Purchase Right granted hereunder. Such terms and conditions include, but are not limited to, the exercise price, the time or times when Options or Stock Purchase Rights may be exercised (which may be based
on performance criteria), any vesting acceleration or waiver of forfeiture restrictions, and any restriction or limitation regarding any Option or Stock Purchase Right or the Common Stock relating thereto, based in each case on such factors as the
Administrator, in its sole discretion, shall determine; 
 (vi) to prescribe, amend and rescind rules and regulations relating
to the Plan, including rules and regulations relating to sub-plans established for the purpose of satisfying applicable foreign laws; 
 (vii) to allow Optionees to satisfy withholding tax obligations by electing to have the Company withhold from the Shares to be issued upon exercise of an Option or Stock Purchase Right that number of Shares having a Fair Market Value equal
to the minimum amount required to be withheld. The Fair Market Value of the Shares to be withheld shall be determined on the date that the amount of tax to be withheld is to be determined. All elections by Optionees to have Shares withheld for this
purpose shall be made in such form and under such conditions as the Administrator may deem necessary or advisable; and 
 (viii) to construe and interpret the terms of the Plan and Options granted pursuant to the Plan. 
 (c)
Effect of Administrator’s Decision. All decisions, determinations and interpretations of the Administrator shall be final and binding on all Optionees. 
  

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 5. Eligibility. Nonstatutory Stock Options and Stock Purchase Rights may be granted
to Service Providers. Incentive Stock Options may be granted only to Employees. 
 6. Limitations. 
 (a) Incentive Stock Option Limit. Each Option shall be designated in the Option Agreement as either an Incentive Stock Option or a
Nonstatutory Stock Option. However, notwithstanding such designation, to the extent that the aggregate Fair Market Value of the Shares with respect to which Incentive Stock Options are exercisable for the first time by the Optionee during any
calendar year (under all plans of the Company and any Parent or Subsidiary) exceeds $100,000, such Options shall be treated as Nonstatutory Stock Options. For purposes of this Section 6(a), Incentive Stock Options shall be taken into account in
the order in which they were granted. The Fair Market Value of the Shares shall be determined as of the time the Option with respect to such Shares is granted. 
 (b) At-Will Employment. Neither the Plan nor any Option or Stock Purchase Right shall confer upon any Optionee any right with respect to continuing the Optionee’s relationship as a Service
Provider with the Company, nor shall it interfere in any way with his or her right or the Company’s right to terminate such relationship at any time, with or without cause, and with or without notice. 
 7. Term of Plan. Subject to stockholder approval in accordance with Section 19, the Plan shall become effective upon
its adoption by the Board. Unless sooner terminated under Section 15, it shall continue in effect for a term of ten (10) years from the later of (i) the effective date of the Plan, or (ii) the earlier of the most recent Board or
stockholder approval of an increase in the number of Shares reserved for issuance under the Plan. 
 8. Term of Option.
The term of each Option shall be stated in the Option Agreement; provided, however, that the term shall be no more than ten (10) years from the date of grant thereof. In the case of an Incentive Stock Option granted to an Optionee who, at the
time the Option is granted, owns stock representing more than ten percent (10%) of the voting power of all classes of stock of the Company or any Parent or Subsidiary, the term of the Option shall be five (5) years from the date of grant
or such shorter term as may be provided in the Option Agreement. 
 9. Option Exercise Price and Consideration.

 (a) Exercise Price. The per share exercise price for the Shares to be issued upon exercise of an Option shall be such
price as is determined by the Administrator, but shall be subject to the following: 
 (i) In the case of an Incentive Stock
Option 
 (A) granted to an Employee who, at the time of grant of such Option, owns stock representing more than ten percent
(10%) of the voting power of all classes of stock of the Company or any Parent or Subsidiary, the exercise price shall be no less than 110% of the Fair Market Value per Share on the date of grant. 
  

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 (B) granted to any other Employee, the per Share exercise price shall be no less than 100%
of the Fair Market Value per Share on the date of grant. 
 (ii) In the case of a Nonstatutory Stock Option 
 (A) granted to a Service Provider who, at the time of grant of such Option, owns stock representing more than ten percent (10%) of the
voting power of all classes of stock of the Company or any Parent or Subsidiary, the exercise price shall be no less than 110% of the Fair Market Value per Share on the date of grant. 
 (B) granted to any other Service Provider, the per Share exercise price shall be no less than 85% of the Fair Market Value per Share on the
date of grant. 
 (iii) Notwithstanding the foregoing, Options may be granted with a per Share exercise price other than as
required above pursuant to a merger or other corporate transaction. 
 (b) Forms of Consideration. The consideration to
be paid for the Shares to be issued upon exercise of an Option, including the method of payment, shall be determined by the Administrator (and, in the case of an Incentive Stock Option, shall be determined at the time of grant). Such consideration
may consist of, without limitation, (1) cash, (2) check, (3) promissory note, (4) other Shares, provided Shares acquired directly from the Company (x) have been owned by the Optionee for more than six months on the date of
surrender, and (y) have a Fair Market Value on the date of surrender equal to the aggregate exercise price of the Shares as to which such Option shall be exercised, (5) consideration received by the Company under a cashless exercise
program implemented by the Company in connection with the Plan, or (6) any combination of the foregoing methods of payment. In making its determination as to the type of consideration to accept, the Administrator shall consider if acceptance of
such consideration may be reasonably expected to benefit the Company. 
 10. Exercise of Option. 
 (a) Procedure for Exercise; Rights as a Stockholder. Any Option granted hereunder shall be exercisable according to the
terms hereof at such times and under such conditions as determined by the Administrator and set forth in the Option Agreement. An Option may not be exercised for a fraction of a Share. Except in the case of Options granted to officers, Directors and
Consultants, Options shall become exercisable at a rate of no less than 20% per year over five (5) years from the date the Options are granted. 
 An Option shall be deemed exercised when the Company receives (i) written or electronic notice of exercise (in accordance with the Option Agreement) from the person entitled to exercise the Option,
and (ii) full payment for the Shares with respect to which the Option is exercised. Full payment may consist of any consideration and method of payment authorized by the Administrator and permitted by the Option Agreement and the Plan. Shares
issued upon exercise of an Option shall be issued in the name of the Optionee or, if requested by the Optionee, in the name of the Optionee and his or her spouse. Until the Shares are issued (as evidenced by the appropriate entry on the books of the
Company or of a duly authorized transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to the Shares, notwithstanding the exercise of the Option. The Company shall issue
(or cause to be issued) such

  

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Shares promptly after the Option is exercised. No adjustment will be made for a dividend or other right for which the record date is prior to the date the Shares are issued, except as provided in
Section 13 of the Plan. 
 Exercise of an Option in any manner shall result in a decrease in the number of Shares
thereafter available, both for purposes of the Plan and for sale under the Option, by the number of Shares as to which the Option is exercised. 
 (b) Termination of Relationship as a Service Provider. If an Optionee ceases to be a Service Provider, such Optionee may exercise his or her Option within thirty (30) days of termination,
or such longer period of time as specified in the Option Agreement, to the extent that the Option is vested on the date of termination (but in no event later than the expiration of the term of the Option as set forth in the Option Agreement). If, on
the date of termination, the Optionee is not vested as to his or her entire Option, the Shares covered by the unvested portion of the Option shall revert to the Plan. If, after termination, the Optionee does not exercise his or her Option within the
time specified by the Administrator, the Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (c) Disability of Optionee. If an Optionee ceases to be a Service Provider as a result of the Optionee’s Disability, the Optionee may exercise his or her Option within six (6) months of termination, or such longer period of
time as specified in the Option Agreement, to the extent the Option is vested on the date of termination (but in no event later than the expiration of the term of such Option as set forth in the Option Agreement). If, on the date of termination, the
Optionee is not vested as to his or her entire Option, the Shares covered by the unvested portion of the Option shall revert to the Plan. If, after termination, the Optionee does not exercise his or her Option within the time specified herein, the
Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (d)
Death of Optionee. If an Optionee dies while a Service Provider, the Option may be exercised within six (6) months following Optionee’s death, or such longer period of time as specified in the Option Agreement, to the
extent that the Option is vested on the date of death (but in no event later than the expiration of the term of such Option as set forth in the Option Agreement) by the Optionee’s designated beneficiary, provided such beneficiary has been
designated prior to Optionee’s death in a form acceptable to the Administrator. If no such beneficiary has been designated by the Optionee, then such Option may be exercised by the personal representative of the Optionee’s estate or by the
person(s) to whom the Option is transferred pursuant to the Optionee’s will or in accordance with the laws of descent and distribution. If, at the time of death, the Optionee is not vested as to his or her entire Option, the Shares covered by
the unvested portion of the Option shall immediately revert to the Plan. If the Option is not so exercised within the time specified herein, the Option shall terminate, and the Shares covered by such Option shall revert to the Plan. 
 (e) Leaves of Absence. 
 (i) A Service Provider shall not cease to be an Employee in the case of (A) any leave of absence approved by the Company or (B) transfers between locations of the Company or between the Company,
its Parent, any Subsidiary, or any successor. 
  

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 (ii) For purposes of Incentive Stock Options, no such leave may exceed ninety
(90) days, unless reemployment upon expiration of such leave is guaranteed by statute or contract. If reemployment upon expiration of a leave of absence approved by the Company is not so guaranteed, then three (3) months following the 91st
day of such leave, any Incentive Stock Option held by the Optionee shall cease to be treated as an Incentive Stock Option and shall be treated for tax purposes as a Nonstatutory Stock Option. 
 11. Stock Purchase Rights. 
 (a) Rights to Purchase. Stock Purchase Rights may be issued either alone, in addition to, or in tandem with other awards granted under the Plan and/or cash awards made outside of the Plan. After
the Administrator determines that it will offer Stock Purchase Rights under the Plan, it shall advise the offeree in writing or electronically of the terms, conditions and restrictions related to the offer, including the number of Shares that such
person shall be entitled to purchase, the price to be paid, and the time within which such person must accept such offer. The terms of the offer shall comply in all respects with Section 260.140.42 of Title 10 of the California Code of
Regulations. The offer shall be accepted by execution of a Restricted Stock Purchase Agreement in the form determined by the Administrator. 
 (b) Repurchase Option. Unless the Administrator determines otherwise, the Restricted Stock Purchase Agreement shall grant the Company a repurchase option exercisable within 90 days of the voluntary
or involuntary termination of the purchaser’s service with the Company for any reason (including death or disability). The purchase price for Shares repurchased pursuant to the Restricted Stock Purchase Agreement shall be the original price
paid by the purchaser and may be paid by cancellation of any indebtedness of the purchaser to the Company. The repurchase option shall lapse at such rate as the Administrator may determine. Except with respect to Shares purchased by officers,
Directors and Consultants, the repurchase option shall in no case lapse at a rate of less than 20% per year over five (5) years from the date of purchase. 
 (c) Other Provisions. The Restricted Stock Purchase Agreement shall contain such other terms, provisions and conditions not inconsistent with the Plan as may be determined by the Administrator in
its sole discretion. 
 (d) Rights as a Stockholder. Once the Stock Purchase Right is exercised, the purchaser shall have
rights equivalent to those of a stockholder and shall be a stockholder when his or her purchase is entered upon the records of the duly authorized transfer agent of the Company. No adjustment shall be made for a dividend or other right for which the
record date is prior to the date the Stock Purchase Right is exercised, except as provided in Section 13 of the Plan. 
 12. Limited Transferability of Options and Stock Purchase Rights. Unless determined otherwise by the Administrator, Options and Stock Purchase Rights may not be sold, pledged, assigned, hypothecated, transferred, or
disposed of in any manner other than by will or the laws of descent and distribution, and may be exercised during the lifetime of the Optionee, only by the Optionee. If the Administrator in its sole discretion makes an Option or Stock Purchase Right
transferable, such Option or Stock Purchase Right may only be transferred (i) by will, (ii) by the laws of descent and distribution, or (iii) to family members (within the meaning of Rule 701 of the Securities Act) through gifts or
domestic relations orders, as permitted by Rule 701 of the Securities Act. 
  

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 13. Adjustments; Dissolution or Liquidation; Merger or Change in Control. 

(a) Adjustments. In the event that any dividend or other distribution (whether in the form of cash, Shares, other securities, or
other property), recapitalization, stock split, reverse stock split, reorganization, merger, consolidation, split-up, spin-off, combination, repurchase, or exchange of Shares or other securities of the Company, or other change in the corporate
structure of the Company affecting the Shares occurs, the Administrator, in order to prevent diminution or enlargement of the benefits or potential benefits intended to be made available under the Plan and in order to comply with
Section 25102(o) of the California Corporations Code, shall adjust the number and class of Shares that may be delivered under the Plan and/or the number, class, and price of Shares covered by each outstanding Option or Stock Purchase Right.

 (b) Dissolution or Liquidation. In the event of the proposed dissolution or liquidation of the Company, the
Administrator shall notify each Optionee as soon as practicable prior to the effective date of such proposed transaction. The Administrator in its discretion may provide for an Optionee to have the right to exercise his or her Option until ten
(10) days prior to such transaction as to all of the Optioned Stock, including Shares as to which the Option would not otherwise be exercisable. In addition, the Administrator may provide that any Company repurchase option applicable to any
Shares purchased upon exercise of an Option or Stock Purchase Right shall lapse as to all such Shares, provided the proposed dissolution or liquidation takes place at the time and in the manner contemplated. To the extent it has not been previously
exercised, an Option or Stock Purchase Right will terminate immediately prior to the consummation of such proposed action. 
 (c)
Merger or Change in Control. In the event of a merger of the Company with or into another corporation, or a Change in Control, each outstanding Option and Stock Purchase Right shall be assumed or an equivalent option substituted by the
successor corporation or a Parent or Subsidiary of the successor corporation. In the event that the successor corporation in a merger or Change in Control refuses to assume or substitute for the Option or Stock Purchase Right, then the Optionee
shall fully vest in and have the right to exercise the Option or Stock Purchase Right as to all of the Optioned Stock, including Shares as to which it would not otherwise be vested or exercisable. If an Option or Stock Purchase Right becomes fully
vested and exercisable in lieu of assumption or substitution in the event of a merger or Change in Control, the Administrator shall notify the Optionee in writing or electronically that this Option or Stock Purchase Right shall be fully exercisable
for a period of fifteen (15) days from the date of such notice, and the Option or Stock Purchase Right shall terminate upon expiration of such period. For the purposes of this paragraph, the Option or Stock Purchase Right shall be considered
assumed if, following the merger or Change in Control, the option or right confers the right to purchase or receive, for each Share of Optioned Stock subject to the Option or Stock Purchase Right immediately prior to the merger or Change in Control,
the consideration (whether stock, cash, or other securities or property) received in the merger or Change in Control by holders of Common Stock for each Share held on the effective date of the transaction (and if holders were offered a choice of
consideration, the type of consideration chosen by the holders of a majority of the outstanding Shares); provided, however, that if such consideration received in the merger or Change in Control is not solely common stock of the successor
corporation or its Parent, the Administrator may, with the consent of the successor

  

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corporation, provide for the consideration to be received upon the exercise of the Option or Stock Purchase Right, for each Share of Optioned Stock subject to the Option or Stock Purchase Right,
to be solely common stock of the successor corporation or its Parent equal in fair market value to the per share consideration received by holders of common stock in the merger or Change in Control. 
 14. Time of Granting Options and Stock Purchase Rights. The date of grant of an Option or Stock Purchase Right shall,
for all purposes, be the date on which the Administrator makes the determination granting such Option or Stock Purchase Right, or such later date as is determined by the Administrator. Notice of the determination shall be given to each Service
Provider to whom an Option or Stock Purchase Right is so granted within a reasonable time after the date of such grant. 
 15.
Amendment and Termination of the Plan. 
 (a) Amendment and Termination. The Board may at
any time amend, alter, suspend or terminate the Plan. 
 (b) Stockholder Approval. The Board shall obtain stockholder
approval of any Plan amendment to the extent necessary and desirable to comply with Applicable Laws. 
 (c)
Effect of Amendment or Termination. No amendment, alteration, suspension or termination of the Plan shall impair the rights of any Optionee, unless mutually agreed otherwise between the Optionee and the Administrator,
which agreement must be in writing and signed by the Optionee and the Company. Termination of the Plan shall not affect the Administrator’s ability to exercise the powers granted to it hereunder with respect to Options granted under the Plan
prior to the date of such termination. 
 16. Conditions Upon Issuance of Shares. 
 (a) Legal Compliance. Shares shall not be issued pursuant to the exercise of an Option unless the exercise of such Option and the
issuance and delivery of such Shares shall comply with Applicable Laws and shall be further subject to the approval of counsel for the Company with respect to such compliance. 
 (b) Investment Representations. As a condition to the exercise of an Option, the Administrator may require the person exercising such
Option to represent and warrant at the time of any such exercise that the Shares are being purchased only for investment and without any present intention to sell or distribute such Shares if, in the opinion of counsel for the Company, such a
representation is required. 
 17. Inability to Obtain Authority. The inability of the Company to obtain authority from
any regulatory body having jurisdiction, which authority is deemed by the Company’s counsel to be necessary to the lawful issuance and sale of any Shares hereunder, shall relieve the Company of any liability in respect of the failure to issue
or sell such Shares as to which such requisite authority shall not have been obtained. 
 18.
Reservation of Shares. The Company, during the term of this Plan, shall at all times reserve and keep available such number of Shares as shall be sufficient to satisfy the requirements of the Plan. 
  

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 19. Stockholder Approval. The Plan shall be subject to approval by the stockholders
of the Company within twelve (12) months after the date the Plan is adopted. Such stockholder approval shall be obtained in the degree and manner required under Applicable Laws. 
 20. Information to Optionees. The Company shall provide to each Optionee and to each individual who acquires Shares pursuant to the
Plan, not less frequently than annually during the period such Optionee has one or more Options or Stock Purchase Rights outstanding, and, in the case of an individual who acquires Shares pursuant to the Plan, during the period such individual owns
such Shares, copies of annual financial statements. The Company shall not be required to provide such statements to key employees whose duties in connection with the Company assure their access to equivalent information. 
 21. Rules Particular to Specific Countries. Notwithstanding anything herein to the contrary, the terms and conditions of the Plan
with respect to Optionees who are tax residents of a particular country may be subject to an addendum to the Plan in the form of an Appendix. To the extent that the terms and conditions set forth in an Appendix conflict with any provisions of the
Plan, the provisions of the Appendix shall govern. The adoption of any such Appendix shall be pursuant to Section 15 above. 
  

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 CODEXIS, INC. 
 2002 STOCK PLAN 
 APPENDIX 
 FOR GERMANY 
  

	1.	General 

 Each of the provisions of the Codexis, Inc. 2002 Stock Plan shall apply to this Appendix subject to the alterations below. This Appendix shall apply in relation to Options and Stock Purchase Rights granted to Service Providers residing and
providing services in Germany. 
  

	2.	Exercise of Discretion 

 The Administrator’s discretion with respect to the Plan, including, but not limited to, Section 4 (b), will be exercised in a way complying with German law, in particular with the labour law
principle of equal treatment (arbeitsrechtlicher Gleichbehandlungsgrundsatz) and with the prohibition of discrimination (Diskriminierungsverbot). 
  

	3.	Disability 

 Section 2(k) shall read as follows: “Disability” means total and permanent disability to perform work if it results in termination of employment by the Service Provider or, if valid under German law, by the Company or the
Subsidiary. 
  

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	4.	Vesting Requirement 

 The
last sentence of the first paragraph of Section 10(a) and the last sentence of Section 11(b) shall not apply. 
  

	5.	Leaves of Absence 

 Section 10(e)(i) is amended to read in its entirety as follows: “(i) A Service Provider shall not cease to be an Employee: (A) in the case of any leave of absence approved by the Company; (B) in the case of transfers
between locations of the Company or between the Company, its Parent, any Subsidiary, or any successor; or (C) if required by German law.” 
  

	6.	Ex-gratia benefit 

 The grant of an Option or a Stock Purchase Right is an ex-gratia benefit (freiwillige Leistung). It does not create a legal claim; and even repeated granting will not create such a legal
claim. 
 The Option or Stock Purchase Right granted shall not form, or be considered, part of any normal or
expected compensation that is or may be subject to severance, resignation, redundancy or similar pay nor does it affect or change in any way the terms and conditions of employment. 
  

	7.	Adjustments upon Changes in Capitalization, Merger or Asset Sale 

 The Administrator’s discretion with respect to any Adjustments pursuant to Section 13 and to any Investment
Representation pursuant to Section 16(b) will be exercised taking into fair consideration the circumstances why such adjustment or representation is deemed appropriate. 
  

	8.	Taxes/Withholding 

 The
following summary of certain German income tax considerations for German Employees is based on the tax law effective at the date of this Appendix which may be changed, even with retroactive effect. The summary does not describe all tax
considerations that may be relevant to a German Employee’s decision to accept or exercise any of the rights under the Plan. It is not a substitute for tax advice. 
  

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 Capital gains realized upon exercise of an Option or a Stock Purchase Right is deemed to be
a benefit in kind subject to income tax. Such gain is subject to the personal income tax rate (as of 2008 between 15.8 % and 47.5 % including solidarity surcharge). The capital gain realized upon exercise of an Option or a Stock Purchase
Right is determined by the difference between the fair market value of the Shares at the date the Shares are booked out (Ausbuchung) of the account of the Company or of any transfer agent of the Company and the purchase price. The fair market
value is defined on the basis of the prices quoted on the respective stock exchange or, if the Shares are not listed, according to an appropriate appraisal method available for unlisted shares of corporations. A reduced tax rate may apply if the
grant of the option qualifies as salary for several years. 
 The employer company is obligated to deduct wage tax from the gross
salary of the Employee. Additionally, the usual social security contributions, up to the relevant maximum amount, have to be paid on the difference between the exercise price and the market value at the time the Option or Stock Purchase Right is
exercised. – If the regular salary of the Employee is not sufficient for the employer company to deduct wage tax and pay such tax to the competent tax office, the company will request the Employee to make a payment to the company in order to
enable it to pay the wage tax. The employer company will inform the tax office if the Employee fails to fulfill such request. 
 If the Employee is obliged to retransfer the Shares to the Company under the Repurchase Option, such retransfer should be considered as negative income for the Employee thereby reducing the Employee’s overall income for the respective
calendar year. The amount of the negative income is determined by the difference between the fair market value of the Shares at the date the Shares are retransferred and the purchase price. The fair market value is defined as described above.

 Capital gains from the sale of Shares are only subject to taxation, (i) if the sale takes place within one year from the
purchase as a so-called private transaction (privates Veräußerungsgeschäft) or – after this period has lapsed – (ii) if the Optionee (or the

  

 -14- 

 
predecessor in the case of a transfer of Shares without consideration), at any time during the five years preceding the sale, directly or indirectly held or holds a participation of 1% or more.
Capital gains deriving from a disposal of Shares as private transactions are tax exempt for Employees if the total gains from private transactions in the respective calendar year amounts to less than € 512 p.a. and per person. To the
extent that capital gains upon sale of Shares are subject to German income tax, 50% of such capital gains are subject to the progressive income tax rate plus a solidarity surcharge of 5.5% thereon. According to the newly enacted Corporate Tax Reform
Act 2008 (Unternehmensteuerreform 2008) capital gains will generally be subject to a uniform 25% tax (plus solidarity surcharge and, if applicable, church tax) as of 2009 if the respective Shares have been acquired after 31 December 2008
unless a shareholder holds, or held at any time during the five years preceding the sale, directly or indirectly, an interest of 1% or more in the company, in which case 60% from any such sale will be subject to tax at personal rates (instead of
currently only 50%). Generally, the bank will levy the 25% tax on the capital gain by way of withholding if the Shares are held through a domestic bank or a domestic branch of a foreign bank (a “Bank”). However, since the purchase price of
the Shares cannot be verified for withholding purposes , the Bank will be obliged to levy the 25% tax (plus solidarity surcharge and, if applicable, church tax) on 30% of the sales price of the Shares from which parts may possibly be recovered later
by the shareholder by way of filing an income tax return. Capital gains stemming from Shares acquired before 1 January 2009 will continue to be taxed pursuant to the current tax regime (see above). 
 In principle, 50% of the gross dividends received by Employees until 31 December 2008 will be subject to income tax at the progressive
tax rate plus solidarity surcharge. Investment income received by the Employee, including dividends, after deduction of half the income-related expenses in economic connection with the dividends or the standard amount for income-related expenses of
€ 51 (€ 102 for married couples filing jointly), are tax-free up to the maximum amount of tax-free savings allowances of € 750 (or € 1,500 for married couples filing jointly) until 31 December 2008.
Dividends received thereafter will be subject to the 25% tax rate as described above which will be collected by way of withholding provided the Shares are held through a Bank. The current tax allowances and deductions will be replaced from 2009
onward by a joint lump-sum deduction for capital income (i.e., interest and

  

 -15- 

 
dividend income as well as capital gains) of €801 (€1,602 for married couples filing tax returns jointly) per annum, whereby higher expenses directly attributable to a capital
investment will not be deductible as expenses any more. 
 Please note that a taxpayer will be able to apply for a tax assessment
if his or her personal tax rate is lower than the 25% flat-rate (Günstigerprüfung) or if the taxpayer can claim a tax credit for tax imposed by foreign Tax Authorities that has not been recognized yet by way of withholding.

  

	9.	Insider Dealings 

 Please
note that Germany has adopted the EC-Directive on Insider Dealings. Insiders are, among others, persons who by virtue of their position as members of managing or supervisory boards of the issuing company or its subsidiaries or by their profession or
work, have knowledge of not publicly known facts which may influence the market value of the securities issued. Insiders are subject to certain restrictions in selling or purchasing such securities or otherwise making use of their insider knowledge.
Anyone in breach of those provisions will be liable to imprisonment or fine. 
  

	10.	Administrator’s decisions 

 The decisions of the Administrator in connection with any interpretation of the Plan or in any dispute relating to an Option or a Stock Purchase Right or other matters relating to the Plan shall be final
and conclusive and binding on the relevant parties. It may only be revised by competent courts. 
  

	11.	Governing Law 

 The Plan shall be governed by and construed in accordance with the laws of the State of Delaware but mandatory provisions of German law may be applied. 
  

 -16- 

 CODEXIS, INC. 
 2002 STOCK PLAN 
 STOCK OPTION AGREEMENT

 Unless otherwise defined herein, the terms defined in the 2002 Stock Plan shall have the same defined meanings in this
Stock Option Agreement. 
  

	I.	NOTICE OF STOCK OPTION GRANT 

 Name: 
 Address: 
 The undersigned Optionee has been granted an Option to purchase Common Stock of the Company, subject to the terms and conditions of the Plan
and this Option Agreement, as follows: 
  

							
	Date of Grant	 	                                       
                                         
   	  	
			
	Vesting Commencement Date	 	                                       
                                         
   	  	
			
	Exercise Price per Share	 	$                                       
                                         
	  	
			
	Total Number of Shares Granted	 	                                       
                                         
   	  	
			
	Total Exercise Price	 	$                                       
                                         
	  	
				
	Type of Option:	 	—	  	Incentive Stock Option	  	
				
		 	—	  	Nonstatutory Stock Option	  	
			
	Term/Expiration Date:	 	                                       
                                         
   	  	

 Vesting Schedule: 
 This Option shall be exercisable, in whole or in part, according to the following vesting schedule: 
 25% of the Shares subject to the Option shall vest on the one (1) year anniversary of the Vesting Commencement Date, and 1/48 of the
Option shall vest each month thereafter, subject to Optionee continuing to be a Service Provider on such dates. 

 Termination Period: 
 This Option shall be exercisable for three (3) months after Optionee ceases to be a Service Provider. Upon Optionee’s death or
Disability, this Option may be exercised for one (1) year after Optionee ceases to be a Service Provider. In no event may Optionee exercise this Option after the Term/Expiration Date as provided above. 
  

	II.	AGREEMENT 

 1.
Grant of Option. The Plan Administrator of the Company hereby grants to the Optionee named in the Notice of Grant (the “Optionee”), an option (the “Option”) to purchase the number of Shares set forth in the Notice of
Grant, at the exercise price per Share set forth in the Notice of Grant (the “Exercise Price”), and subject to the terms and conditions of the Plan, which is incorporated herein by reference. Subject to Section 15(c) of the Plan, in
the event of a conflict between the terms and conditions of the Plan and this Option Agreement, the terms and conditions of the Plan shall prevail. 
 If designated in the Notice of Grant as an Incentive Stock Option (“ISO”), this Option is intended to qualify as an Incentive Stock Option as defined in Section 422 of the Code.
Nevertheless, to the extent that it exceeds the $100,000 rule of Code Section 422(d), this Option shall be treated as a Nonstatutory Stock Option (“NSO”). 
 2. Exercise of Option. 
 (a) Right to Exercise. This Option shall be
exercisable during its term in accordance with the Vesting Schedule set out in the Notice of Grant and with the applicable provisions of the Plan and this Option Agreement. 
 (b) Method of Exercise. This Option shall be exercisable by delivery of an exercise notice in the form attached as
Exhibit A (the “Exercise Notice”) which shall state the election to exercise the Option, the number of Shares with respect to which the Option is being exercised, and such other representations and agreements as may be required
by the Company. The Exercise Notice shall be accompanied by payment of the aggregate Exercise Price as to all Exercised Shares. This Option shall be deemed to be exercised upon receipt by the Company of such fully executed Exercise Notice
accompanied by the aggregate Exercise Price. 
 No Shares shall be issued pursuant to the exercise of an Option unless such
issuance and such exercise complies with Applicable Laws. Assuming such compliance, for income tax purposes the Shares shall be considered transferred to the Optionee on the date on which the Option is exercised with respect to such Shares.

 3. Optionee’s Representations. In the event the Shares have not been registered under the Securities Act of 1933,
as amended, at the time this Option is exercised, the Optionee shall, if required by the Company, concurrently with the exercise of all or any portion of this Option, deliver to the Company his or her Investment Representation Statement in the form
attached hereto as Exhibit B. 
  

 -2- 

 4. Lock-Up Period. Optionee hereby agrees that Optionee shall not offer, pledge,
sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, lend, or otherwise transfer or dispose of, directly or indirectly, any Common Stock (or other
securities) of the Company or enter into any swap, hedging or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of any Common Stock (or other securities) of the Company held by Optionee
(other than those included in the registration) for a period specified by the representative of the underwriters of Common Stock (or other securities) of the Company not to exceed one hundred eighty (180) days following the effective date of
any registration statement of the Company filed under the Securities Act. 
 Optionee agrees to execute and deliver such other
agreements as may be reasonably requested by the Company or the underwriter which are consistent with the foregoing or which are necessary to give further effect thereto. In addition, if requested by the Company or the representative of the
underwriters of Common Stock (or other securities) of the Company, Optionee shall provide, within ten (10) days of such request, such information as may be required by the Company or such representative in connection with the completion of any
public offering of the Company’s securities pursuant to a registration statement filed under the Securities Act. The obligations described in this Section shall not apply to a registration relating solely to employee benefit plans on Form S-1
or Form S-8 or similar forms that may be promulgated in the future, or a registration relating solely to a Commission Rule 145 transaction on Form S-4 or similar forms that may be promulgated in the future. The Company may impose stop-transfer
instructions with respect to the shares of Common Stock (or other securities) subject to the foregoing restriction until the end of said one hundred eighty (180) day period. Optionee agrees that any transferee of the Option or Shares acquired
pursuant to the Option shall be bound by this Section. 
 5. Method of Payment. Payment of the aggregate Exercise Price
shall be by any of the following, or a combination thereof, at the election of the Optionee: 
 (a) cash or check; 
 (b) consideration received by the Company under a formal cashless exercise program adopted by the Company in connection with the Plan; or

 (c) surrender of other Shares which, (i) in the case of Shares acquired from the Company, either directly or indirectly,
have been owned by the Optionee for more than six (6) months on the date of surrender, and (ii) have a Fair Market Value on the date of surrender equal to the aggregate Exercise Price of the Exercised Shares. 
 6. Restrictions on Exercise. This Option may not be exercised until such time as the Plan has been approved by the stockholders of
the Company, or if the issuance of such Shares upon such exercise or the method of payment of consideration for such Shares would constitute a violation of any Applicable Law. 
 7. Non-Transferability of Option. This Option may not be transferred in any manner otherwise than by will or by the laws of descent
or distribution and may be exercised during the lifetime of Optionee only by Optionee. The terms of the Plan and this Option Agreement shall be binding upon the executors, administrators, heirs, successors and assigns of the Optionee. 
  

 -3- 

 8. Term of Option. This Option may be exercised only within the term set out in the
Notice of Grant, and may be exercised during such term only in accordance with the Plan and the terms of this Option. 
 9.
Tax Obligations. 
 (a) Withholding Taxes. Optionee agrees to make appropriate arrangements with the Company (or
the Parent or Subsidiary employing or retaining Optionee) for the satisfaction of all Federal, state, local and foreign income and employment tax withholding requirements applicable to the Option exercise. Optionee acknowledges and agrees that the
Company may refuse to honor the exercise and refuse to deliver Shares if such withholding amounts are not delivered at the time of exercise. 
 (b) Notice of Disqualifying Disposition of ISO Shares. If the Option granted to Optionee herein is an ISO, and if Optionee sells or otherwise disposes of any of the Shares acquired pursuant to the
ISO on or before the later of (1) the date two years after the Date of Grant, or (2) the date one year after the date of exercise, the Optionee shall immediately notify the Company in writing of such disposition. Optionee agrees that
Optionee may be subject to income tax withholding by the Company on the compensation income recognized by the Optionee. 
 10.
Entire Agreement; Governing Law. The Plan is incorporated herein by reference. The Plan and this Option Agreement constitute the entire agreement of the parties with respect to the subject matter hereof and supersede in their entirety all
prior undertakings and agreements of the Company and Optionee with respect to the subject matter hereof, and may not be modified adversely to the Optionee’s interest except by means of a writing signed by the Company and Optionee. This
agreement is governed by the internal substantive laws but not the choice of law rules of California. 
 11. No Guarantee of
Continued Service. OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO THE VESTING SCHEDULE HEREOF IS EARNED ONLY BY CONTINUING AS A SERVICE PROVIDER AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF BEING HIRED, BEING
GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER). OPTIONEE FURTHER ACKNOWLEDGES AND AGREES THAT THIS AGREEMENT, THE TRANSACTIONS CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO NOT CONSTITUTE AN EXPRESS OR IMPLIED PROMISE OF
CONTINUED ENGAGEMENT AS A SERVICE PROVIDER FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND SHALL NOT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE OPTIONEE’S RELATIONSHIP AS A SERVICE PROVIDER
AT ANY TIME, WITH OR WITHOUT CAUSE. 
 Optionee acknowledges receipt of a copy of the Plan and represents that he or she is
familiar with the terms and provisions thereof, and hereby accepts this Option subject to all of the terms and provisions thereof. Optionee has reviewed the Plan and this Option in their entirety, has had an

  

 -4- 

 
opportunity to obtain the advice of counsel prior to executing this Option and fully understands all provisions of the Option. Optionee hereby agrees to accept as binding, conclusive and final
all decisions or interpretations of the Administrator upon any questions arising under the Plan or this Option. Optionee further agrees to notify the Company upon any change in the residence address indicated below. 
  

			
	OPTIONEE	  	CODEXIS, INC.
		
	  
	  	  

	Signature	  	By
		
	  
	  	  

	Print Name	  	Title
		
	  
	  	
	  
	  	
	Residence Address	  	

  

 -5- 

 EXHIBIT A 
 2002 STOCK PLAN 
 EXERCISE NOTICE 
 CODEXIS, INC. 
 Address:                         
 Attention:                         
 1. Exercise of Option. Effective as of today,             ,         , the
undersigned (“Optionee”) hereby elects to exercise Optionee’s option to purchase              shares of the Common Stock (the “Shares”) of Codexis, Inc. (the
“Company”) under and pursuant to the 2002 Stock Plan (the “Plan”) and the Stock Option Agreement dated             ,
         (the “Option Agreement”). 
 2. Delivery of Payment.
Purchaser herewith delivers to the Company the full purchase price of the Shares, as set forth in the Option Agreement, and any and all withholding taxes due in connection with the exercise of the Option. 
 3. Representations of Optionee. Optionee acknowledges that Optionee has received, read and understood the Plan and the Option
Agreement and agrees to abide by and be bound by their terms and conditions. 
 4. Rights as Stockholder. Until the
issuance of the Shares (as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to
the Optioned Stock, notwithstanding the exercise of the Option. The Shares shall be issued to the Optionee as soon as practicable after the Option is exercised in accordance with the Option Agreement. No adjustment shall be made for a dividend or
other right for which the record date is prior to the date of issuance except as provided in Section 13 of the Plan. 
 5.
Company’s Right of First Refusal Before any Shares held by Optionee or any transferee (either being sometimes referred to herein as the “Holder”) may be sold or otherwise transferred (including transfer by gift or operation of
law), the Company or its assignee(s) shall have a right of first refusal to purchase the Shares on the terms and conditions set forth in this Section (the “Right of First Refusal”). 
 (a) Notice of Proposed Transfer. The Holder of the Shares shall deliver to the Company a written notice (the “Notice”)
stating: (i) the Holder’s bona fide intention to sell or otherwise transfer such Shares; (ii) the name of each proposed purchaser or other transferee (“Proposed Transferee”); (iii) the number of Shares to be transferred
to each Proposed Transferee; and (iv) the bona fide cash price or other consideration for which the Holder proposes to transfer the Shares (the “Offered Price”), and the Holder shall offer the Shares at the Offered Price to the
Company or its assignee(s). 

 (b) Exercise of Right of First Refusal. At any time within thirty (30) days
after receipt of the Notice, the Company and/or its assignee(s) may, by giving written notice to the Holder, elect to purchase all, but not less than all, of the Shares proposed to be transferred to any one or more of the Proposed Transferees, at
the purchase price determined in accordance with subsection (c) below. 
 (c) Purchase Price. The purchase price
(“Purchase Price”) for the Shares purchased by the Company or its assignee(s) under this Section shall be the Offered Price. If the Offered Price includes consideration other than cash, the cash equivalent value of the non-cash
consideration shall be determined by the Board of Directors of the Company in good faith. 
 (d) Payment. Payment of the
Purchase Price shall be made, at the option of the Company or its assignee(s), in cash (by check), by cancellation of all or a portion of any outstanding indebtedness of the Holder to the Company (or, in the case of repurchase by an assignee, to the
assignee), or by any combination thereof within thirty (30) days after receipt of the Notice or in the manner and at the times set forth in the Notice. 
 (e) Holder’s Right to Transfer. If all of the Shares proposed in the Notice to be transferred to a given Proposed Transferee are not purchased by the Company and/or its assignee(s) as provided
in this Section, then the Holder may sell or otherwise transfer such Shares to that Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other transfer is consummated within 60 days after the date of the Notice,
that any such sale or other transfer is effected in accordance with any applicable securities laws and that the Proposed Transferee agrees in writing that the provisions of this Section shall continue to apply to the Shares in the hands of such
Proposed Transferee. If the Shares described in the Notice are not transferred to the Proposed Transferee within such period, a new Notice shall be given to the Company, and the Company and/or its assignees shall again be offered the Right of First
Refusal before any Shares held by the Holder may be sold or otherwise transferred. 
 (f) Exception for Certain Family
Transfers. Anything to the contrary contained in this Section notwithstanding, the transfer of any or all of the Shares during the Optionee’s lifetime or on the Optionee’s death by will or intestacy to the Optionee’s immediate
family or a trust for the benefit of the Optionee’s immediate family shall be exempt from the provisions of this Section. “Immediate Family” as used herein shall mean spouse, lineal descendant or antecedent, father, mother, brother or
sister. In such case, the transferee or other recipient shall receive and hold the Shares so transferred subject to the provisions of this Section, and there shall be no further transfer of such Shares except in accordance with the terms of this
Section. 
 (g) Termination of Right of First Refusal. The Right of First Refusal shall terminate as to any Shares upon
the earlier of (i) the first sale of Common Stock of the Company to the general public, or (ii) a Change in Control in which the successor corporation has equity securities that are publicly traded. 
  

 -2- 

 6. Tax Consultation. Optionee understands that Optionee may suffer adverse tax
consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents that Optionee has consulted with any tax consultants Optionee deems advisable in connection with the purchase or disposition of the Shares and
that Optionee is not relying on the Company for any tax advice. 
 7. Restrictive Legends and Stop-Transfer Orders.

 (a) Legends. Optionee understands and agrees that the Company shall cause the legends set forth below or legends
substantially equivalent thereto, to be placed upon any certificate(s) evidencing ownership of the Shares together with any other legends that may be required by the Company or by state or federal securities laws: 
 THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”).
THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT UNDER THE ACT COVERING THE SECURITIES OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

 THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS ON TRANSFER AND A RIGHT OF FIRST REFUSAL HELD
BY THE ISSUER OR ITS ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE BETWEEN THE ISSUER AND THE ORIGINAL HOLDER OF THESE SHARES, A COPY OF WHICH MAY BE OBTAINED AT THE PRINCIPAL OFFICE OF THE ISSUER. SUCH TRANSFER RESTRICTIONS AND RIGHT OF FIRST
REFUSAL ARE BINDING ON TRANSFEREES OF THESE SHARES. 
 THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO RESTRICTIONS ON
TRANSFER FOR A PERIOD NOT TO EXCEED 180 DAYS FOLLOWING THE EFFECTIVE DATE OF THE UNDERWRITTEN PUBLIC OFFERING OF THE COMPANY’S SECURITIES AND MAY NOT BE SOLD OR OTHERWISE DISPOSED OF BY THE HOLDER WITHOUT THE CONSENT OF THE COMPANY OR THE
MANAGING UNDERWRITER. 
 (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with the
restrictions referred to herein, the Company may issue appropriate “stop transfer” instructions to its transfer agent, if any, and that, if the Company transfers its own securities, it may make appropriate notations to the same effect
in its own records. 
 (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its books any
Shares that have been sold or otherwise transferred in violation of any of the provisions of this Exercise Notice or (ii) to treat as owner of such Shares or to accord the right to vote or pay dividends to any purchaser or other transferee to
whom such Shares shall have been so transferred. 
  

 -3- 

 8. Successors and Assigns. The Company may assign any of its rights under this
Exercise Notice to single or multiple assignees, and this Exercise Notice shall inure to the benefit of the successors and assigns of the Company. Subject to the restrictions on transfer herein set forth, this Exercise Notice shall be binding upon
Optionee and his or her heirs, executors, administrators, successors and assigns. 
 9. Interpretation. Any dispute
regarding the interpretation of this Exercise Notice shall be submitted by Optionee or by the Company forthwith to the Administrator, which shall review such dispute at its next regular meeting. The resolution of such a dispute by the Administrator
shall be final and binding on all parties. 
 10. Governing Law; Severability. This Exercise Notice is governed by the
internal substantive laws, but not the choice of law rules, of California. In the event that any provision hereof becomes or is declared by a court of competent jurisdiction to be illegal, unenforceable or void, this Exercise Notice will continue in
full force and effect. 
 11. Entire Agreement. The Plan and Option Agreement are incorporated herein by reference. This
Exercise Notice, the Plan, the Option Agreement and the Investment Representation Statement constitute the entire agreement of the parties with respect to the subject matter hereof and supersede in their entirety all prior undertakings and
agreements of the Company and Optionee with respect to the subject matter hereof, and may not be modified adversely to the Optionee’s interest except by means of a writing signed by the Company and Optionee. 
  

			
	 Submitted by:
	  	Accepted by:
	OPTIONEE	  	CODEXIS, INC.
		
	  
	  	  

	Signature	  	By
		
	  
	  	  

	Print Name	  	Title
		
	Address:	  	Address:
	  
	  	  

	  
	  	  

	  
	  	
		
		  	  

		  	Date Received

  

 -4- 

 EXHIBIT B 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	OPTIONEE:	  	
		
	COMPANY:	  	CODEXIS, INC.
		
	SECURITY:	  	COMMON STOCK
		
	AMOUNT:	  	
		
	DATE:	  	

 In connection with the purchase of the above-listed Securities, the undersigned
Optionee represents to the Company the following: 
 (a) Optionee is aware of the Company’s business affairs and financial
condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s own account only and not with a
view to, or for resale in connection with, any “distribution” thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”). 
 (b) Optionee acknowledges and understands that the Securities constitute “restricted securities” under the Securities Act and have
not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Optionee’s investment intent as expressed herein. In this connection,
Optionee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Optionee’s representation was predicated solely upon a present intention to hold these Securities for
the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the Securities, or for a period of one year or any other fixed period in the future. Optionee further
understands that the Securities must be held indefinitely unless they are subsequently registered under the Securities Act or an exemption from such registration is available. Optionee further acknowledges and understands that the Company is under
no obligation to register the Securities. Optionee understands that the certificate evidencing the Securities will be imprinted with any legend required under applicable state securities laws. 
 (c) Optionee is familiar with the provisions of Rule 701 and Rule 144, each promulgated under the Securities Act, which, in
substance, permit limited public resale of “restricted securities” acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to the satisfaction of certain conditions. Rule 701 provides that if the
issuer qualifies under Rule 701 at the time of the grant of the Option to the Optionee, the exercise will be exempt from registration under the Securities Act. In the event the Company becomes subject to the reporting requirements of

 
Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days thereafter (or such longer period as any market stand-off agreement may require) the Securities exempt under
Rule 701 may be resold, subject to the satisfaction of certain of the conditions specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited “broker’s transaction” or in transactions
directly with a market maker (as said term is defined under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability of certain public information about the Company, (3) the amount of Securities
being sold during any three month period not exceeding the limitations specified in Rule 144(e), and (4) the timely filing of a Form 144, if applicable. 
 In the event that the Company does not qualify under Rule 701 at the time of grant of the Option, then the Securities may be resold in certain limited circumstances subject to the provisions of
Rule 144, which requires the resale to occur not less than one year after the later of the date the Securities were sold by the Company or the date the Securities were sold by an affiliate of the Company, within the meaning of
Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a non-affiliate who subsequently holds the Securities less than two years, the satisfaction of the conditions set forth in sections (1), (2), (3) and
(4) of the paragraph immediately above. 
 (d) Optionee further understands that in the event all of the applicable
requirements of Rule 701 or 144 are not satisfied, registration under the Securities Act, compliance with Regulation A, or some other registration exemption will be required; and that, notwithstanding the fact that Rules 144 and 701 are
not exclusive, the Staff of the Securities and Exchange Commission has expressed its opinion that persons proposing to sell private placement securities other than in a registered offering and otherwise than pursuant to Rules 144 or 701 will
have a substantial burden of proof in establishing that an exemption from registration is available for such offers or sales, and that such persons and their respective brokers who participate in such transactions do so at their own risk. Optionee
understands that no assurances can be given that any such other registration exemption will be available in such event. 
  

	
	Signature of Optionee:
	
	  

	
	Date:             ,         

  

 -2- 

 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 
 STOCK OPTION AGREEMENT

 Early Exercise Permitted 
 Codexis, Inc., a Delaware corporation (the “Company”), pursuant to its 2002 Stock Plan, as amended from time to time (the “Plan”), hereby grants to the Optionee listed below
(“Optionee”), an option to purchase the number of shares of the Company’s Common Stock set forth below (the “Option”), subject to the terms and conditions of the Plan and this Stock Option Agreement (this “Option
Agreement”). Unless otherwise defined herein, the terms defined in the Plan shall have the same defined meanings in this Option Agreement. 
  

	I.	NOTICE OF STOCK OPTION GRANT 

  

					
	Optionee:	 		  	  

			
	Date of Grant:	 		  	  

			
	Vesting Commencement Date:	 		  	  

			
	Exercise Price per Share:	 		  	  

			
	Total Number of Shares Granted:	 		  	  

			
	Total Exercise Price:	 		  	  

			
	Term/Expiration Date:	 		  	  

  

			
	Type of Option:	  	Nonstatutory Stock Option
		
	Exercise Schedule:	  	 ̈  Same as Vesting Schedule    x  Early
Exercise Permitted
		
	Vesting Schedule:	  	 This Option is exercisable immediately, in whole or in part, at such times as are established by the Administrator, conditioned upon
Optionee entering into a Restricted Stock Purchase Agreement with respect to any unvested Shares (as defined below). The Shares subject to this Option shall vest and/or be released from the Company’s Repurchase Option, as set forth in the
Restricted Stock Purchase Agreement attached hereto as Exhibit C-1, according to the following schedule:
  
 Twenty-five percent (25%) of the Shares subject to the Option (rounded down to the next whole number of shares) shall vest on the first anniversary of the Date of Grant and 1/48th of the Shares subject to the Option shall vest monthly thereafter so
that one hundred percent (100%) of the Shares subject to the Option are vested on the fourth anniversary of the Date of Grant.

			
	Termination Period:	  	This Option may be exercised, to the extent vested, for three (3) months after Optionee ceases to be a Service Provider, or such longer period as may be applicable upon the death
or disability of Optionee as provided herein (or, if not provided herein, then as provided in the Plan), but in no event later than the Term/Expiration Date as set forth above.

  

	II.	AGREEMENT 

 1.
Grant of Option. The Company hereby grants to Optionee an Option to purchase the number of shares of Common Stock (the “Shares”) set forth in the Notice of Grant, at the exercise price per share set forth in the Notice of Grant (the
“Exercise Price”). Notwithstanding anything to the contrary anywhere else in this Option Agreement, this grant of an Option is subject to the terms, definitions and provisions of the Plan, which is incorporated herein by reference.

 2. Exercise of Option. This Option is exercisable as follows: 
 (a) Right to Exercise. 
 (i) This Option shall be exercisable cumulatively according to the vesting schedule set out in the Notice of Grant. Alternatively, at the election of Optionee, this Option may be exercised in whole or in
part at such times as are established by the Administrator as to Shares which have not yet vested. For purposes of this Option Agreement, Shares subject to this Option shall vest based on Optionee’s continued status as a Service Provider.
Vested Shares shall not be subject to the Company’s Repurchase Option (as set forth in the Restricted Stock Purchase Agreement). 
 (ii) As a condition to exercising this Option for unvested Shares, Optionee shall execute the Restricted Stock Purchase Agreement. 
 (iii) This Option may not be exercised for a fraction of a Share. 
 (iv) In the
event of Optionee’s death, disability or other termination of Optionee’s status as a Service Provider, the exercisability of the Option shall be governed by Sections 7, 8 and 9 hereof. 
 (v) In no event may this Option be exercised after the Expiration Date of this Option as set forth in the Notice of Grant. 
 (b) Method of Exercise. This Option shall be exercisable by written notice to the Company (in the form attached as Exhibit A)
(the “Exercise Notice”). The Exercise Notice shall state the number of Shares for which the Option is being exercised, and such other representations and agreements with respect to such Shares of Common Stock as may be required by the
Company pursuant to the provisions of the Plan. The Exercise Notice shall be signed by Optionee and, together with an executed copy of the Restricted Stock Purchase Agreement, if applicable, shall be delivered in person or by certified mail to the
Secretary of the Company. The Exercise Notice and Restricted Stock Purchase Agreement shall be accompanied by payment of the Exercise Price, including payment of any applicable withholding tax. 
  

 2 

 No Shares shall be issued pursuant to the exercise of an Option unless such issuance and
such exercise comply with all relevant provisions of law and the requirements of any stock exchange upon which the Shares may then be listed. Assuming such compliance, for income tax purposes the Shares shall be considered transferred to Optionee on
the date on which the Option is exercised with respect to such Shares. 
 3. Optionee’s Representations. If the
Shares purchasable pursuant to the exercise of this Option have not been registered under the Securities Act of 1933, as amended (the “Securities Act”), at the time this Option is exercised, Optionee shall, if required by the Company,
concurrently with the exercise of all or any portion of this Option, deliver to the Company his or her Investment Representation Statement in the form attached hereto as Exhibit B. 
 4. Lock-Up Period. Optionee hereby agrees that if so requested by the Company or any representative of the underwriters (the
“Managing Underwriter”) in connection with any registration of the offering of any securities of the Company under the Securities Act, Optionee shall not sell or otherwise transfer any Shares or other securities of the Company during
the 180-day period (or such longer period as may be requested in writing by the Managing Underwriter and agreed to in writing by the Company) (the “Market Standoff Period”) following the effective date of a registration statement of the
Company filed under the Securities Act; provided, however, that such restriction shall apply only to the first registration statement of the Company to become effective under the Securities Act that includes securities to be sold on behalf of
the Company to the public in an underwritten public offering under the Securities Act. The Company may impose stop-transfer instructions with respect to securities subject to the foregoing restrictions until the end of such Market Standoff Period
and these restrictions shall be binding on any transferee of such Shares. Notwithstanding the foregoing, the 180-day period may be extended for up to such number of additional days as is deemed necessary by the Company or the Managing Underwriter to
continue coverage by research analysts in accordance with NASD Rule 2711 or any successor rule. 
 5. Method of Payment.
Payment of the Exercise Price shall be by any of the following, or a combination thereof, at the election of Optionee: 
 (a)
cash; 
 (b) check; 
 (c) with the consent of the Administrator, a full recourse promissory note bearing interest (at no less than such rate as is a market rate of interest and which then precludes the imputation of interest
under the Code), payable upon such terms as may be prescribed by the Administrator and structured to comply with Applicable Laws; 
 (d) with the consent of the Administrator, surrender of other Shares of Common Stock of the Company which (A) in the case of Shares acquired from the Company, have been owned by Optionee for more than six (6) months on the date of
surrender, and (B) have a Fair Market Value on the date of surrender equal to the Exercise Price of the Shares as to which the Option is being exercised; 
  

 3 

 (e) with the consent of the Administrator, surrendered Shares issuable upon the exercise of
the Option having an aggregate Fair Market Value on the date of exercise equal to the aggregate Exercise Price of the Option or exercised portion thereof; 
 (f) with the consent of the Administrator, property of any kind which constitutes good and valuable consideration; 
 (g) following the consummation of the initial public offering of the Company’s Common Stock pursuant to a registration statement on Form S-1 under the Securities Act, with the consent of the
Administrator, delivery of a notice that Optionee has placed a market sell order with a broker with respect to Shares then issuable upon exercise of the Option and that the broker has been directed to pay a sufficient portion of the net proceeds of
the sale to the Company in satisfaction of the aggregate Exercise Price; provided, that payment of such proceeds is then made to the Company upon settlement of such sale; or 
 (h) with the consent of the Administrator, any combination of the foregoing methods of payment. 
 6. Restrictions on Exercise. This Option may not be exercised until the Plan has been approved by the stockholders of the Company. If
the issuance of Shares upon such exercise or if the method of payment for such Shares would constitute a violation of any applicable federal or state securities or other law or regulation, then the Option may also not be exercised. The Company may
require Optionee to make any representation and warranty to the Company as may be required by any applicable law or regulation before allowing the Option to be exercised. 
 7. Termination of Relationship. If Optionee ceases to be a Service Provider (other than by reason of Optionee’s death or the total and permanent disability of Optionee within the meaning of
Internal Revenue Code Section 22(e)(3)), Optionee may exercise this Option during the Termination Period set out in the Notice of Grant, to the extent the Option was vested on the date on which Optionee ceases to be a Service Provider. To the
extent that the Option is not vested on the date on which Optionee ceases to be a Service Provider, or if Optionee does not exercise this Option within the time specified herein, the Option shall terminate. 
 8. Disability of Optionee. If Optionee ceases to be a Service Provider as a result of his or her total and permanent disability
within the meaning of Internal Revenue Code Section 22(e)(3), Optionee may exercise the Option to the extent the Option was vested at the date on which Optionee ceases to be a Service Provider, but only within twelve (12) months from such
date (and in no event later than the expiration date of the term of this Option as set forth in the Notice of Grant). To the extent that the Option is not vested at the date on which Optionee ceases to be a Service Provider, or if Optionee does not
exercise such Option within the time specified herein, the Option shall terminate. 
 9. Death of Optionee. If Optionee
ceases to be a Service Provider as a result of the death of Optionee, the vested portion of the Option may be exercised at any time within twelve (12) months following the date of death (and in no event later than the expiration date of

  

 4 

 
the term of this Option as set forth in the Notice of Grant) by Optionee’s estate or by a person who acquires the right to exercise the Option by bequest or inheritance. To the extent that
the Option is not vested on the date of death, or if the Option is not exercised within the time specified herein, the Option shall terminate. 
 10. Non-Transferability of Option. This Option may not be transferred in any manner except by will or by the laws of descent or distribution. It may be exercised during the lifetime of Optionee
only by Optionee. The terms of this Option shall be binding upon the executors, administrators, heirs, successors and assigns of Optionee. 
 11. Term of Option. This Option may be exercised only within the term set out in the Notice of Grant. 
 12. Restrictions on Shares. Optionee hereby agrees that Shares purchased upon the exercise of the Option shall be subject to such terms and conditions as the Administrator shall determine in its
sole discretion, including, without limitation, restrictions on the transferability of Shares, the right of the Company to repurchase Shares, and a right of first refusal in favor of the Company with respect to permitted transfers of Shares. Such
terms and conditions may, in the Administrator’s sole discretion, be contained in the Exercise Notice with respect to the Option or in such other agreement as the Administrator shall determine and which Optionee hereby agrees to enter into at
the request of the Company. 
 (Signature Page Follows) 
  

 5 

 This Agreement may be executed in two or more counterparts, each of which shall be deemed an
original and all of which shall constitute one document. 
  

			
	CODEXIS, INC.
		
	 By:
	 	  

	 Name:
	 	  

	 Title:
	 	  

 OPTIONEE ACKNOWLEDGES AND AGREES THAT THE VESTING OF SHARES PURSUANT TO THE
OPTION HEREOF IS EARNED ONLY BY CONTINUING SERVICE AS A SERVICE PROVIDER (INCLUDING AS AN EMPLOYEE, DIRECTOR OR CONSULTANT) AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF BEGINNING SERVICE, BEING GRANTED THIS OPTION OR ACQUIRING SHARES
HEREUNDER). OPTIONEE FURTHER ACKNOWLEDGES AND AGREES THAT NOTHING IN THIS AGREEMENT, NOR IN THE COMPANY’S 2002 STOCK PLAN, AS AMENDED FROM TIME TO TIME, WHICH IS INCORPORATED HEREIN BY REFERENCE, SHALL CONFER UPON OPTIONEE ANY RIGHT WITH
RESPECT TO CONTINUATION OF SERVICE AS A SERVICE PROVIDER TO THE COMPANY, NOR SHALL IT INTERFERE IN ANY WAY WITH OPTIONEE’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE SERVICE AS A SERVICE PROVIDER AT ANY TIME, WITH OR WITHOUT CAUSE AND WITH
OR WITHOUT PRIOR NOTICE. 
 Optionee acknowledges receipt of a copy of the Plan and represents that he or she is familiar with
the terms and provisions thereof. Optionee hereby accepts this Option subject to all of the terms and provisions hereof. Optionee has reviewed the Plan and this Option in their entirety, has had an opportunity to obtain the advice of counsel prior
to executing this Option and fully understands all provisions of the Option. Optionee hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Administrator upon any questions arising under the Plan or this
Option. Optionee further agrees to notify the Company upon any change in the residence address indicated below. 
  

			
	Dated:                     	 	  

		 	OPTIONEE
		
		 	Residence Address:

 [Signature Page to Stock Option Agreement] 

 EXHIBIT A 
 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 

 EXERCISE NOTICE 
 Codexis, Inc. 
 Attention: Stock Administration 
 1. Exercise of Option. Effective as of today,             ,         , the
undersigned (“Optionee”) hereby elects to exercise Optionee’s option to purchase              shares of the Common Stock (the “Shares”) of Codexis, Inc., a
Delaware corporation (the “Company”), under and pursuant to the Codexis, Inc. 2002 Stock Plan, as amended from time to time (the “Plan”) and the Stock Option Agreement dated
                     (the “Option Agreement”). Capitalized terms used herein without definition shall have the meanings given in the
Option Agreement. 
  

							
	Date of Grant:	 		  	  
	  	
				
	Number of Shares as to which Option is Exercised:	 		  	  
	  	
				
	Exercise Price per Share:	 		  	$                        	  	
				
	Total Exercise Price:	 		  	$                        	  	
				
	Certificate to be issued in name of:	 		  	  
	  	
				
	Cash Payment delivered herewith:	 		  	$                        	  	
				
	Other form of consideration delivered herewith:	 		  	 Form of Consideration:
 $                        
	  	

 Type of
Option:            Nonstatutory Stock Option 
 2.
Representations of Optionee. Optionee acknowledges that Optionee has received, read and understood the Plan and the Option Agreement. Optionee agrees to abide by and be bound by their terms and conditions. 
 3. Rights as Stockholder. Until the stock certificate evidencing Shares purchased pursuant to the exercise of the Option is issued
(as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company), no right to vote or receive dividends or any other rights as a stockholder shall exist with respect to Shares subject to the
Option, notwithstanding the exercise of the Option. The Company shall issue (or cause to be issued) such stock certificate promptly after the Option is exercised. No adjustment will be made for a dividend or other right for which the record date is
prior to the date the stock certificate is issued, except as provided in Section 13 of the Plan. 

 Optionee shall enjoy rights as a stockholder until such time as Optionee disposes of the
Shares or the Company and/or its assignee(s) exercises the Right of First Refusal (as defined below) hereunder. Upon such exercise, Optionee shall have no further rights as a holder of the Shares so purchased except the right to receive payment for
the Shares so purchased in accordance with the provisions of this Agreement, and Optionee shall forthwith cause the certificate(s) evidencing the Shares so purchased to be surrendered to the Company for transfer or cancellation. 
 4. Optionee’s Rights to Transfer Shares 
 (a) Company’s Right of First Refusal. Before any Shares held by Optionee or any permitted transferee (each, a “Holder”) may be sold, pledged, assigned, hypothecated, transferred, or
otherwise disposed of (each, a “Transfer”), the Company or its assignee(s) shall have a right of first refusal to purchase the Shares proposed to be Transferred on the terms and conditions set forth in this Section 4 (the “Right
of First Refusal”). 
 (i) Notice of Proposed Transfer. In the event any Holder desires to Transfer any Shares, the
Holder shall deliver to the Company a written notice (the “Notice”) stating: (w) the Holder’s bona fide intention to sell or otherwise Transfer such Shares; (x) the name of each proposed purchaser or other transferee
(“Proposed Transferee”); (y) the number of Shares to be Transferred to each Proposed Transferee; and (z) the bona fide cash price or other consideration for which the Holder proposes to Transfer the Shares (the “Offered
Price”), and the Holder shall offer such Shares at the Offered Price to the Company or its assignee(s). 
 (ii)
Exercise of Right of First Refusal. Within thirty (30) days after receipt of the Notice, the Company and/or its assignee(s) may elect in writing to purchase all, but not less than all, of the Shares proposed to be Transferred to any one
or more of the Proposed Transferees. The purchase price shall be determined in accordance with Section 4(iii) hereof. 
 (iii) Purchase Price. The purchase price (“Purchase Price”) for the Shares repurchased under this Section 4 shall be the Offered Price. If the Offered Price includes consideration other than cash, the cash equivalent
value of the non-cash consideration shall be determined by the Board in good faith. 
 (iv) Payment. Payment of the
Purchase Price shall be made, at the option of the Company or its assignee(s), in cash (by check), by cancellation of all or a portion of any outstanding indebtedness of the Holder to the Company (or, in the case of purchase by an assignee, of the
assignee to the Company), or by any combination thereof within thirty (30) days after receipt of the Notice or in the manner and at the times mutually agreed to by the Company and the Holder. 
 (v) Holder’s Right to Transfer. If all of the Shares proposed in the Notice to be Transferred are not purchased by the Company
and/or its assignee(s) as provided in this Section 4, then the Holder may sell or otherwise Transfer such Shares to that Proposed Transferee at the Offered Price or at a higher price, provided that such sale or other Transfer is consummated
within one hundred twenty (120) days after the date of the Notice and provided further that any such sale or other Transfer is effected in accordance with any applicable

 
securities laws and the Proposed Transferee agrees in writing that the provisions of this Section 4 and the Restricted Stock Purchase Agreement, if applicable, shall continue to apply to the
Shares in the hands of such Proposed Transferee. If the Shares described in the Notice are not Transferred to the Proposed Transferee within such 120-day period, a new Notice shall be given to the Company, and the Company and/or its assignees shall
again be offered the Right of First Refusal as provided herein before any Shares held by the Holder may be sold or otherwise Transferred. 
 (b) Exception for Certain Family Transfers. Anything to the contrary contained in this Section 4 notwithstanding, the Transfer of any or all of the Shares during Optionee’s lifetime or
upon Optionee’s death by will or intestacy to Optionee’s Immediate Family or a trust for the benefit of Optionee’s Immediate Family shall be exempt from the Right of First Refusal. As used herein, “Immediate Family” shall
mean spouse, lineal descendant or antecedent, father, mother, brother or sister or stepchild (whether or not adopted). In such case, the transferee or other recipient shall receive and hold the Shares so Transferred subject to the provisions of this
Section 4 (including the Right of First Refusal) and the Restricted Stock Purchase Agreement, if applicable, and there shall be no further Transfer of such Shares except in accordance with the terms of this Section 4. 
 (c) Termination of Right of First Refusal. The Right of First Refusal shall terminate as to all Shares upon a sale of Common Stock of
the Company to the general public pursuant to a registration statement filed with and declared effective by the Securities and Exchange Commission under the Securities Act of 1933, as amended (a “Public Offering”). 
 5. Transfer Restrictions. Any transfer or sale of the Shares is subject to restrictions on transfer imposed by any applicable state
and federal securities laws. Any Transfer or attempted Transfer of any of the Shares not in accordance with the terms of this Agreement, including the Right of First Refusal provided in this Agreement, shall be void and the Company may enforce the
terms of this Agreement by stop transfer instructions or similar actions by the Company and its agents or designees. 
 6.
Tax Consultation. Optionee understands that Optionee may suffer adverse tax consequences as a result of Optionee’s purchase or disposition of the Shares. Optionee represents that Optionee has consulted with any tax consultants Optionee
deems advisable in connection with the purchase or disposition of the Shares and that Optionee is not relying on the Company for any tax advice. 
 7. Restrictive Legends and Stop-Transfer Orders. 
 (a) Legends.
Optionee understands and agrees that the Company shall cause the legends set forth below or legends substantially equivalent thereto, to be placed upon any certificate(s) evidencing ownership of the Shares together with any other legends that may be
required by state or federal securities laws: 
 THE SECURITIES REPRESENTED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED (THE “ACT”), AND MAY NOT BE

 
OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER THE ACT OR, IN THE OPINION OF COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE
SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS IN COMPLIANCE THEREWITH. 
 THE SHARES REPRESENTED BY THIS
CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS ON TRANSFER AND RIGHT OF FIRST REFUSAL OPTIONS HELD BY THE ISSUER OR ITS ASSIGNEE(S) AS SET FORTH IN THE EXERCISE NOTICE BETWEEN THE ISSUER AND THE ORIGINAL HOLDER OF THESE SHARES, A COPY OF WHICH MAY
BE OBTAINED AT THE PRINCIPAL OFFICE OF THE ISSUER. SUCH TRANSFER RESTRICTIONS AND RIGHT OF FIRST REFUSAL ARE BINDING ON TRANSFEREES OF THESE SHARES. 
 (b) Stop-Transfer Notices. Optionee agrees that, in order to ensure compliance with the restrictions referred to herein, the Company may issue appropriate “stop transfer” instructions to
its transfer agent, if any, and that, if the Company transfers its own securities, it may make appropriate notations to the same effect in its own records. 
 (c) Refusal to Transfer. The Company shall not be required (i) to transfer on its books any Shares that have been sold or otherwise transferred in violation of any of the provisions of this
Agreement or (ii) to treat as owner of such Shares or to accord the right to vote or pay dividends to any purchaser or other transferee to whom such Shares shall have been so transferred. 
 8. Successors and Assigns. The Company may assign any of its rights under this Agreement to single or multiple assignees, and this
Agreement shall inure to the benefit of the successors and assigns of the Company. Subject to the restrictions on transfer herein set forth, this Agreement shall be binding upon Optionee and his or her heirs, executors, administrators, successors
and assigns. 
 9. Interpretation. Any dispute regarding the interpretation of this Agreement shall be submitted by
Optionee or by the Company forthwith to the Company’s Board of Directors or committee thereof that is responsible for the administration of the Plan (the “Administrator”), which shall review such dispute at its next regular meeting.
The resolution of such a dispute by the Administrator shall be final and binding on the Company and on Optionee. 
 10.
Governing Law; Severability. The laws of the State of California shall govern the interpretation, validity, administration, enforcement and performance of the terms of this Agreement regardless of the law that might be applied under
principles of conflicts of laws. Should any provision of this Agreement be determined by a court of law to be illegal or unenforceable, the other provisions shall nevertheless remain effective and shall remain enforceable. 

 11. Notices. Any notice required or permitted hereunder shall be given in writing and
shall be deemed effectively given upon personal delivery or upon deposit in the United States mail by certified mail, with postage and fees prepaid, addressed to the other party at its address as shown below beneath its signature, or to such other
address as such party may designate in writing from time to time to the other party. 
 12. Further Instruments. Optionee
hereby agrees to execute such further instruments and to take such further action as may be reasonably necessary to carry out the purposes and intent of this Agreement, including, without limitation, the Investment Representation Statement in the
form attached to the Option Agreement as Exhibit B. 
 13. Delivery of Payment. Optionee herewith delivers to the
Company the full Exercise Price for the Shares, as well as any applicable withholding tax. 
 14. Entire Agreement. The
Plan and Option Agreement are incorporated herein by reference. This Agreement, the Plan, the Option Agreement, the Investment Representation Statement and the Restricted Stock Purchase Agreement, if applicable, constitute the entire agreement of
the parties and supersede in their entirety all prior undertakings and agreements of the Company and Optionee with respect to the subject matter hereof. 
 (Signature Page Follows) 

					
	Accepted by:	  	Submitted by:
		
	CODEXIS, INC.	  	OPTIONEE
			
	By:	 	  
	  	  

		 		  	Optionee
	Name:	 	  
	  	
			
	Title:	 	  
	  	Address:

 [Signature Page to Exercise Notice] 

 EXHIBIT B 
 INVESTMENT REPRESENTATION STATEMENT 
  

					
	OPTIONEE	 	:	    	
			
	COMPANY	 	:	    	Codexis, Inc.
			
	SECURITY	 	:	    	Common Stock
			
	AMOUNT	 	:	    	
			
	DATE	 	:	    	

 In connection with the purchase of the above-listed shares of Common Stock (the
“Securities”) of Codexis, Inc., a Delaware corporation (the “Company”), the undersigned (“Optionee”) represents to the Company the following: 
 (a) Optionee is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the
Company to reach an informed and knowledgeable decision to acquire the Securities. Optionee is acquiring these Securities for investment for Optionee’s own account only and not with a view to, or for resale in connection with, any
“distribution” thereof within the meaning of the Securities Act of 1933, as amended (the “Securities Act”). 
 (b) Optionee acknowledges and understands that the Securities constitute “restricted securities” under the Securities Act and have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which
exemption depends upon, among other things, the bona fide nature of Optionee’s investment intent as expressed herein. Optionee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may
be unavailable if Optionee’s representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in
the market price of the Securities, or for a period of one year or any other fixed period in the future. Optionee further understands that the Securities must be held indefinitely unless they are subsequently registered under the Securities Act or
an exemption from such registration is available. Optionee further acknowledges and understands that the Company is under no obligation to register the Securities. Optionee understands that the certificate evidencing the Securities will be imprinted
with a legend which prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel satisfactory to the Company and any other legend required under applicable state securities laws.

 (c) Optionee is familiar with the provisions of Rule 701 and Rule 144, each promulgated under the Securities Act,
which, in substance, permit limited public resale of “restricted securities” acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to

 
the satisfaction of certain conditions. Rule 701 provides that if the issuer qualifies under Rule 701 at the time of the grant of the Option to Optionee, the exercise will be exempt
from registration under the Securities Act. In the event the Company becomes subject to the reporting requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), ninety (90) days
thereafter (or such longer period as any market stand-off agreement may require) the Securities exempt under Rule 701 may be resold, subject to the satisfaction of certain of the conditions specified by Rule 144, including: (1) the
resale being made through a broker in an unsolicited “broker’s transaction” or in transactions directly with a market maker (as said term is defined under the Exchange Act); and, in the case of an affiliate, (2) the
availability of certain public information about the Company, (3) the amount of Securities being sold during any three (3) month period not exceeding the limitations specified in Rule 144(e) and (4) the timely filing of a Form
144, if applicable. 
 In the event that the Company does not qualify under Rule 701 at the time of grant of the Option,
then the Securities may be resold in certain limited circumstances subject to the provisions of Rule 144, which requires the resale to occur not less than one year after the later of the date the Securities were sold by the Company or the
date the Securities were sold by an affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a non-affiliate who subsequently holds the Securities less than two
(2) years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of the paragraph immediately above. 
 (d) Optionee further understands that in the event all of the applicable requirements of Rule 701 or 144 are not satisfied, registration under the Securities Act, compliance with Regulation A, or
some other registration exemption will be required; and that, notwithstanding the fact that Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange Commission has expressed its opinion that persons proposing to sell private
placement securities other than in a registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden of proof in establishing that an exemption from registration is available for such offers or sales, and that such
persons and their respective brokers who participate in such transactions do so at their own risk. Optionee understands that no assurances can be given that any such other registration exemption will be available in such event. 
  

			
		 	Signature of Optionee:
		
		 	  

		 	Optionee
		
	Date:             ,         	 	

 EXHIBIT C-1 
 CODEXIS, INC. 
 2002 STOCK PLAN, AS AMENDED 

 RESTRICTED STOCK PURCHASE AGREEMENT 
 THIS RESTRICTED STOCK PURCHASE AGREEMENT (this “Agreement”) is made between
                                        
(the “Purchaser”) and Codexis, Inc. (the “Company”), as of             ,         . 
 RECITALS 
 (1) Unless otherwise defined herein, the terms defined in the Plan shall have the same defined meanings in this Agreement. Pursuant to the exercise of the Option granted to Purchaser under the Company’s 2002 Stock Plan, as amended, and
pursuant to the Stock Option Agreement (the “Option Agreement”) dated                     , by and between the Company and Purchaser
with respect to such grant, which Option Agreement is hereby incorporated by reference, Purchaser has elected to purchase              of those shares which have not become vested
under the vesting schedule set forth in the Option Agreement (“Unvested Shares”). The Unvested Shares and the shares subject to the Option Agreement which have become vested are sometimes collectively referred to herein as the
“Shares”. 
 (2) As required by the Option Agreement, as a condition to Purchaser’s election to exercise the
option, Purchaser must execute this Agreement, which sets forth the rights and obligations of the parties with respect to Shares acquired upon exercise of the Option. 
 1. Repurchase Option. 
 (a) If Purchaser ceases to be a Service Provider for
any reason, including for cause, death and disability, the Company or its assignee shall have the right and option to purchase from Purchaser, or Purchaser’s personal representative, as the case may be, all of Purchaser’s Unvested Shares
as of the date on which Purchaser ceases to be a Service Provider at the exercise price paid by Purchaser for such Shares in connection with the exercise of the Option (the “Repurchase Option”). 
 (b) The Company may exercise its Repurchase Option by delivering, personally or by registered mail, to Purchaser (or his or her transferee
or legal representative, as the case may be), within ninety (90) days of the date on which Purchaser ceases to be a Service Provider, a notice in writing indicating the Company’s intention to exercise the Repurchase Option and setting
forth a date for closing not later than thirty (30) days from the mailing of such notice. The closing shall take place at the Company’s office. At the closing, the holder of the certificates for the Unvested Shares being transferred shall
deliver the stock certificate or certificates evidencing the Unvested Shares, and the Company shall deliver the purchase price therefor. 

 (c) At its option, the Company may elect to make payment for the Unvested Shares to a bank
selected by the Company. The Company shall avail itself of this option by a notice in writing to Purchaser stating the name and address of the bank, date of closing, and waiving the closing at the Company’s office. 
 (d) If the Company does not elect to exercise the Repurchase Option conferred above by giving the requisite notice within ninety
(90) days following the date on which Purchaser ceases to be a Service Provider, the Repurchase Option shall terminate. 
 (e) One hundred percent (100%) of the Unvested Shares shall initially be subject to the Repurchase Option. The Unvested Shares shall be released from the Repurchase Option in accordance with the Vesting Schedule set forth in the Notice
of Grant until all Shares are released from the Repurchase Option. Fractional Shares shall be rounded to the nearest whole share. 
 2. Transferability of the Shares; Escrow. 
 (a) Purchaser hereby authorizes and directs the secretary of the
Company, or such other person designated by the Company from time to time, to transfer the Unvested Shares as to which the Repurchase Option has been exercised from Purchaser to the Company. 
 (b) To insure the availability for delivery of Purchaser’s Unvested Shares upon repurchase by the Company pursuant to the Repurchase
Option under Section 1, Purchaser hereby appoints the Secretary, or any other person designated by the Company from time to time as escrow agent, as its attorney-in-fact to sell, assign and transfer unto the Company, such Unvested Shares, if
any, repurchased by the Company pursuant to the Repurchase Option and shall, upon execution of this Agreement, deliver and deposit with the Secretary of the Company, or such other person designated by the Company from time to time, the share
certificate(s) representing the Unvested Shares, together with the stock assignment duly endorsed in blank, attached hereto as Exhibit C-2. The Unvested Shares and stock assignment shall be held by the Secretary in escrow, pursuant to the
Joint Escrow Instructions of the Company and Purchaser attached as Exhibit C-3 hereto, until the Company exercises its Repurchase Option as provided in Section 1, until such Unvested Shares are vested, or until such time as this
Agreement no longer is in effect. As a further condition to the Company’s obligations under this Agreement, the spouse of Purchaser, if any, shall execute and deliver to the Company the Consent of Spouse attached hereto as Exhibit C-4.
Upon vesting of the Unvested Shares, the escrow agent shall promptly deliver to Purchaser the certificate or certificates representing such Shares in the escrow agent’s possession belonging to Purchaser, and the escrow agent shall be discharged
of all further obligations hereunder; provided, however, that the escrow agent shall nevertheless retain such certificate or certificates as escrow agent if so required pursuant to other restrictions imposed pursuant to this Agreement. 

(c) The Company, or its designee, shall not be liable for any act it may do or omit to do with respect to holding the Shares in escrow
and while acting in good faith and in the exercise of its judgment. 

 (d) Transfer or sale of the Shares is subject to restrictions on transfer imposed by any
applicable state and federal securities laws. Any transferee shall hold such Shares subject to all of the provisions hereof and the Exercise Notice executed by Purchaser with respect to any Unvested Shares purchased by Purchaser and shall
acknowledge the same by signing a copy of this Agreement. Any transfer or attempted transfer of any of the Shares not in accordance with the terms of this Agreement shall be void and the Company may enforce the terms of this Agreement by stop
transfer instructions or similar actions by the Company and its agents or designees. 
 3. Ownership, Voting Rights,
Duties. This Agreement shall not affect in any way the ownership, voting rights or other rights or duties of Purchaser, except as specifically provided herein. 
 4. Adjustment for Stock Split. All references to the number of Shares and the purchase price of the Shares in this Agreement shall be appropriately adjusted to reflect any stock split, stock
dividend or other change in the Shares which may be made by the Company after the date of this Agreement. 
 5. Notices.
Notices required hereunder shall be given in person or by registered mail to the address of Purchaser shown on the records of the Company, and to the Company at its principal executive office. 
 6. Survival of Terms. This Agreement shall apply to and bind Purchaser and the Company and their respective permitted assignees and
transferees, heirs, legatees, executors, administrators and legal successors. 
 7. Section 83(b) Election for Unvested
Shares Purchased Pursuant to a Nonstatutory Stock Option. Purchaser hereby acknowledges that he or she has been informed that, with respect to the exercise of a Nonstatutory Stock Option for Unvested Shares, that unless an election, as set forth
on Exhibit C-5, is filed by Purchaser with the Internal Revenue Service and, if necessary, the proper state taxing authorities, within thirty (30) days of the purchase of the Shares, electing pursuant to Section 83(b) of the
Internal Revenue Code (and similar state tax provisions if applicable) to be taxed currently on any difference between the purchase price of the Shares and their Fair Market Value on the date of purchase, there will be a recognition of taxable
income to the Purchaser, measured by the excess, if any, of the fair market value of the Shares, at the time the Company’s Repurchase Option lapses over the purchase price for the Shares. Purchaser represents that Purchaser has consulted any
tax consultant(s) Purchaser deems advisable in connection with the purchase of the Shares or the filing of the Election under Section 83(b) and similar tax provisions. 
 PURCHASER ACKNOWLEDGES THAT IT IS PURCHASER’S SOLE RESPONSIBILITY AND NOT THE COMPANY’S TO FILE TIMELY THE ELECTION UNDER
SECTION 83(b), EVEN IF PURCHASER REQUESTS THE COMPANY OR ITS REPRESENTATIVE TO MAKE THIS FILING ON PURCHASER’S BEHALF. 
 8. Representations. Purchaser has reviewed with his or her own tax advisors the federal, state, local and foreign tax consequences of this investment and the transactions contemplated by

 
this Agreement. Purchaser is relying solely on such advisors and not on any statements or representations of the Company or any of its agents. Purchaser understands that Purchaser (and not the
Company) shall be responsible for his or her own tax liability that may arise as a result of this investment or the transactions contemplated by this Agreement. 
 9. Governing Law; Severability. The laws of the State of California shall govern the interpretation, validity, administration, enforcement and performance of the terms of this Agreement regardless
of the law that might be applied under principles of conflicts of laws. Should any provision of this Agreement be determined by a court of law to be illegal or unenforceable, the other provisions shall nevertheless remain effective and shall remain
enforceable. 
 (Signature Page Follows) 

 Purchaser represents that he or she has read this Agreement and is familiar with its terms
and provisions. Purchaser hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Board upon any questions arising under this Agreement. 
 IN WITNESS WHEREOF, this Agreement is deemed made as of the date first set forth above. 
  

			
	 CODEXIS, INC.

		
	 By:
	 	  

	 Name:
	 	  

	 Title:
	 	  

	
	 PURCHASER

		
	 By:
	 	  

	 Name:
	 	  

	 Address:
	 	

 [Signature Page to Restricted Stock Purchase Agreement] 

 EXHIBIT C-2 
 ASSIGNMENT SEPARATE FROM CERTIFICATE 
 FOR VALUE
RECEIVED I,                             , hereby sell, assign and transfer unto
                                        
                                    
(            ) shares of the Common Stock of Codexis, Inc. registered in my name on the books of said corporation represented by Certificate
No.          herewith and do hereby irrevocably constitute and appoint
                     to transfer the said stock on the books of the within named corporation with full power of substitution in the
premises. 
 This Assignment Separate from Certificate may be used only in accordance with the Restricted Stock Purchase
Agreement between Codexis, Inc. and the undersigned dated             ,         . 
 Dated:             ,          

 

			
	Signature:	 	  

 INSTRUCTIONS: Please do not fill in any blanks other than the signature line. The
purpose of this assignment is to enable the Company to exercise the Repurchase Option, as set forth in the Restricted Stock Purchase Agreement, without requiring additional signatures on the part of Purchaser. 

 EXHIBIT C-3 
 JOINT ESCROW INSTRUCTIONS 
             ,          
 Secretary 
 Codexis, Inc. 
 As Escrow Agent for both Codexis, Inc. (the “Company”) and the undersigned purchaser of stock of the Company (the “Purchaser”), you are hereby authorized and directed to hold the
documents delivered to you pursuant to the terms of that certain Restricted Stock Purchase Agreement (“Agreement”) between the Company and the undersigned, in accordance with the following instructions: 
 1. In the event the Company and/or any assignee of the Company (referred to collectively for convenience herein as the “Company”)
exercises the Company’s Repurchase Option set forth in the Agreement, the Company shall give to Purchaser and you a written notice specifying the number of shares of stock to be purchased, the purchase price, and the time for a closing
hereunder at the principal office of the Company. Purchaser and the Company hereby irrevocably authorize and direct you to close the transaction contemplated by such notice in accordance with the terms of said notice. 
 2. At the closing, you are directed (a) to date the stock assignments necessary for the transfer in question, (b) to fill in the
number of shares being transferred, and (c) to deliver the same, together with the certificate evidencing the shares of stock to be transferred, to the Company or its assignee, against the simultaneous delivery to you of the purchase price (by
cash, a check, or a combination thereof) for the number of shares of stock being purchased pursuant to the exercise of the Company’s Repurchase Option. 
 3. Purchaser irrevocably authorizes the Company to deposit with you any certificates evidencing shares of stock to be held by you hereunder and any additions and substitutions to said shares as defined in
the Agreement. Purchaser does hereby irrevocably constitute and appoint you as Purchaser’s attorney-in-fact and agent for the term of this escrow to execute, with respect to such securities, all documents necessary or appropriate to make such
securities negotiable and to complete any transaction herein contemplated, including but not limited to the filing with any applicable state blue sky authority of any required applications for consent to, or notice of transfer of, the securities.
Subject to the provisions of this paragraph 3, Purchaser shall exercise all rights and privileges of a stockholder of the Company while the stock is held by you. 
 4. Upon written request of Purchaser, but no more than once per calendar year, unless the Company’s Repurchase Option has been exercised, you will deliver to Purchaser a certificate or certificates
representing the number of shares of stock as are not then subject to the Company’s Repurchase Option. Within one hundred twenty (120) days after Purchaser ceases to be a Service

 
Provider, you will deliver to Purchaser a certificate or certificates representing the aggregate number of shares held or issued pursuant to the Agreement and not purchased by the Company or its
assignees pursuant to exercise of the Company’s Repurchase Option. 
 5. If at the time of termination of this escrow you
should have in your possession any documents, securities, or other property belonging to Purchaser, you shall deliver all of the same to Purchaser and shall be discharged of all further obligations hereunder. 
 6. Your duties hereunder may be altered, amended, modified or revoked only by a writing signed by all of the parties hereto. 
 7. You shall be obligated only for the performance of such duties as are specifically set forth herein and may rely and shall be protected
in relying or refraining from acting on any instrument reasonably believed by you to be genuine and to have been signed or presented by the proper party or parties. You shall not be personally liable for any act you may do or omit to do hereunder as
Escrow Agent or as attorney-in-fact for Purchaser while acting in good faith, and any act done or omitted by you pursuant to the advice of your own attorneys shall be conclusive evidence of such good faith. 
 8. You are hereby expressly authorized to disregard any and all warnings given by any of the parties hereto or by any other person or
corporation, excepting only orders or process of courts of law and are hereby expressly authorized to comply with and obey orders, judgments or decrees of any court. In case you obey or comply with any such order, judgment or decree, you shall not
be liable to any of the parties hereto or to any other person, firm or corporation by reason of such compliance, notwithstanding any such order, judgment or decree being subsequently reversed, modified, annulled, set aside, vacated or found to have
been entered without jurisdiction. 
 9. You shall not be liable in any respect on account of the identity, authorities or
rights of the parties executing or delivering or purporting to execute or deliver the Agreement or any documents or papers deposited or called for hereunder. 
 10. You shall not be liable for the expiration of any rights under any applicable state, federal or local statute of limitations or similar statute or regulation with respect to these Joint Escrow
Instructions or any documents deposited with you. 
 11. You shall be entitled to employ such legal counsel and other experts as
you may deem necessary properly to advise you in connection with your obligations hereunder, may rely upon the advice of such counsel, and may pay such counsel reasonable compensation therefor. 
 12. Your responsibilities as Escrow Agent hereunder shall terminate if you shall cease to be an officer or agent of the Company or if you
shall resign by written notice to each party. In the event of any such termination, the Company shall appoint a successor Escrow Agent. 
  

 2 

 13. If you reasonably require other or further instruments in connection with these Joint
Escrow Instructions or obligations in respect hereto, the necessary parties hereto shall join in furnishing such instruments. 
 14. It is understood and agreed that should any dispute arise with respect to the delivery and/or ownership or right of possession of the securities held by you hereunder, you are authorized and directed to retain in your possession without
liability to anyone all or any part of said securities until such disputes shall have been settled either by mutual written agreement of the parties concerned or by a final order, decree or judgment of a court of competent jurisdiction after the
time for appeal has expired and no appeal has been perfected, but you shall be under no duty whatsoever to institute or defend any such proceedings. 
 15. Any notice required or permitted hereunder shall be given in writing and shall be deemed effectively given upon personal delivery or upon deposit in the United States Post Office, by registered or
certified mail with postage and fees prepaid, addressed to each of the other parties thereunto entitled at such addresses as a party may designate by written notice to each of the other parties hereto. 
 16. By signing these Joint Escrow Instructions, you become a party hereto only for the purpose of said Joint Escrow Instructions; you do not
become a party to the Agreement. 
 17. This instrument shall be binding upon and inure to the benefit of the parties hereto,
and their respective successors and permitted assigns. 
 18. These Joint Escrow Instructions shall be governed by, and
construed and enforced in accordance with, the laws of the State of California, excluding that body of law pertaining to conflicts of law. 
 (Signature Page Follows) 
  

 3 

 IN WITNESS WHEREOF, these Joint Escrow Instructions shall be effective as of the date first
set forth above. 
  

			
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	
	PURCHASER:
		
	By:	 	  

	Name:	 	  

	Address:	 	
	
	ESCROW AGENT:
		
	By:	 	  

	Name:	 	  

	Title:	 	  

 EXHIBIT C-4 
 CONSENT OF SPOUSE 
 I,
                                        ,
spouse of
                                        ,
have read and approve the Restricted Stock Purchase Agreement dated             ,         , between my spouse and Codexis, Inc. In
consideration of granting the right to my spouse to purchase shares of Codexis, Inc. set forth in the Restricted Stock Purchase Agreement, I hereby appoint my spouse as my attorney-in-fact in respect to the exercise of any rights under the Agreement
and agree to be bound by the provisions of the Restricted Stock Purchase Agreement insofar as I may have any rights in said Restricted Stock Purchase Agreement or any shares issued pursuant thereto under the community property laws or similar laws
relating to marital property in effect in the state of our residence as of the date of the signing of the foregoing Restricted Stock Purchase Agreement. 
 Dated:             ,          
  

	
	  

	Signature of Spouse

 EXHIBIT C-5 
 INFORMATION CONCERNING THE FILING OF SECTION 83(b) ELECTION 
 This information is supplied to you in connection with your recent purchase of shares of Common Stock of Codexis, Inc. (the “Company”), at a purchase price equal to the current fair market value of the stock and subject to
an Agreement for purchase of shares that gives the Company the right to repurchase the shares under the terms stated in the Agreement in the event that you terminate your continuous status as an employee, consultant or director of the Company prior
to the full vesting. 
 Section 83 of the Internal Revenue Code taxes as ordinary income the difference between the amount
paid for the stock and its fair market value as of the date any restrictions on that stock lapse. In this context, “restriction” means the right of the Company to buy back the stock at less than its fair market value, in connection with
the termination of your continuous status as an employee, consultant or director of the Company, which right expires as your stock vests pursuant to the Agreement. Thus, if the shares are worth $12.50 a share at the time the first 25% of the shares
becomes fully vested (no longer subject to repurchase) and if you purchased such shares for $0.10 per share, then you would be required to report ordinary income in the amount of $12.40 for each such share in the first year that such shares are
first vested (no longer subject to repurchase). Upon the vesting of the final portion of the shares and if the fair market value of the shares at that time is $15.00 per share, then you would be required to report ordinary income in the amount of
$14.90 per share for the tax year in which such final portion of the shares is no longer subject to repurchase. 
 To avoid the
assessment of ordinary income tax at the time the restrictions end, there is an election that can be filed under Section 83(b). This is an election to include in income in the year the stock is purchased the difference between what is paid for
the stock and its then fair market value. Even though in your case the fair market value of the stock may equal the amount paid and therefore there may be no income at this time, the Internal Revenue Service nonetheless requires that the election be
filed in order to avoid adverse tax consequences in the future. 
 You must file one executed copy of the 83(b) election
form with the Internal Revenue Service within 30 days of the purchase of the shares. The steps outlined below should be followed to ensure the election is filed correctly and timely: 
  

	1)	Complete 83(b) election form; 

  

	2)	Prepare cover letter to the IRS (sample letter attached); 

  

	3)	Send cover letter with originally executed 83(b) election form and one (1) additional copy via certified mail or Federal Express to the IRS, within 30 days of
the date of purchase, with a self-addressed stamped envelope and retain receipt of mailing; 

  

	4)	Retain IRS file stamped copy for your records when returned; and 

  

	5)	One copy should be returned to the Company for its records and one copy should be filed along with your federal income tax return for the tax year.

 For your information, the address of the IRS (if you live in Northern California, except for
the Central Valley) is as follows: 
 Internal Revenue Service 
 5045 East Butler Avenue 
 Fresno, California 93888 

 SECTION 83(b) ELECTION 
 This statement is being made under Section 83(b) of the Internal Revenue Code, pursuant to Treas. Reg. Section 1.83-2. 

The taxpayer who performed the service is: 
 Name: 
 Address: 
 Taxpayer Ident. No. 
 The property
with respect to which the election is being made is              shares of common stock of Codexis, Inc. 
 The property was issued on             , 200  . 
 The taxable year in which the election is being made in the calendar year 200  . 
 The property is subject to a repurchase right pursuant to which the issuer has the right to acquire the property at the original purchase price if for any reason the taxpayer’s service provider relationship with the issuer is
terminated. The issuer’s repurchase right lapses in a series of annual and monthly installments over a             -year period ending on
            , 200  . 
 The fair market value at the time of
transfer (determined without regard to any restriction other than a restriction which by its terms will never lapse) is $             per share. 
 The amount paid for such property is $             per share. 
 A copy of this statement was furnished to Codexis, Inc. for whom taxpayer rendered the services underlying the transfer of property. 
 This statement is executed on             , 200  . 
  

			
	  
	  	  

	Spouse (if any)	  	Taxpayer

 This election must be filed with the Internal Revenue Service Center with which taxpayer files his
or her Federal income tax returns and must be made within thirty (30) days after the execution date of the Stock Purchase Agreement. This filing should be made by registered or certified mail, return receipt requested. Optionee must retain two
(2) copies of the completed form for filing with his or her Federal and state tax returns for the current tax year and an additional copy for his or her records. 

 IMPORTANT: READ THIS — 
 IF YOU WISH TO MAKE A SECTION 83(B) ELECTION, THE FILING OF SUCH ELECTION IS YOUR RESPONSIBILITY. 
 THE FORM FOR MAKING THIS SECTION 83(B) ELECTION IS ATTACHED TO THIS AGREEMENT AS PART OF EXHIBIT C-5. 
 YOU MUST FILE THIS FORM WITHIN 30 DAYS OF PURCHASING THE SHARES. 
 YOU (AND NOT THE COMPANY OR ANY OF ITS AGENTS) SHALL BE SOLELY RESPONSIBLE FOR FILING SUCH FORM WITH THE IRS, EVEN IF YOU
REQUEST THE COMPANY OR ITS AGENTS TO MAKE THIS FILING ON YOUR BEHALF AND EVEN IF THE COMPANY OR ITS AGENTS HAVE PREVIOUSLY MADE THIS FILING ON YOUR BEHALF. 
 The election should be filed by mailing a signed election form by certified mail, return receipt requested to the IRS Service Center where you file your tax returns. See www.irs.gov 

             ,          
 Internal Revenue Service 
 5045 East Butler Avenue 
 Fresno, California 93888 
  

			
	Re:	  	83(b) Election for Purchase of Codexis, Inc. Common Stock

 Ladies and Gentlemen: 
 Enclosed is a completed form of election under Section 83(b) of the Internal Revenue Code of 1986 (the “83(b) Election”) relating to my recent purchase of
             shares of Common Stock of Codexis, Inc. 
 Please acknowledge
receipt of the 83(b) Election by stamping as filed the enclosed copy and returning it to me in the self-addressed stamped envelope provided. 
  

	
	 Sincerely,

	
	  

 EnclosuresOffer Letter - Alan Shaw

 Exhibit 10.12A 
  

					
	

	  		  	     Codexis, Inc.
     200 Penobscot Drive
     Redwood City, California 94063

     Tel : 650.980.5600
     Fax : 650.298.5449
     www.codexis.com

	July 29, 2003	  	  

 Alan Shaw 
 [Address] 
 Dear Alan: 
 On behalf of Codexis, I am pleased to confirm your status as a full-time employee of Codexis effective July 29, 2003. Your current position will remain as Chief Executive Officer. 
 Compensation 
 This letter confirms that you
will continue to receive a salary of $23,750 per month (equivalent to $285,000 per year), payable in periodic installments on our regular paydays. For 2003, you also will be eligible to participate in the Codexis Executive Bonus Plan, which is a
performance-based program that allows for a bonus stock option award based upon achievement of Codexis objectives. You must be employed by Codexis on the date that the bonus is to be paid in order to be eligible for the bonus. 
 Stock Options 
 As previously communicated
to you, you have elected to participate in the offer to exchange certain outstanding options for new options. Your new Codexis options, once granted, will be subject to the terms of the Codexis, Inc. 2002 Stock Plan. 
 Employee Benefits 
 As a full-time employee,
you will be eligible for the Codexis employee benefit plans, which currently include medical, dental, vision, EAP, long and short-term disability plans, life insurance, Flex Plan, a 401(k) savings plan, employee stock purchase plan (through
August 31, 2003), and our flexible time off plan that allows full-time employees to accrue 20 or 25 days of flexible time off (FTO) each year of employment, depending upon years of service. 
 Codexis has agreed to continue to participate in the Maxygen benefit plans providing medical, dental, vision, EAP, life insurance, Flex Plan and long and
short-term disability coverage and intends to continue to participate in those plans at least through the end of the year under the terms and conditions as set forth in the documents and instruments governing those plans and subject to the same
rights to alter, amend or modify any of those plans and programs. There will be no gap in any of those coverages. 
 Codexis will also continue
to participate as an employer in the Maxygen 401(k) retirement plan under the terms and conditions set forth in the documents and instruments governing that plan, which will require preparation of new plan documents. Copies of the new plan will be
distributed upon their completion. The 401(k) plan previously was amended to eliminate the employer matching contribution for employees in Codexis effective January 1, 2003, and that change will remain in effect. Some additional documentation
will be provided upon its completion. 

 Human Resources Policies 
 At this time, Codexis intends to adopt Maxygen’s human resource and other Company policies for all it’s employees except for those provisions of Maxygen’s policies that specifically exclude
Codexis employees, e.g., Codexis Travel Policy. 
 Other Terms and Conditions of Employment 
 All employment with Codexis is at will. “Employment at will” means that you are free to resign from your employment at any time, for any reason or
no reason at all, with or without cause and with or without notice. Similarly, Codexis may terminate your employment at any time for any legal reason, or no reason, with or without cause and with or without notice. By accepting this offer of
continuing employment, you agree that your employment is at will, and acknowledge that no one, other than the CEO of Codexis or the Chairman of the Board of Directors of Codexis, has the authority to promise you anything to the contrary. Any such
agreement must be in writing and signed by both you and such Individual to be effective. 
 Employment with any other entity, or for yourself in
competition with Codexis, Maxygen or any affiliate or subsidiary of Maxygen is not permitted. If you want to take an outside job, you should discuss the outside opportunity with your manager and the Human Resources Department in advance so that we
can determine if any actual or potential conflict of interest exists. 
 During the course of your employment, you may create, develop or have
access to confidential information belonging to Codexis and/or third parties such as Maxygen, including trade secrets and proprietary information, such as technical and scientific research and/or protocols, customer and supplier information,
business plans, marketing plans, unpublished financial information, designs, drawings, innovations, inventions, discoveries, specifications, software, source codes, and personnel information. You agree that as a condition of your employment with
Codexis, you will sign and comply with the attached Codexis Confidential Information, Secrecy and Invention Agreement. 
 Arbitration of
Disputes 
 You agree that, except as described below, any dispute relating to your employment or the termination of your employment with
Codexis shall be finally settled by binding arbitration in Palo Alto, California before a neutral arbitrator of the American Arbitration Association (“AAA”) under its National Rules for the Resolution of Employment Disputes. Claims subject
to arbitration shall include, but shall not be limited to, claims under Title VII of the Civil Rights Act of 1964 (as amended) and other civil rights statutes of the United States, the Age Discrimination in Employment Act, the Americans with
Disabilities Act, the Family and Medical Leave Act, the Employee Retirement Income Security Act of 1974, the California Fair Employment and Housing Act, the California Labor Code, and any other federal, state or local statute or regulation, and the
common law of contract and tort. However, this agreement to arbitrate shall not apply to claims (a) for workers’ compensation, (b) for unemployment compensation or (c) injunctive relief arising out of or related to
misappropriation of trade secrets or misuse or improper disclosure of confidential information, unfair competition or breach of any non-competition or non-solicitation agreement between you and Codexis. 
 You understand that by this agreement, you and Codexis are waiving your respective rights to trial by jury, and that judgment upon any arbitration award may
be entered in any court having jurisdiction of the matter. Any controversy or claim subject to arbitration shall be waived and forever barred if arbitration is not initiated within one year after the date the controversy or claim first arose, or if
statutory rights are involved, within the time limit established by the applicable statute of limitations. 

 You and Codexis will have the same remedies available in arbitration as those available had the claim been
filed in a court of law, including, where authorized by statute, compensatory and punitive damages, injunctive relief and attorneys’ fees. Although Codexis will pay all costs of the AAA and the arbitrator, you agree to pay all costs you would
otherwise be required to pay were your claims litigated in a court of law, such as costs of your attorney, deposition transcripts and expert witness fees and expenses. 
 The terms described in this letter replace all prior agreements, understandings, and promises between Codexis or Maxygen and you concerning the terms and conditions of your employment with Codexis.

 We are pleased that you will continue to work with Codexis, and hope that your association with Codexis will be successful and rewarding.
Please indicate your acceptance of this offer by signing this letter below and a copy of the attached Codexis Confidential Information, Secrecy and Invention Agreement and returning both to Rose Sturgess by no later than August 1, 2003. A copy of
the letter is enclosed for your records. 
  

			
	Sincerely,
	
	Codexis, Inc.
		
	By:	 	 /s/ Marc Ketzel

		 	Marc Ketzel
		 	 Vice President, Human Resources
 (On behalf of the Codexis Board of Directors)

 I understand and agree to the foregoing terms and conditions of employment with Codexis.

  

					
	 Alan Shaw
	 		 	
	Print Name	 		 	
			
	 /s/ Alan Shaw
	 		 	 29TH July 2003

	Signature	 		 	Date

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