Document:

Fourth Amended and Restated Investor Rights Agreement

 Exhibit 4.2 
 CODEXIS, INC. 
 FOURTH AMENDED AND RESTATED 
 INVESTOR RIGHTS AGREEMENT 
 November 13, 2007 

 TABLE OF CONTENTS 
  

							
	 	 	 	  	 	  	 Page

	 SECTION 1.
	 	GENERAL	  	2
		 	 1.1
	  	Definitions	  	2
			
	 SECTION 2.
	 	REGISTRATION; RESTRICTIONS ON TRANSFER	  	3
		 	 2.1
	  	Restrictions on Transfer	  	3
		 	 2.2
	  	Demand Registration	  	5
		 	 2.3
	  	Piggyback Registrations	  	6
		 	 2.4
	  	Form S-3 Registration	  	7
		 	 2.5
	  	Expenses of Registration	  	8
		 	 2.6
	  	Obligations of the Company	  	9
		 	 2.7
	  	Termination of Registration Rights	  	10
		 	 2.8
	  	Delay of Registration; Furnishing Information	  	10
		 	 2.9
	  	Indemnification	  	11
		 	 2.10
	  	Assignment of Registration Rights	  	13
		 	 2.11
	  	Limitation on Subsequent Registration Rights	  	13
		 	 2.12
	  	“Market Stand-Off” Agreement	  	13
		 	 2.13
	  	Agreement to Furnish Information	  	14
		 	 2.14
	  	Rule 144 Reporting	  	14
			
	 SECTION 3.
	 	COVENANTS OF THE COMPANY	  	15
		 	 3.1
	  	Basic Financial Information and Reporting	  	15
		 	 3.2
	  	Stockholder/Option Lists	  	15
		 	 3.3
	  	Inspection Rights	  	15
		 	 3.4
	  	Confidentiality of Records	  	16
		 	 3.5
	  	Reservation of Common Stock	  	16
		 	 3.6
	  	Stock Vesting	  	16
		 	 3.7
	  	Proprietary Information and Inventions Agreement	  	17
		 	 3.8
	  	Approval of Director/Management Transactions	  	17
		 	 3.9
	  	Approval of Maxygen Transactions	  	17
		 	 3.10
	  	Directors’ Liability and Indemnification	  	17
		 	 3.11
	  	Compensation Committee	  	17
		 	 3.12
	  	Budget Approval	  	17
		 	 3.13
	  	Observer Rights	  	17

  

 i 

							
		 	 3.14
	  	Termination of Covenants	  	18
			
	 SECTION 4.
	 	SUBSCRIPTION RIGHT	  	18
		 	 4.1
	  	Subsequent Offerings	  	18
		 	 4.2
	  	Exercise of Rights	  	18
		 	 4.3
	  	Issuance of Equity Securities to Other Persons	  	19
		 	 4.4
	  	Termination and Waiver of Subscription Rights	  	19
		 	 4.5
	  	Transfer of Subscription Rights	  	19
		 	 4.6
	  	Excluded Securities	  	19
		 	 4.7
	  	Waiver of Subscription Rights	  	20
			
	 SECTION 5.
	 	MISCELLANEOUS	  	20
		 	 5.1
	  	Governing Law	  	20
		 	 5.2
	  	Survival	  	20
		 	 5.3
	  	Successors and Assigns	  	20
		 	 5.4
	  	Entire Agreement	  	21
		 	 5.5
	  	Severability	  	21
		 	 5.6
	  	Amendment and Waiver	  	21
		 	 5.7
	  	Delays or Omissions	  	21
		 	 5.8
	  	Notices	  	22
		 	 5.9
	  	Attorneys’ Fees	  	22
		 	 5.10
	  	Titles and Subtitles	  	22
		 	 5.11
	  	Additional Investors	  	22
		 	 5.12
	  	Counterparts	  	22
		 	 5.13
	  	Aggregation of Stock	  	22
		 	 5.14
	  	Specific Performance	  	23

  

 ii 

 CODEXIS, INC. 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 
 This Fourth Amended and Restated
Investor Rights Agreement (the “Agreement”) is entered into as of November 13, 2007, by and among Codexis, Inc., a Delaware corporation (the “Company”) and the investors listed on Exhibit A hereto,
referred to hereinafter as the “Investors” and each individually as an “Investor.” 
 RECITALS

 WHEREAS, certain of the Investors hold shares of the Company’s Series A Preferred Stock, $.0001 par value per share (the
“Series A Stock”), Series B Preferred Stock, $.0001 par value per share (the “Series B Stock”), Series C Preferred Stock, $.0001 par value per share (the “Series C Stock”) and/or Series D Preferred
Stock, $.0001 par value per share (the “Series D Stock”), and possess registration rights, information rights, rights of first offer, and other rights pursuant to that certain Third Amended and Restated Investors’ Rights
Agreement dated as of August 22, 2006, as amended, by and among the Company and such Investors (the “Prior Agreement”); 
 WHEREAS, certain of the Investors and the Company are parties to that certain Series E Preferred Stock Purchase Agreement of even date herewith (the “Purchase Agreement”) which contemplates the sale of Series E Preferred
Stock, $.0001 par value per share (the “Series E Stock”) to such Investors (the “Financing”); 
 WHEREAS,
the parties to the Prior Agreement desire to terminate the Prior Agreement and accept the rights and covenants hereof in lieu of their rights and covenants under the Prior Agreement; 
 WHEREAS, the obligations in the Purchase Agreement are conditioned upon the execution and delivery of this Agreement; and 
 WHEREAS, in connection with the consummation of the Financing, the parties desire to enter into this Agreement in order to grant registration,
information rights and other rights to the Investors as set forth below. 
 AGREEMENT 
 NOW, THEREFORE, in consideration of the representations, warranties, covenants and agreements contained in this Agreement and for other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree that the Prior Agreement shall be superseded and replaced in its entirety by this Agreement, and the parties hereto further agree as follows:

 SECTION 1. GENERAL. 
 1.1 Definitions. As used in this Agreement the following terms shall have the following respective meanings: 
 (a) “Affiliate” means any corporation or other entity that is directly or indirectly controlling, controlled by or under common control with a party hereto, or any investment funds with the same manager or advisor as a
party hereto. For the purpose of this definition, “control” shall mean the direct or indirect ownership of at least fifty percent (50%) of the outstanding shares or other voting rights of the subject entity to elect directors or the
equivalent governing body, or if not meeting the preceding, any entity owned or controlled by or owning or controlling the maximum control or ownership right permitted in the country where such entity exists. 
 (b) “Exchange Act” means the Securities Exchange Act of 1934, as amended. 
 (c) “Form S-3” means such form under the Securities Act as in effect on the date hereof or any successor or similar registration form
under the Securities Act subsequently adopted by the SEC that permits inclusion or incorporation of substantial information by reference to other documents filed by the Company with the SEC. 
 (d) “Holder” means any person owning of record Registrable Securities that have not been sold to the public or any assignee of record of
such Registrable Securities in accordance with Section 2.10 hereof. 
 (e) “Initial Offering” means the Company’s
first firm commitment underwritten public offering of its Common Stock registered under the Securities Act that results in the Preferred Stock being converted into Common Stock. 
 (f) “Initating Holders” shall mean Holders of Registrable Securities who in the aggregate hold not less than thirty percent
(30%) of the outstanding Registrable Securities. 
 (g) “Preferred Stock” means the Series A Stock, the Series B Stock,
the Series C Stock, the Series D Stock and the Series E Stock. 
 (h) “Register,” “registered,” and
“registration” refer to a registration effected by preparing and filing a registration statement in compliance with the Securities Act, and the declaration or ordering of effectiveness of such registration statement or document.

 (i) “Registrable Securities” means (a) Common Stock of the Company issued or issuable upon conversion of the Shares
and the exercise of any warrants and (b) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in
exchange for or in replacement of, such above-described securities. Notwithstanding the foregoing, Registrable Securities shall not include any securities sold by a person to the public either pursuant to a registration statement or Rule 144 or
sold in a private transaction in which the transferor’s rights under Section 2 of this Agreement are not assigned. 
  

 2 

 (j) “Registrable Securities then outstanding” shall be the number of shares determined
by calculating the total number of shares of the Company’s Common Stock that are Registrable Securities and either (a) are then issued and outstanding or (b) are issuable pursuant to then exercisable or convertible securities.

 (k) “Registration Expenses” shall mean all expenses incurred by the Company in complying with Sections 2.2, 2.3, 2.4
and 2.6 hereof, including, without limitation, all registration and filing fees, printing expenses, fees and disbursements of counsel for the Company, reasonable fees and disbursements of counsel for the Holders not to exceed (a) fifty thousand
dollars ($50,000) in the aggregate in the case of a registration on Form S-1 or its equivalent or (b) twenty five thousand dollars ($25,000) in the aggregate in the case of a registration on Form S-3 or its equivalent, blue sky fees and
expenses and the expense of any special audits incident to or required by any such registration (but excluding the compensation of regular employees of the Company, which shall be paid in any event by the Company). 
 (l) “SEC” or “Commission” means the Securities and Exchange Commission. 
 (m) “Securities Act” shall mean the Securities Act of 1933, as amended. 
 (n) “Selling Expenses” shall mean all underwriting discounts and selling commissions applicable to the sale. 
 (o) “Senior Officer” shall mean the Chief Executive Officer, Chief Financial Officer, General Counsel, President or any Senior Vice
President of the Company. 
 (p) “Shares” shall mean the Company’s Series E Stock issued pursuant to the Purchase
Agreement and the Series A Stock, Series B Stock, Series C Stock and the Series D Stock of the Company held by certain Investors listed on Exhibit A hereto and their permitted assigns. 
 (q) “Special Registration Statement” shall mean (i) a registration statement relating to any employee benefit plan or
(ii) with respect to any corporate reorganization or transaction under Rule 145 of the Securities Act, including any registration statements related to the resale of securities issued in such a transaction or (iii) a registration
related to stock issued or issuable upon conversion of debt securities. 
 SECTION 2. REGISTRATION; RESTRICTIONS ON TRANSFER. 
 2.1 Restrictions on Transfer. 
 (a)
Each Holder agrees not to make any disposition of all or any portion of the Shares or Registrable Securities unless and until: 
 (i) There
is then in effect a registration statement under the Securities Act covering such proposed disposition and such disposition is made in accordance with such registration statement; or 
  

 3 

 (ii) (A) The transferee has agreed in writing to be bound by the terms of this Agreement,
(B) such Holder shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances surrounding the proposed disposition, and (C) if reasonably requested by the
Company, such Holder shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, that such disposition will not require registration of such shares under the Securities Act. It is agreed that the Company will
not require opinions of counsel for transactions made pursuant to Rule 144, except in unusual circumstances. After its Initial Offering, the Company will not require the transferee to be bound by the terms of Section 2.1(a)(ii) of this
Agreement. 
 (iii) Notwithstanding the provisions of paragraphs (i) and (ii) above, no such registration statement or opinion of
counsel shall be necessary for a transfer by a Holder that is (A) a partnership transferring to its partners or former partners in accordance with partnership interests, (B) a corporation transferring to a wholly-owned subsidiary or a
parent corporation that owns all of the capital stock of the Holder, (C) a limited liability company transferring to its members or former members in accordance with their interest in the limited liability company, (D) an individual
transferring to the Holder’s family member or trust for the benefit of an individual Holder, or (E) an Affiliate; provided, however, that in each case the transferee will be subject to the terms of this Agreement to the same
extent as if he were an original Holder hereunder. 
 (b) Each certificate representing Shares or Registrable Securities shall (unless
otherwise permitted by the provisions of the Agreement) be stamped or otherwise imprinted with a legend substantially similar to the following (in addition to any legend required under applicable state securities laws): 
 THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO THE TERMS AND CONDITIONS OF AN INVESTOR RIGHTS AGREEMENT THAT PLACES CERTAIN RESTRICTIONS ON
THE TRANSFER OF THE SHARES REPRESENTED HEREBY. A COPY OF SUCH INVESTOR RIGHTS AGREEMENT WILL BE FURNISHED TO THE RECORD HOLDER OF THIS CERTIFICATE WITHOUT CHARGE UPON WRITTEN REQUEST TO THE COMPANY AT ITS PRINCIPAL PLACE OF BUSINESS. 
 (c) The Company shall be obligated to reissue promptly unlegended certificates at the request of any Holder thereof if the Holder shall have obtained an
opinion of counsel (which counsel may be counsel to the Company) reasonably acceptable to the Company to the effect that the securities proposed to be disposed of may lawfully be so disposed of without registration, qualification or legend.

 (d) Any legend endorsed on an instrument pursuant to applicable state securities laws and the stop-transfer instructions with respect to
such securities shall be removed upon receipt by the Company of an order of the appropriate blue sky authority authorizing such removal. 
  

 4 

 2.2 Demand Registration. 
 (a) Subject to the conditions of this Section 2.2, if the Company shall receive a written request from the Initiating Holders that the Company file a
registration statement under the Securities Act covering the registration of Registrable Securities with an anticipated aggregate offering price, net of underwriting discounts and commissions, of at least ten million dollars ($10,000,000) (a
“Qualified Public Offering”), then the Company shall, within thirty (30) days of the receipt thereof, give written notice of such request to all Holders, and subject to the limitations of this Section 2.2, effect, as
expeditiously as reasonably possible, the registration under the Securities Act of all Registrable Securities that the Holders request to be registered. 
 (b) If the Initiating Holders intend to distribute the Registrable Securities covered by their request by means of an underwriting, they shall so advise the Company as a part of their request made pursuant to this
Section 2.2 or any request pursuant to Section 2.4 and the Company shall include such information in the written notice referred to in Section 2.2(a) or Section 2.4(a), as applicable. In such event, the right of any Holder to
include its Registrable Securities in such registration shall be conditioned upon such Holder’s participation in such underwriting and the inclusion of such Holder’s Registrable Securities in the underwriting to the extent provided herein.
All Holders proposing to distribute their securities through such underwriting shall enter into an underwriting agreement in customary form with the underwriter or underwriters selected for such underwriting by a majority in interest of the
Initiating Holders (which underwriter or underwriters shall be reasonably acceptable to the Company). Notwithstanding any other provision of this Section 2.2 or Section 2.4, if the underwriter advises the Company that marketing factors
require a limitation of the number of securities to be underwritten (including Registrable Securities) then the Company shall so advise all Holders of Registrable Securities that would otherwise be underwritten pursuant hereto, and the number of
shares that may be included in the underwriting shall be allocated to the Holders of such Registrable Securities on a pro rata basis based on the number of Registrable Securities held by all such Holders (including the Initiating Holders);
provided, however, that the number of shares of Registrable Securities to be included in such underwriting and registration shall not be reduced unless all other securities of the Company are first entirely excluded from the
underwriting and registration. Any Registrable Securities excluded or withdrawn from such underwriting shall be withdrawn from the registration. 
 (c) The Company shall not be required to effect a registration pursuant to this Section 2.2: 
 (i) prior to the earlier of
(A) November 13, 2010 or (B) one hundred eighty (180) days following the effective date of the registration statement pertaining to the Initial Offering; 
 (ii) after the Company has effected two (2) registrations pursuant to this Section 2.2, and such registrations have been declared or ordered
effective; 
 (iii) during the period starting with the date of filing of, and ending on the date one hundred eighty (180) days
following the effective date of the registration statement pertaining to the Initial Offering; provided, however, that the Company makes reasonable best efforts to cause such registration statement to become effective; 
  

 5 

 (iv) if within thirty (30) days of receipt of a written request from Initiating Holders pursuant to
Section 2.2(a), the Company gives notice to the Holders of the Company’s intention to file a registration statement for its Initial Offering within ninety (90) days; 
 (v) if the Company shall furnish to Holders requesting a registration statement pursuant to this Section 2.2, a certificate signed by the Chairman
of the Board stating that in the good faith judgment of the Board of Directors of the Company, it would be seriously detrimental to the Company and its stockholders for such registration statement to be effected at such time, in which event the
Company shall have the right to defer such filing for a period of not more than one hundred twenty (120) days after receipt of the request of the Initiating Holders; provided that such right to delay a request shall be exercised by the
Company not more than once in any twelve (12) month period; or 
 (vi) in any particular jurisdiction in which the Company would be
required to qualify to do business or to execute a general consent to service of process in effecting such registration, qualification or compliance. 
 2.3 Piggyback Registrations. The Company shall notify all Holders of Registrable Securities in writing at least fifteen (15) days prior to the filing of any registration statement under the
Securities Act for purposes of a public offering of securities of the Company (including, but not limited to, registration statements relating to secondary offerings of securities of the Company, but excluding Special Registration Statements) and
will afford each such Holder an opportunity to include in such registration statement all or part of such Registrable Securities held by such Holder. Each Holder desiring to include in any such registration statement all or any part of the
Registrable Securities held by it shall, within seven (7) days after the above-described notice from the Company, so notify the Company in writing. Such notice shall state the intended method of disposition of the Registrable Securities by such
Holder. If a Holder decides not to include all of its Registrable Securities in any registration statement thereafter filed by the Company, such Holder shall nevertheless continue to have the right to include any Registrable Securities in any
subsequent registration statement or registration statements as may be filed by the Company with respect to offerings of its securities, all upon the terms and conditions set forth herein. 
 (a) Underwriting. If the registration statement under which the Company gives notice under this Section 2.3 is for an underwritten offering,
the Company shall so advise the Holders of Registrable Securities. In such event, the right of any such Holder to be included in a registration pursuant to this Section 2.3 shall be conditioned upon such Holder’s participation in such
underwriting and the inclusion of such Holder’s Registrable Securities in the underwriting to the extent provided herein. All Holders proposing to distribute their Registrable Securities through such underwriting shall enter into an
underwriting agreement in customary form with the underwriter or underwriters selected for such underwriting by the Company. Notwithstanding any other provision of this Agreement, if the underwriter determines in good faith that marketing factors
require a limitation of the number of shares to be underwritten, the number of shares that 

  

 6 

 
may be included in the underwriting shall be allocated, first, to the Company; second, to the Holders on a pro rata basis based on the total number of
Registrable Securities held by the Holders; and third, to any stockholder of the Company (other than a Holder) on a pro rata basis. No such reduction shall reduce the amount of securities of the selling Holders included in the registration
below twenty-five percent (25%) of the total amount of securities included in such registration, unless such offering is the Initial Offering and such registration does not include shares of any other selling stockholders, in which event any or
all of the Registrable Securities of the Holders may be excluded in accordance with the immediately preceding sentence. If any Holder disapproves of the terms of any such underwriting, such Holder may elect to withdraw therefrom by written notice to
the Company and the underwriter, delivered at least ten (10) business days prior to the effective date of the registration statement. Any Registrable Securities excluded or withdrawn from such underwriting shall be excluded and withdrawn from
the registration. For any Holder that is a partnership, limited liability company or corporation, the partners, retired partners, members, retired members and stockholders of such Holder, or the estates and family members of any such partners,
retired partners, member and retired members and any trusts for the benefit of any of the foregoing person shall be deemed to be a single “Holder,” and any pro rata reduction with respect to such “Holder” shall be based
upon the aggregate amount of shares carrying registration rights owned by all entities and individuals included in such “Holder,” as defined in this sentence. 
 (b) Right to Terminate Registration. The Company shall have the right to terminate or withdraw any registration initiated by it under this Section 2.3 prior to the effectiveness of such registration
whether or not any Holder has elected to include securities in such registration. The Registration Expenses of such withdrawn registration shall be borne by the Company in accordance with Section 2.5 hereof. 
 2.4 Form S-3 Registration. In case the Company shall receive from any Holder or Holders of Registrable Securities a written request or requests
that the Company effect a registration on Form S-3 (or any successor to Form S-3) or any similar short-form registration statement and any related qualification or compliance with respect to all or a part of the Registrable Securities
owned by such Holder or Holders, the Company will: 
 (a) promptly give written notice of the proposed registration, and any related
qualification or compliance, to all other Holders of Registrable Securities; and 
 (b) as soon as practicable, effect such registration and
all such qualifications and compliances as may be so requested and as would permit or facilitate the sale and distribution of all or such portion of such Holder’s or Holders’ Registrable Securities as are specified in such request,
together with all or such portion of the Registrable Securities of any other Holder or Holders joining in such request as are specified in a written request given within fifteen (15) days after receipt of such written notice from the Company;
provided, however, that the Company shall not be obligated to effect any such registration, qualification or compliance pursuant to this Section 2.4: 
 (i) if Form S-3 is not available for such offering by the Holders; 
  

 7 

 (ii) if the Holders, together with the holders of any other securities of the Company entitled to
inclusion in such registration, propose to sell Registrable Securities and such other securities (if any) at an aggregate price to the public of less than one million dollars ($1,000,000); 
 (iii) if within thirty (30) days of receipt of a written request from any Holder or Holders pursuant to this Section 2.4, the Company gives
notice to such Holder or Holders of the Company’s intention to make a public offering within ninety (90) days, other than pursuant to a Special Registration Statement; 
 (iv) if the Company shall furnish to the Holders a certificate signed by the Chairman of the Board of Directors of the Company stating that in the good
faith judgment of the Board of Directors of the Company, it would be seriously detrimental to the Company and its stockholders for such Form S-3 registration to be effected at such time, in which event the Company shall have the right to defer
the filing of the Form S-3 registration statement for a period of not more than ninety (90) days after receipt of the request of the Holder or Holders under this Section 2.4; provided, that such right to delay a request shall
be exercised by the Company not more than once in any twelve (12) month period; 
 (v) if the Company has, within the twelve
(12) month period preceding the date of such request, already effected two (2) registrations on Form S-3 for the Holders pursuant to this Section 2.4; or 
 (vi) in any particular jurisdiction in which the Company would be required to qualify to do business or to execute a general consent to service of
process in effecting such registration, qualification or compliance. 
 (c) Subject to the foregoing, the Company shall file a Form S-3
registration statement covering the Registrable Securities and other securities so requested to be registered as soon as practicable after receipt of the requests of the Holders. Registrations effected pursuant to this Section 2.4 shall not be
counted as demands for registration or registrations effected pursuant to Sections 2.2 or 2.3, respectively. All Registration Expenses incurred in connection with registrations requested pursuant to this Section 2.4 after the first two
(2) registrations shall be paid by the selling Holders pro rata in proportion to the number of shares sold by each such Holder. 
 2.5 Expenses of Registration. Except as specifically provided herein, all Registration Expenses incurred in connection with any registration, qualification or compliance pursuant to Section 2.2 or any registration under
Section 2.3 or Section 2.4 herein shall be borne by the Company. All Selling Expenses incurred in connection with any registrations hereunder shall be borne by the holders of the securities so registered pro rata on the basis of the
number of shares so registered. The Company shall not, however, be required to pay for expenses of any registration proceeding begun pursuant to Section 2.2 or 2.4, the request of which has been subsequently withdrawn by the Initiating Holders
unless (a) the withdrawal is based upon material adverse information concerning the Company of which the Initiating Holders were not aware at the time of such request or (b) the Holders of a majority of Registrable Securities agree to
forfeit their right to one requested registration pursuant to Section 2.2 or Section 2.4, as 

  

 8 

 
applicable, in which event such right shall be forfeited by all Holders. If the Holders are required to pay the Registration Expenses, such expenses shall be
borne by the holders of securities (including Registrable Securities) requesting such registration in proportion to the number of shares for which registration was requested. If the Company is required to pay the Registration Expenses of a withdrawn
offering pursuant to clause (a) above, then the Holders shall not forfeit their rights pursuant to Section 2.2 or Section 2.4 to a demand registration. 
 2.6 Obligations of the Company. Whenever required to effect the registration of any Registrable Securities, the Company shall, as expeditiously as reasonably possible: 
 (a) Prepare and file with the SEC a registration statement with respect to such Registrable Securities and use all reasonable best efforts to cause such
registration statement to become effective, and, upon the request of the Holders of a majority of the Registrable Securities registered thereunder, keep such registration statement effective for up to one hundred twenty (120) days or, if
earlier, until the Holder or Holders have completed the distribution related thereto; provided, however, that at any time, upon written notice to the participating Holders and for a period not to exceed sixty (60) days thereafter
(the “Suspension Period”), the Company may delay the filing or effectiveness of any registration statement or suspend the use or effectiveness of any registration statement (and the Initiating Holders hereby agree not to offer or
sell any Registrable Securities pursuant to such registration statement during the Suspension Period) if the Company reasonably believes that the Company may, in the absence of such delay or suspension hereunder, be required under state or federal
securities laws to disclose any corporate development the disclosure of which could reasonably be expected to have an adverse effect upon the Company, its stockholders, a potentially significant transaction or event involving the Company, or any
negotiations, discussions, or proposals directly relating thereto. No more than two (2) such Suspension Periods shall occur in any twelve (12) month period. In the event that the Company shall exercise its rights hereunder, the applicable
time period during which the registration statement is to remain effective shall be extended by a period of time equal to the duration of the Suspension Period. The Company may extend the Suspension Period for an additional consecutive sixty
(60) days with the consent of the holders of a majority of the Registrable Securities proposed to be sold by the Initiating Holders, which consent shall not be unreasonably withheld. If so directed by the Company, the Initiating Holders shall
use their reasonable efforts to deliver to the Company (at the Company’s expense) all copies, other than permanent file copies then in such Initiating Holders’ possession, of the prospectus relating to such Registrable Securities current
at the time of receipt of such notice. 
 (b) Prepare and file with the SEC such amendments and supplements to such registration statement
and the prospectus used in connection with such registration statement as may be necessary to comply with the provisions of the Securities Act with respect to the disposition of all securities covered by such registration statement for the period
set forth in paragraph (a) above. 
 (c) Furnish to the Holders such number of copies of a prospectus, including a preliminary
prospectus, in conformity with the requirements of the Securities Act, and such other documents as they may reasonably request in order to facilitate the disposition of Registrable Securities owned by them. 
  

 9 

 (d) Use its reasonable best efforts to register and qualify the securities covered by such registration
statement under such other securities or Blue Sky laws of such jurisdictions as shall be reasonably requested by the Holders; provided, however that the Company shall not be required in connection therewith or as a condition
thereto to qualify to do business or to file a general consent to service of process in any such states or jurisdictions. 
 (e) In the event
of any underwritten public offering, enter into and perform its obligations under an underwriting agreement, in usual and customary form, with the managing underwriter(s) of such offering. Each Holder participating in such underwriting shall also
enter into and perform its obligations under such an agreement. 
 (f) Notify each Holder of Registrable Securities covered by such
registration statement at any time when a prospectus relating thereto is required to be delivered under the Securities Act of the happening of any event as a result of which the prospectus included in such registration statement, as then in effect,
includes an untrue statement of a material fact or omits to state a material fact required to be stated therein or necessary to make the statements therein not misleading in the light of the circumstances then existing. The Company will use
reasonable best efforts to amend or supplement such prospectus in order to cause such prospectus not to include any untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the
statements therein not misleading in the light of the circumstances then existing. 
 (g) Furnish, on the date that such Registrable
Securities are delivered to the underwriters for sale, if such securities are being sold through underwriters, (i) an opinion, dated as of such date, of the counsel representing the Company for the purposes of such registration, in form and
substance as is customarily given to underwriters in an underwritten public offering, addressed to the underwriters, if any, and (ii) a letter, dated as of such date, from the independent certified public accountants of the Company, in form and
substance as is customarily given by independent certified public accountants to underwriters in an underwritten public offering addressed to the underwriters. 
 2.7 Termination of Registration Rights. All registration rights granted under this Section 2 shall terminate and be of no further force and effect five (5) years after the date of the Company’s
Initial Offering. In addition, a Holder’s registration rights shall expire if (a) the Company has completed its Initial Offering and is subject to the provisions of the Exchange Act, (b) such Holder (together with its affiliates)
holds less than 1% of the Company’s outstanding Common Stock (treating all shares of convertible Preferred Stock on an as converted basis) and (c) all Registrable Securities held by and issuable to such Holder (and its affiliates) may be
sold under Rule 144 promulgated under Securities Act during any ninety (90) day period. 
 2.8 Delay of Registration; Furnishing
Information. 
 (a) No Holder shall have any right to obtain or seek an injunction restraining or otherwise delaying any such registration
as the result of any controversy that might arise with respect to the interpretation or implementation of this Section 2. 
  

 10 

 (b) It shall be a condition precedent to the obligations of the Company to take any action pursuant to
Section 2.2, 2.3 or 2.4 that the selling Holders shall furnish to the Company such information regarding themselves, the Registrable Securities held by them and the intended method of disposition of such securities as shall be required to
effect the registration of their Registrable Securities. 
 (c) The Company shall have no obligation with respect to any registration
requested pursuant to Section 2.2 or Section 2.4 if, due to the operation of subsection 2.2(b), the anticipated aggregate offering price of the Registrable Securities to be included in the registration does not equal or exceed the
anticipated aggregate offering price required to originally trigger the Company’s obligation to initiate such registration as specified in Section 2.2 or Section 2.4, whichever is applicable. 
 2.9 Indemnification. In the event any Registrable Securities are included in a registration statement under Sections 2.2, 2.3 or 2.4:

 (a) To the extent permitted by law, the Company will indemnify and hold harmless each Holder, the partners, members, officers and directors
of each Holder, any underwriter (as defined in the Securities Act) for such Holder and each person, if any, who controls such Holder or underwriter within the meaning of the Securities Act or the Exchange Act, against any losses, claims, damages, or
liabilities (joint or several) to which they may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages or liabilities (or actions in respect thereof) arise out of or are
based upon any of the following statements, omissions or violations (collectively, “Violations”) by the Company: (i) any untrue statement or alleged untrue statement of a material fact contained in such registration statement,
including any preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto, (ii) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the
statements therein not misleading, or (iii) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation promulgated under the Securities Act, the Exchange Act or
any state securities law in connection with the offering covered by such registration statement; and the Company will pay as incurred to each such Holder, partner, member, officer, director, underwriter or controlling person for any legal or other
expenses reasonably incurred by them in connection with investigating or defending any such loss, claim, damage, liability or action; provided, however, that the indemnity agreement contained in this Section 2.9(a) shall not apply
to amounts paid in settlement of any such loss, claim, damage, liability or action if such settlement is effected without the consent of the Company, which consent shall not be unreasonably withheld, nor shall the Company be liable in any such case
for any such loss, claim, damage, liability or action to the extent that it arises out of or is based upon a Violation that occurs in reliance upon and in conformity with written information furnished expressly for use in connection with such
registration by such Holder, partner, member, officer, director, underwriter or controlling person of such Holder. 
 (b) To the extent
permitted by law, each Holder will, severally but not jointly, if Registrable Securities held by such Holder are included in the securities as to which such registration qualifications or compliance is being effected, indemnify and hold harmless the
Company, each of its directors, its officers and each person, if any, who controls the Company 

  

 11 

 
within the meaning of the Securities Act, any underwriter and any other Holder selling securities under such registration statement or any of such other
Holder’s partners, members, directors or officers or any person who controls such Holder, against any losses, claims, damages or liabilities to which the Company or any such director, officer, controlling person, underwriter or other such
Holder, or partner, member, director, officer or controlling person of such other Holder may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages or liabilities (or actions
in respect thereto) arise out of or are based upon any Violation, in each case to the extent (and only to the extent) that such Violation occurs in reliance upon and in conformity with written information furnished by such Holder under an instrument
duly executed by such Holder and stated to be specifically for use in connection with such registration; and each such Holder will pay as incurred any legal or other expenses reasonably incurred by the Company or any such director, officer,
controlling person, underwriter or other Holder, or partner, member, officer, director or controlling person of such other Holder in connection with investigating or defending any such loss, claim, damage, liability or action if it is judicially
determined that there was such a Violation; provided, however, that the indemnity agreement contained in this Section 2.9(b) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability or
action if such settlement is effected without the consent of the Holder, which consent shall not be unreasonably withheld; provided further, that in no event shall any indemnity under this Section 2.9 exceed the net proceeds from
the offering received by such Holder. 
 (c) Promptly after receipt by an indemnified party under this Section 2.9 of notice of the
commencement of any action (including any governmental action), such indemnified party will, if a claim in respect thereof is to be made against any indemnifying party under this Section 2.9, deliver to the indemnifying party a written notice
of the commencement thereof and the indemnifying party shall have the right to participate in, and, to the extent the indemnifying party so desires, jointly with any other indemnifying party similarly noticed, to assume the defense thereof with
counsel mutually satisfactory to the parties; provided, however, that an indemnified party shall have the right to retain its own counsel, with the fees and expenses to be paid by the indemnifying party, if representation
of such indemnified party by the counsel retained by the indemnifying party would be inappropriate due to actual or potential differing interests between such indemnified party and any other party represented by such counsel in such proceeding. The
failure to deliver written notice to the indemnifying party within a reasonable time of the commencement of any such action, if materially prejudicial to its ability to defend such action, shall relieve such indemnifying party of any liability to
the indemnified party under this Section 2.9, but the omission so to deliver written notice to the indemnifying party will not relieve it of any liability that it may have to any indemnified party otherwise than under this Section 2.9.

 (d) If the indemnification provided for in this Section 2.9 is held by a court of competent jurisdiction to be unavailable to an
indemnified party with respect to any losses, claims, damages or liabilities referred to herein, the indemnifying party, in lieu of indemnifying such indemnified party thereunder, shall to the extent permitted by applicable law contribute to the
amount paid or payable by such indemnified party as a result of such loss, claim, damage or liability in such proportion as is appropriate to reflect the relative fault of the indemnifying party on the one hand and of the indemnified party on the
other in connection with the Violation(s) that resulted in such loss, claim, damage or liability, as well as any other relevant equitable 

  

 12 

 
considerations. The relative fault of the indemnifying party and of the indemnified party shall be determined by a court of law by reference to, among other
things, whether the untrue or alleged untrue statement of a material fact or the omission to state a material fact relates to information supplied by the indemnifying party or by the indemnified party and the parties’ relative intent,
knowledge, access to information and opportunity to correct or prevent such statement or omission; provided, that, in no event shall any contribution by a Holder hereunder exceed the net proceeds from the offering received by such
Holder. 
 (e) The obligations of the Company and Holders under this Section 2.9 shall survive completion of any offering of Registrable
Securities in a registration statement and the termination of this Agreement. No indemnifying party, in the defense of any such claim or litigation, shall, except with the consent of each indemnified party, consent to entry of any judgment or enter
into any settlement which does not include as an unconditional term thereof the giving by the claimant or plaintiff to such Indemnified Party of a release from all liability in respect to such claim or litigation. 
 2.10 Assignment of Registration Rights. The rights to cause the Company to register Registrable Securities pursuant to this Section 2 may be
assigned by a Holder to a transferee or assignee of Registrable Securities that (a) is a subsidiary, parent, general partner, limited partner, retired partner, member or retired member of a Holder, (b) is a Holder’s family member or
trust for the benefit of an individual Holder, or (c) acquires at least fifty thousand (50,000) shares of Registrable Securities (as adjusted for stock splits and combinations); or (d) is an Affiliate of such Holder
provided, however, (i) the transferor shall, within ten (10) days after such transfer, furnish to the Company written notice of the name and address of such transferee or assignee and the securities with respect
to which such registration rights are being assigned and (ii) such transferee shall agree in writing to be subject to all restrictions set forth in this Agreement. 
 2.11 Limitation on Subsequent Registration Rights. Other than as provided in Section 5.11, after the date of this Agreement, the Company shall not, without the prior written consent of the Holders of at
least two-thirds of the Registrable Securities then outstanding, enter into any agreement with any holder or prospective holder of any securities of the Company that would grant such holder registration rights pari passu or senior to those granted
to the Holders hereunder, other than the right to a Special Registration Statement (“Subsequent Registration Rights”). 
 2.12 “Market Stand-Off” Agreement. Each Holder hereby agrees that such Holder shall not sell, transfer, make any short sale of, grant any option for the purchase of, or enter into any hedging or similar transaction with the
same economic effect as a sale, any Common Stock (or other securities) of the Company held by such Holder (other than those included in the registration and Common Stock purchased by a Holder in the open market after the effective date of such
registration statement) 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 a registration statement
of the Company filed under the Securities Act (or such longer period, not to exceed eighteen (18) days after the expiration of the 180-day period as the underwriters or the Company shall request in order to facilitate compliance with National
Association of Securities Dealers Rule 2711); provided that: 
 (i) such agreement shall apply only to the Company’s Initial Offering;
and 
  

 13 

 (ii) all executive officers and directors of the Company and holders of at least one percent
(1%) of the Company’s capital stock (on an as converted basis) and all other persons with registration rights (whether or not pursuant to this Agreement) enter into similar agreements. 
 2.13 Agreement to Furnish Information. Each Holder agrees to execute and deliver such other agreements as may be reasonably requested by the
Company or the underwriter that are consistent with the Holder’s obligations under Section 2.12 or that 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, each Holder 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 Section 2.12 and this Section 2.13 shall not apply to a Special Registration. 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 the one hundred eighty (180) day (or one hundred and ninety eight (198) day) period,
if applicable. Each Holder agrees that any transferee of any shares of Registrable Securities shall be bound by Sections 2.12 and 2.13. The underwriters of the Company’s stock are intended third party beneficiaries of Sections 2.12 and
2.13 and shall have the right, power and authority to enforce the provisions hereof as though they were a party hereto. 
 2.14 Rule 144
Reporting. With a view to making available to the Holders the benefits of certain rules and regulations of the SEC that may permit the sale of the Registrable Securities to the public without registration, the Company agrees to use its
reasonable best efforts to: 
 (a) Make and keep public information available, as those terms are understood and defined in SEC Rule 144
or any similar or analogous rule promulgated under the Securities Act, at all times after the effective date of the first registration filed by the Company for an offering of its securities to the general public; 
 (b) File with the SEC, in a timely manner, all reports and other documents required of the Company under the Exchange Act; and 
 (c) So long as a Holder owns any Registrable Securities, furnish to such Holder forthwith upon request: a written statement by the Company as to its
compliance with the reporting requirements of Rule 144 of the Securities Act, and of the Exchange Act (at any time after it has become subject to such reporting requirements); a copy of the most recent annual or quarterly report of the Company; and
such other reports and documents as a Holder may reasonably request in availing itself of any rule or regulation of the SEC allowing it to sell any such securities without registration. 
  

 14 

 SECTION 3. COVENANTS OF THE COMPANY. 
 3.1 Basic Financial Information and Reporting. 
 (a) The Company will maintain true books and records of account in which full and correct entries will be made of all its business transactions pursuant to a system of accounting established and administered in accordance with United States
generally accepted accounting principles consistently applied, and will set aside on its books all such proper accruals and reserves as shall be required under generally accepted accounting principles consistently applied. 
 (b) As soon as practicable after the end of each fiscal year of the Company, and in any event within one hundred and twenty (120) days thereafter,
the Company will furnish each Investor a balance sheet of the Company, as at the end of such fiscal year, and a statement of income and a statement of cash flows of the Company, for such year, all prepared in accordance with United States generally
accepted accounting principles consistently applied and setting forth in each case in comparative form the figures for the previous fiscal year, all in reasonable detail. Such financial statements shall be accompanied by a report and opinion thereon
by independent public accountants of national standing selected by the Company’s Board of Directors. 
 (c) The Company will furnish
each Investor, as soon as practicable after the end of the first, second and third quarterly accounting periods in each fiscal year of the Company, and in any event within forty-five (45) days thereafter, a balance sheet of the Company as of
the end of each such quarterly period and a statement of income of the Company for such period and for the current fiscal year to date, prepared in accordance with United States generally accepted accounting principles, with the exception that no
notes need be attached to such statements and year-end audit adjustments may not have been made. 
 (d) So long as an Investor (with its
Affiliates) shall own not less than one hundred thousand (100,000) shares of Registrable Securities (as adjusted for stock splits and combinations) (a “Major Investor”), the Company will furnish each such Major Investor:
(i) at least sixty (60) days prior to the beginning of each fiscal year an annual budget and operating plans for such fiscal year (and as soon as available, any subsequent revisions thereto); and (ii) as soon as practicable after the
end of each month, and in any event within thirty (30) days thereafter, a statement of income of the Company for such month and for the current fiscal year to date, including a comparison to plan figures for such period, prepared in accordance
with United States generally accepted accounting principles consistently applied, with the exception that no notes need be attached to such statements and year-end audit adjustments may not have been made. 
 3.2 Stockholder/Option Lists. The Company will furnish each Major Investor, as soon as practicable after the end of each calendar quarter, and in
any event within twenty (20) days thereafter, a stockholder list for the Company and an option holder list for the Company as of the last day of the applicable calendar quarter. 
 3.3 Inspection Rights. Each Major Investor shall have the right to visit and inspect any of the properties of the Company or any of its
subsidiaries, and to discuss the affairs, finances and 

  

 15 

 
accounts of the Company or any of its subsidiaries with its officers, and to review such information as is reasonably requested all at such reasonable times
and as often as may be reasonably requested; provided, however, that the Company shall not be obligated under this Section 3.3 with respect to a competitor of the Company or with respect to information that the Board of Directors
determines in good faith is confidential and should not, therefore, be disclosed. 
 3.4 Confidentiality of Records. Each Holder
agrees to use, and to use reasonable efforts to ensure that its authorized representatives use, the same degree of care as such recipient uses to protect its own confidential information to keep confidential any information furnished to it pursuant
to this Section 3 and any other information identified as proprietary or confidential except such information that (i) was in the public domain prior to the time it was furnished to such recipient, (ii) is or becomes (through no
willful or improper action or inaction by such recipient) generally available to the public, (iii) was in its possession or known by such recipient (as evidenced by written records) without restriction prior to receipt from the Company,
(iv) was rightfully disclosed to such recipient by a third party without restriction or (v) was independently developed (as evidenced by written records) without any use of the Company’s confidential information. Furthermore, nothing
contained herein shall prevent any Holder or Permitted Disclosee (as defined below) from (a) entering into any business, entering into any agreement with a third party, or investing in or engaging in investment discussions with any other
company (whether or not competitive with the Company), provided that such Holder or Permitted Disclosee does not, except as permitted in accordance with this Section 3.4, disclose any proprietary or confidential information of the Company in
connection with such activities, or (b) making any disclosures required by law, rule, regulation or court or other governmental order. Notwithstanding the foregoing, any such Holder may disclose such proprietary or confidential information to
any former, current or prospective partner, affiliated company, limited partner, general partner or management company of such Holder (or any employee or representative of any of the foregoing) (each of the foregoing persons, a “Permitted
Disclosee”) or legal counsel, accountants or representatives for such Holder or Permitted Disclosee, so long as such Permitted Disclosees are subject to equivalent confidentiality obligations. Notwithstanding the foregoing confidentiality
provisions, a Holder (and any of the Holder’s respective employees, representatives, or other agents) may disclose to any and all persons, without limitation of any kind, the tax treatment and tax structure of the transaction contemplated by
the Purchase Agreement and all materials of any kind (including opinions or other tax analyses) that are provided relating to such tax treatment and tax structure. In addition, at no time will a Holder be subject to any restriction concerning its
consultation with its tax advisors regarding the tax treatment or tax structure of the transaction contemplated by the Purchase Agreement. 
 3.5 Reservation of Common Stock. The Company will at all times reserve and keep available, solely for issuance and delivery upon the conversion of the Preferred Stock, all Common Stock issuable from time to time upon such conversion.

 3.6 Stock Vesting. Unless otherwise approved by the Board of Directors, all stock options and other stock equivalents issued after
the date of this Agreement to employees, directors, consultants and other service providers shall be subject to vesting as follows: (a) twenty-five percent (25%) of such stock shall vest at the end of the first year following the earlier
of the date of issuance or such person’s services commencement date with the company, 

  

 16 

 
and (b) seventy-five percent (75%) of such stock shall vest over the remaining three (3) years. With respect to any shares of stock purchased
by any such person, the Company’s repurchase option shall provide that upon such person’s termination of employment or service with the Company, with or without cause, the Company or its assignee shall have the option to purchase at cost
any unvested shares of stock held by such person. 
 3.7 Proprietary Information and Inventions Agreement. The Company shall require
all employees and consultants to execute and deliver a Proprietary Information and Inventions Agreement substantially in the form provided to the Investors. 
 3.8 Approval of Director/Management Transactions. The Company shall not, without the approval of a majority of the non-interested directors, authorize or enter into any transactions with any director or
management employee, or such director’s or employee’s immediate family. 
 3.9 Approval of Maxygen Transactions. From and
after October 1, 2002, the Company has not and shall not authorize or enter into any contracts or agreements with Maxygen, Inc. (“Maxygen”) or its Affiliates without the approval of a majority of the non-interested directors.

 3.10 Directors’ Liability and Indemnification. The Company’s Certificate of Incorporation and Bylaws shall provide
(a) for elimination of the liability of directors to the maximum extent permitted by law and (b) for indemnification of directors for acts on behalf of the Company to the maximum extent permitted by law. In addition, the Company shall
enter into and at all times maintain indemnification contracts substantially in the form attached as Exhibit B hereto with each of its directors to indemnify such directors to the maximum extent permissible under Delaware law. 
 3.11 Compensation Committee. The Company shall maintain a compensation committee of the Board of Directors. The approval of the compensation
committee will be required to (i) hire or terminate any Senior Officer, (ii) change the base salary of any Senior Officer or (iii) grant any cash bonus to any Senior Officer. 
 3.12 Budget Approval. The Company shall not, without the approval of the Board of Directors, approve any annual budget of the Company or any
formal amendment thereto. 
 3.13 Observer Rights. As long as Biomedical Sciences Investment Fund Pte Ltd (“Bio*One”)
owns not less than fifty percent (50%) of the number of shares of Series D Preferred Stock (or an equivalent amount of Common Stock issued upon conversion thereof) originally purchased by Bio*One, the Company shall invite a representative
of Bio*One to attend all meetings of its Board of Directors in a nonvoting observer capacity and, in this respect, shall give such representative copies of all notices, minutes, consents and other materials that it provides to its directors;
provided, however, that such representative shall agree to hold in confidence and trust and to act in a fiduciary manner with respect to all information so provided; and, provided further, that the Company reserves the
right to withhold any information and to exclude such representative from any meeting or portion thereof (i) to protect confidential proprietary information, or (ii) if access to such information or attendance at such meeting could
adversely affect the attorney-client privilege between the Company and its counsel or would result in disclosure of trade secrets to such representative or if such Investor or its representative is or is affiliated with a direct competitor of the
Company. 
  

 17 

 3.14 Termination of Covenants. All covenants of the Company contained in Section 3 of this
Agreement shall expire and terminate as to each Investor upon the earlier of (i) the effective date of the registration statement pertaining to the Initial Offering that results in the Preferred Stock being converted into Common Stock or
(ii) upon (a) the sale, lease or other disposition of all or substantially all of the assets of the Company or (b) an acquisition of the Company by another corporation or entity by consolidation, merger or other reorganization in
which the holders of the Company’s outstanding voting stock immediately prior to such transaction own, immediately after such transaction, securities representing less than fifty percent (50%) of the voting power of the corporation or
other entity surviving such transaction, provided, however, that this Section 3.14(ii)(b) shall not apply to a merger effected exclusively for the purpose of changing the domicile of the Company (a “Change in
Control”). 
 SECTION 4. SUBSCRIPTION RIGHT. 
 4.1 Subsequent Offerings. Each Investor shall have a subscription right to purchase its pro rata share of all Equity Securities, as defined below, that the Company may, from time to time, propose to sell
and issue after the date of this Agreement, other than the Equity Securities excluded by Section 4.6 hereof. Each Investor’s pro rata share is equal to the ratio of (a) the sum of the number of shares of the Company’s
Common Stock issued or issuable upon conversion of the Series B Stock, the Series C Stock, the Series D Stock and/or the Series E Stock which such Investor is deemed to be a holder immediately prior to the issuance of such Equity Securities plus the
number of shares of Common Stock issuable upon the exercise of warrants or options held by such Investor to (b) the total number of shares of the Company’s outstanding Common Stock (including all shares of Common Stock issued or issuable
upon conversion of the Shares or upon the exercise of any outstanding warrants or options) immediately prior to the issuance of the Equity Securities. The term “Equity Securities” shall mean (i) any Common Stock, Shares or
other security of the Company, (ii) any security convertible, with or without consideration, into any Common Stock, Shares or other security (including any option to purchase such a convertible security), (iii) any security carrying any
warrant or right to subscribe to or purchase any Common Stock, Shares or other security or (iv) any such warrant or right. 
 4.2
Exercise of Rights. If the Company proposes to issue any Equity Securities, it shall give each Investor written notice (“Notice”) of its bona fide intention, describing the Equity Securities, the price and the terms and
conditions upon which the Company proposes to issue the same. Each Investor shall have fifteen (15) days from the giving of such Notice to agree to purchase up to that portion of such Equity Securities that equals the proportion that the number
of shares of Common Stock issued and held, or issuable upon conversion of the Series B Stock, the Series C Stock, the Series D Stock and/or the Series E Stock then held by such Investor bears to the total number of shares of Common Stock issued and
held, or issuable upon conversion of the Series B Stock, the Series C Stock, the Series D Stock and/or the Series E Stock then outstanding, for the price and upon the terms and conditions specified in the Notice by giving written notice to the
Company and stating therein the quantity of Equity Securities to be purchased. The Company shall promptly, in writing, inform each Investor that purchases all the 

  

 18 

 
shares available to it (“Fully Exercising Investor”) of any other Investor’s failure to do likewise. During the ten (10) day
period commencing after receipt of such information, each Fully Exercising Investor shall be entitled to obtain that portion of the shares subject to such subscription right and not subscribed for by the Investors that is equal to the proportion
that the number of shares of Common Stock issued and held, or issuable upon conversion of the Series B Stock, the Series C Stock, the Series D Stock and/or the Series E Stock then held, by such Fully Exercising Investor bears to the total number of
shares of Common Stock issued and held, or issuable upon conversion of Series B Stock, the Series C Stock, the Series D Stock and the Series E Stock then held, by all Fully Exercising Investors who wish to purchase some of the unsubscribed shares.
Notwithstanding the foregoing, the Company shall not be required to offer or sell such Equity Securities to any Investor who would cause the Company to be in violation of applicable federal securities laws by virtue of such offer or sale.

 4.3 Issuance of Equity Securities to Other Persons. If the Investors fail to exercise in full the subscription rights, the Company
shall have ninety (90) days thereafter to sell the Equity Securities in respect of which the Investor’s rights were not exercised, at a price and upon general terms and conditions materially no more favorable to the purchasers thereof than
specified in the Company’s notice to the Investors pursuant to Section 4.2 hereof. If the Company has not sold such Equity Securities within ninety (90) days of the notice provided pursuant to Section 4.2, the Company shall not
thereafter issue or sell any Equity Securities, without first offering such securities to the Investors in the manner provided above. 
 4.4
Termination and Waiver of Subscription Rights. The subscription rights established by this Section 4 shall not apply to, and shall terminate upon the earlier of (i) the effective date of the registration statement pertaining to the
Company’s Initial Offering or (ii) a Change in Control. 
 4.5 Transfer of Subscription Rights. The subscription rights of
each Investor under this Section 4 may be transferred to the same persons described in Section 2.10, and shall be subject to the same restrictions, as any transfer of registration rights pursuant to Section 2.10. 
 4.6 Excluded Securities. The subscription rights established by this Section 4 shall have no application to any of the following Equity
Securities (the “Excluded Securities”): 
 (a) options, warrants or other Common Stock purchase rights and the Common Stock
issued pursuant to such options, warrants or other rights (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like after the filing of the Company’s Second Amended and Restated Certificate of Incorporation)
issued or to be issued after the date of this Agreement to employees, officers or directors of, or consultants or advisors to the Company or any subsidiary pursuant to stock purchase or stock option plans or other arrangements, where the primary
purpose of such is not to raise additional equity capital; 
 (b) stock issuable pursuant to any rights or agreements outstanding as of the
date of this Agreement, options and warrants outstanding as of the date of this Agreement; and stock issued pursuant to any such rights or agreements granted after the date of this Agreement; provided, however, that the
subscription rights established by this Section 4 applied with respect to the initial sale or grant by the Company of such rights or agreements; 
  

 19 

 (c) any Equity Securities issued pursuant to a merger, consolidation, acquisition or similar business
combination approved by the Board of Directors; 
 (d) shares of Common Stock issued in connection with any stock split, stock dividend or
recapitalization by the Company; 
 (e) shares of Common Stock issued upon conversion of the Shares; 
 (f) any Equity Securities issued pursuant to any equipment leasing, real property leasing or loan arrangement, or debt financing from a bank or similar
financial or lending institution approved by the Board of Directors; 
 (g) any Equity Securities issued pursuant to any licensing
transaction approved by the Board of Directors; and 
 (h) any Equity Securities issued in connection with strategic alliances, joint
ventures, manufacturing, marketing or distribution arrangements or technology transfer or development arrangements; provided, however, that such strategic transactions and the issuance of shares therein, has been approved by the
Company’s Board of Directors. 
 4.7 Waiver of Subscription Rights. To the extent that any Investor is deemed to have had
subscription rights with respect to the Series E Preferred Stock issued pursuant to the terms of the Purchase Agreement, each Investor hereby waives any and all such subscription rights pursuant to this Section 4, including any notice
provisions relating thereto, on behalf of all Investors, with respect to the issuance of the Series E Preferred Stock pursuant to the Purchase Agreement. 
 SECTION 5. MISCELLANEOUS. 
 5.1 Governing Law. This Agreement shall be governed by and construed under the laws
of the State of California as applied to agreements among California residents entered into and to be performed entirely within California. 
 5.2 Survival. The representations, warranties, covenants, and agreements made herein shall survive the closing of the transactions contemplated hereby. All statements as to factual matters contained in any certificate or other
instrument delivered by or on behalf of the Company pursuant hereto in connection with the transactions contemplated hereby shall be deemed to be representations and warranties by the Company hereunder solely as of the date of such certificate or
instrument. 
 5.3 Successors and Assigns. Except as otherwise expressly provided herein, the provisions hereof shall inure to the
benefit of, and be binding upon, the successors, assigns, heirs, executors, and administrators of the parties hereto and shall inure to the benefit of and be enforceable by each person who shall be a holder of Registrable Securities from time to
time; provided, however, that prior to the receipt by the Company of adequate written notice of the transfer of any Registrable Securities specifying the full name and address of the transferee, the Company may deem and treat the person
listed as the holder of such shares in its records as the absolute owner and holder of such shares for all purposes, including the payment of dividends or any redemption price. 
  

 20 

 5.4 Entire Agreement. This Agreement, the Exhibits and Schedules hereto, the Purchase Agreement
and the other documents delivered pursuant thereto constitute the full and entire understanding and agreement between the parties with regard to the subjects hereof and no party shall be liable or bound to any other in any manner by any
representations, warranties, covenants and agreements except as specifically set forth herein and therein. 
 5.5 Severability. In the
event one or more of the provisions of this Agreement should, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality, or unenforceability shall not affect any other provisions of this Agreement,
and this Agreement shall be construed as if such invalid, illegal or unenforceable provision had never been contained herein. 
 5.6
Amendment and Waiver. 
 (a) Except as otherwise expressly provided, this Agreement may be amended or modified only upon the written
consent of (i) the Company and (ii) the holders of at least a majority of the Preferred Stock, voting together as a single class on an as-converted basis and including any Common Stock issued upon conversion; provided,
however, that no amendment of this Agreement shall materially and adversely affect the rights of an Investor in a manner that materially and disproportionately discriminates against such Investor in relation to the other Investors without
such Investor’s written consent; provided, further, however, that the addition of new parties to this Agreement or the proportionate adjustment in rights that would result from adding new parties shall not be deemed to be
amendments which materially and disproportionately discriminate against such Investor. 
 (b) Except as otherwise expressly provided, the
obligations of the Company and the rights of the Holders under this Agreement may be waived only with the written consent of (i) the Company and (ii) the holders of at least a majority of the Preferred Stock voting together as a single
class on an as-converted basis and including any Common Stock issued upon conversion; provided, however, that no waiver of this Agreement shall materially and adversely affect the rights of an Investor in a manner that materially and
disproportionately discriminates against such Investor in relation to the other Investors without such Investor’s written consent; provided, further, however, that the addition of new parties to this Agreement or the proportionate
adjustment in rights that would result from adding new parties shall not be deemed to be a waiver which materially and disproportionately discriminate against such Investor. 
 (c) For the purposes of determining the number of Holders or Investors entitled to vote or exercise any rights hereunder, the Company shall be entitled
to rely solely on the list of record holders of its stock as maintained by or on behalf of the Company. 
 5.7 Delays or Omissions. It
is agreed that no delay or omission to exercise any right, power, or remedy accruing to any Holder, upon any breach, default or noncompliance of the Company under this Agreement shall impair any such right, power, or remedy, nor shall it be
construed to be a waiver of any such breach, default or noncompliance, or any acquiescence 

  

 21 

 
therein, or of any similar breach, default or noncompliance thereafter occurring. It is further agreed that any waiver, permit, consent, or approval of any
kind or character on any Holder’s part of any breach, default or noncompliance under the Agreement or any waiver on such Holder’s part of any provisions or conditions of this Agreement must be in writing and shall be effective only to the
extent specifically set forth in such writing. All remedies, either under this Agreement, by law, or otherwise afforded to Holders, shall be cumulative and not alternative. 
 5.8 Notices. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal
delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (c) five (5) days after having been sent by registered or
certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be
sent to the party to be notified at the address as set forth on the signature pages hereof or Exhibit A hereto or at such other address as such party may designate by ten (10) days advance written notice to the other parties hereto. 

5.9 Attorneys’ Fees. In the event that any suit or action is instituted to enforce any provision in this Agreement, the prevailing party
in such dispute shall be entitled to recover from the losing party all fees, costs and expenses of enforcing any right of such prevailing party under or with respect to this Agreement, including without limitation, such reasonable fees and expenses
of attorneys and accountants, which shall include, without limitation, all fees, costs and expenses of appeals. 
 5.10 Titles and
Subtitles. The titles of the sections and subsections of this Agreement are for convenience of reference only and are not to be considered in construing this Agreement. 
 5.11 Additional Investors. Notwithstanding anything to the contrary contained herein, if the Company shall issue additional shares of its
Preferred Stock pursuant to the Purchase Agreement, any purchaser of such shares of Preferred Stock may become a party to this Agreement by executing and delivering an additional counterpart signature page to this Agreement and shall be deemed an
“Investor,” a “Holder” and a party hereunder. Notwithstanding anything to the contrary contained herein, if the Company shall issue Equity Securities in accordance with Section 4.6 (c), (f), (g) or (h) of this
Agreement, any purchaser of such Equity Securities may become a party to this Agreement by executing and delivering an additional counterpart signature page to this Agreement and shall be deemed an “Investor,” a “Holder” and a
party hereunder. 
 5.12 Counterparts. This Agreement may be executed in any number of counterparts, each of which shall be an
original, but all of which together shall constitute one instrument. 
 5.13 Aggregation of Stock. All shares of Registrable
Securities held or acquired by Affiliates or persons or persons or entities under common management or control shall be aggregated together for the purpose of determining the availability of any rights under this Agreement. 
  

 22 

 5.14 Specific Performance. The parties hereto hereby declare that it is impossible to measure in
money the damages that will accrue to a party hereto or to their heirs, personal representatives, or assigns by reason of a failure to perform any of the obligations under this Agreement, that such a breach would cause irreparable harm to the
parties and agree that the terms of this Agreement shall be specifically enforceable by equitable remedies, including, but not limited to, temporary, preliminary and injunctive relief, specific performance and the right to compel the breaching party
to vote his or its capital stock of the Company in accordance with the provisions of the Agreement. If any party hereto or his heirs, personal representatives, or assigns institutes any action or proceeding to specifically enforce the provisions
hereof, any person against whom such action or proceeding is brought hereby waives the claim or defense therein that such party or such personal representative has an adequate remedy at law, and such person shall not offer in any such action or
proceeding the claim or defense that such remedy at law exists. 
 (Signature Page Follows) 
  

 23 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	CODEXIS, INC.
		
	By:	 	 /s/ Alan Shaw

	Name:	 	Alan Shaw
	Title:	 	President

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	MAXYGEN, INC.
		
	By:	 	 /s/ Russell J. Howard

	Name:	 	Russell J. Howard, Ph.D.
	Title:	 	Chief Executive Officer

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS
WHEREOF, the parties hereto have executed this FOURTH AMENDED AND
RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof.

  

			
	MALAYSIAN LIFE SCIENCES CAPITAL FUND, LTD.
		
	By:	 	Malaysian Life Sciences Capital Fund Management Company Ltd, its Manager
		
	By:	 	 /s/ Roger Wyse

	Name:	 	Dr. Roger Earl Wyse
	Title:	 	Co-Chairman

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	CMEA VENTURES LIFE SCIENCES 2000, L.P.
		
	By:	 	 /s/ Karl Handelsman

	Name:	 	Karl Handelsman
	Title:	 	Managing Director
	
	CMEA VENTURES LIFE SCIENCES 2000, CIVIL LAW PARTNERSHIP
		
	By:	 	 /s/ Karl Handelsman

	Name:	 	Karl Handelsman
	Title:	 	Managing Director

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	PEQUOT PRIVATE EQUITY FUND III, L.P.
		
	By:	 	PEQUOT CAPITAL MANAGEMENT, INC.,
its investment manager
		
	By:	 	 /s/ Carlos Rodrigues

	Name:	 	Carlos Rodrigues
	Title:	 	Chief Financial Officer
	
	PEQUOT OFFSHORE PRIVATE EQUITY PARTNERS III, L.P.
		
	By:	 	PEQUOT CAPITAL MANAGEMENT, INC.,
its investment manager
		
	By:	 	 /s/ Carlos Rodrigues

	Name:	 	Carlos Rodrigues
	Title:	 	Chief Financial Officer

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	CTTV INVESTMENTS LLC
		
	By:	 	 /s/ Don C. Riley

	Name:	 	Don C. Riley
	Title:	 	Venture Executive

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	BIOMEDICAL SCIENCES INVESTMENT FUND PTE LTD
		
	By:	 	 /s/ Chu Swee Yeok

	Name:	 	Chu Swee Yeok
	Title:	 	Director

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	ROBERT W. CRANMER-BROWN
		
	By:	 	 /s/ RW Cranmer-Brown

	Name:	 	Robert W. Cranmer-Brown

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	THE CONUS FUND, L.P.
		
	By:	 	 /s/ Andrew D. Zacks

	Name:	 	Andrew D. Zacks
	Title:	 	Managing Director, Investment Manager Conus Partners, Inc.
	
	THE CONUS FUND OFFSHORE LTD.
		
	By:	 	 /s/ Andrew D. Zacks

	Name:	 	Andrew D. Zacks
	Title:	 	Managing Director, Investment Manager Conus Partners, Inc.
	
	THE CONUS FUND (QP) L.P.
		
	By:	 	 /s/ Andrew D. Zacks

	Name:	 	Andrew D. Zacks
	Title:	 	Managing Director, Investment Manager Conus Partners, Inc.

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	EQUILON ENTERPRISES LLC DBA SHELL OIL PRODUCTS US
		
	By:	 	 /s/ David A. Sexton

	Name:	 	
	Title:	 	

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	GPSF SECURITIES INC.
		
	By:	 	 /s/ Dawn Pasquin

	Name:	 	Dawn Pasquin
	Title:	 	Vice President

  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 IN WITNESS WHEREOF, the parties hereto have executed
this FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	AFAC EQUITY, L.P.
		
	By:	 	 /s/ Brian M. Feuer

	Name:	 	Brian M. Feuer
	Title:	 	Portfolio Manager

 Address:
 McKinsey & Company, Inc. 
 55 East 52nd Street, 27th Floor 
 New York, New York, 10055 
 Office (212) 446-8029 
 Fax (646) 307-6552 
  

 SIGNATURE PAGE TO 
 FOURTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

 EXHIBIT A 
 SCHEDULE OF INVESTORS 
 Maxygen, Inc. 
 CMEA
Ventures Life Sciences 2000, L.P. 
 CMEA Ventures Life Sciences 2000, Civil Law Partnership 
 CTTV Investments LLC 
 Pequot Offshore Private Equity Partners III, L.P. 
 Pequot Private Equity Fund III, L.P. 
 Pfizer Overseas Pharmaceuticals

 Biomedical Sciences Investment Fund Pte Ltd 
 Robert W.
Cranmer-Brown 
 The Conus Fund, L.P. 
 East Hudson Inc. (BVI)

 The Conus Fund Offshore Ltd. 
 The Conus Fund (QP) L.P.

 Equilon Enterprises LLC dba Shell Oil Products US 
 GPSF
Securities Inc. 
 Malaysian Life Sciences Capital Fund, Ltd. 
 AFAC Equity, L.P. 

 EXHIBIT B 
 FORM OF INDEMNIFICATION AGREEMENTForm of Warrant to purchase shares of Common Stock

 Exhibit 4.3 
 THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “1933 ACT”), OR ANY APPLICABLE STATE SECURITIES LAWS, AND MAY NOT BE SOLD OR TRANSFERRED UNLESS SUCH SALE OR TRANSFER IS IN ACCORDANCE
WITH THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS OR SOME OTHER EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS IS AVAILABLE WITH RESPECT THERETO. 
 COMMON STOCK PURCHASE WARRANT 
  

			
	Warrant No.                     	  	Number of Shares:                     

 CODEXIS, INC. 
 Effective as of February 12, 2004 
 Void
after February 12, 2011 
 1. Issuance. This Common Stock Purchase Warrant (the “Warrant”) is issued to
                                       
  by CODEXIS, INC., a Delaware corporation (hereinafter with its successors called the “Company”). 
 2. Purchase Price; Number of Shares. The registered holder of this Warrant (the “Holder”), commencing on the date hereof, is entitled upon surrender of this Warrant with the subscription form
annexed hereto duly executed, at the principal office of the Company, to purchase from the Company at a price per share of              (the “Purchase Price”),
                     fully paid and nonassessable shares of Common Stock, $0.0001 par value, of the Company (the “Common
Stock”). 
 Until such time as this Warrant is exercised in full or expires, the Purchase Price and the securities issuable upon exercise of this
Warrant are subject to adjustment as hereinafter provided. The person or persons in whose name or names any certificate representing shares of Common Stock is issued hereunder shall be deemed to have become the holder of record of the shares
represented thereby as at the close of business on the date this Warrant is exercised with respect to such shares, whether or not the transfer books of the Company shall be closed. 
 3. Payment of Purchase Price. The Purchase Price may be paid (a) in cash or by check, or (b) by any combination of the foregoing.

 4. Net Issue Election. The Holder may elect to receive, without the payment by the Holder of any additional consideration, shares
of Common Stock equal to the value of this Warrant or any portion hereof by the surrender of this Warrant or such portion to the Company, with the net issue election notice annexed hereto duly executed, at the principal office of the Company.
Thereupon, the Company shall issue to the Holder such number of fully paid and nonassessable shares of Common Stock as is computed using the following formula: 
  

 1 

									
		 	 X
	 	 =
	 	 Y (A-B)
	 	
		 	 	 	A	 	

  

					
	where:	 	X =	 	the number of shares of Common Stock to be issued to the Holder pursuant to this Section 4.
			
		 	Y =	 	the number of shares of Common Stock covered by this Warrant in respect of which the net issue election is made pursuant to this Section 4.
			
		 	A =	 	the Fair Market Value (defined below) of one share of Common Stock as determined at the time the net issue election is made pursuant to this Section 4.
			
		 	B =	 	the Purchase Price in effect under this Warrant at the time the net issue election is made pursuant to this Section 4.

 “Fair Market Value” of a share of Common Stock as of the date that the net issue
election is made (the “Determination Date”) shall mean: 
 (i) If the net issue election is made in connection with
and contingent upon the closing of the sale of the Company’s Common Stock to the public in a public offering pursuant to a Registration Statement under the 1933 Act (a “Public Offering”), and if the Company’s Registration
Statement relating to such Public Offering (“Registration Statement”) has been declared effective by the Securities and Exchange Commission, then the initial “Price to Public” specified in the final prospectus with respect
to such offering. 
 (ii) If the net issue election is not made in connection with and contingent upon a Public Offering, then as
follows: 
 (a) If traded on a securities exchange or the Nasdaq National Market, the fair market value of the Common Stock shall be
deemed to be the average of the closing or last reported sale prices of the Common Stock on such exchange or market over the five day period ending five trading days prior to the Determination Date; 
 (b) If otherwise traded in an over-the-counter market, the fair market value of the Common Stock shall be deemed to be the average of the closing
ask prices of the Common Stock over the five day period ending five trading days prior to the Determination Date; and 
 (c) If there
is no public market for the Common Stock, then fair market value shall be determined in good faith by the Company’s Board of Directors. 
 5. Partial Exercise. This Warrant may be exercised in part, and the Holder shall be entitled to receive a new warrant, which shall be dated as of the date of this Warrant, covering the number of shares in respect of which this
Warrant shall not have been exercised. 
 6. Fractional Shares. In no event shall any fractional share of Common Stock be issued upon
any exercise of this Warrant. If, upon exercise of this Warrant in its entirety, the 

  

 2 

 
Holder would, except as provided in this Section 6, be entitled to receive a fractional share of Common Stock, then the Company shall pay cash
equal to the product of such fraction multiplied by the Common Stock’s fair market value (as determined by the Board of Directors) on the date of exercise. 
 7. Expiration Date; Automatic Exercise. This Warrant shall expire at the close of business on February 12, 2011, and shall be void thereafter. Notwithstanding the foregoing, this Warrant shall
automatically be deemed to be exercised in full pursuant to the provisions of Section 4 hereof, without any further action on behalf of the Holder, immediately prior to the time this Warrant would otherwise expire pursuant to the
preceding sentence. 
 8. Reserved Shares; Valid Issuance. The Company covenants that it will at all times from and after the date
hereof reserve and keep available such number of its authorized shares of Common Stock, free from all preemptive or similar rights therein, as will be sufficient to permit the exercise of this Warrant in full. The Company further covenants that such
shares as may be issued pursuant to such exercise will, upon issuance in accordance with the terms hereof, be duly and validly issued, fully paid and nonassessable and free from all taxes, liens and charges with respect to the issuance thereof.

 9. Stock Splits and Dividends. If after the date hereof the Company shall subdivide the Common Stock, by split-up or otherwise, or
combine the Common Stock, or issue additional shares of Common Stock in payment of a stock dividend on the Common Stock, the number of shares of Common Stock issuable on the exercise of this Warrant shall forthwith be proportionately increased in
the case of a subdivision or stock dividend, or proportionately decreased in the case of a combination, and the Purchase Price shall forthwith be proportionately decreased in the case of a subdivision or stock dividend, or proportionately increased
in the case of a combination. 
 10. Antidilution Rights. The other antidilution rights applicable to the Common Stock of the Company
are set forth in the Amended and Restated Certificate of Incorporation, as amended from time to time (the “Articles”), a true and complete copy in its current form which is attached hereto as Exhibit A. Such
rights shall not be restated, amended or modified in any manner which affects the Holder differently than the holders of Common Stock without such Holder’s prior written consent. The Company shall promptly provide the Holder hereof with any
restatement, amendment or modification to the Articles promptly after the same has been made. 
 11. Dissolutions, Liquidations, Mergers
or Changes in Control. 
 (a) Dissolution or Liquidation. In the event of the proposed dissolution or liquidation of the
Company, the Company shall notify the Holder as soon as practicable prior to the effective date of such proposed transaction. To the extent it has not been previously exercised, the Warrant will terminate immediately prior to the consummation of
such proposed action. 
 (b) Merger or Change in Control. In the event of a merger of the Company with or into another
corporation, or a Change in Control, the Warrant shall be assumed or an equivalent warrant substituted by the successor corporation or a parent or subsidiary of the 

  

 3 

 
successor corporation. In the event that the successor corporation or parent or subsidiary of the successor corporation in a merger or Change in Control
refuses to assume or substitute for the Warrant, then the Company shall notify the Holder in accordance with the provisions of Section 13 hereof of the pending Change of Control and Holder may then elect to exercise the Warrant not less
than three (3) days prior to the effective date of the Change of Control. 
 (c) “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
Securities Exchange Act of 1934, as amended (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. 
 12. Certificate of Adjustment. Whenever
the Purchase Price is adjusted, as herein provided, the Company shall promptly deliver to the Holder a certificate of the Company’s chief financial officer setting forth the Purchase Price after such adjustment and setting forth a brief
statement of the facts requiring such adjustment. 
 13. Notices of Record Date, Etc. In the event of: 
 (a) any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to
receive any dividend or other distribution, or any right to subscribe for, purchase, sell or otherwise acquire or dispose of any shares of stock of any class or any other securities or property, or to receive any other right; 
 (b) any reclassification of the capital stock of the Company, capital reorganization of the Company, consolidation or merger involving the
Company, or sale or conveyance of all or substantially all of its assets; or 
 (c) any voluntary or involuntary dissolution,
liquidation or winding-up of the Company; 
 then in each such event the Company will provide or cause to be provided to the Holder a written notice thereof.
Such notice shall be provided at least ten (10) days prior to the date specified in such notice on which any such action is to be taken. 
  

 4 

 14. Representations, Warranties and Covenants. This Warrant is issued and delivered by the Company
and accepted by each Holder on the basis of the following representations, warranties and covenants made by the Company as of the date of issuance of this initial Warrant to the initial Holder: 
 (a) The Company has all necessary authority to issue, execute and deliver this Warrant and to perform its obligations hereunder. This Warrant has
been duly authorized issued, executed and delivered by the Company and is the valid and binding obligation of the Company, enforceable against the Company in accordance with its terms. 
 (b) The shares of Common Stock issuable upon the exercise of this Warrant have been duly authorized and reserved for issuance by the Company and,
when issued in accordance with the terms hereof, will be validly issued, fully paid and nonassessable. 
 (c) The issuance, execution
and delivery of this Warrant do not, and the issuance of the shares of Common Stock upon the exercise of this Warrant in accordance with the terms hereof will not, (i) violate or contravene the Company’s Articles or by-laws, or any law,
statute, regulation, rule, judgment or order applicable to the Company, (ii) violate, contravene or result in a breach or default under any contract, agreement or instrument to which the Company is a party or by which the Company or any of its
assets are bound or (iii) require the consent or approval of or the filing of any notice or registration with any person or entity. 
 (d) As long as obligations under the                      (the “Loan Agreement”) are outstanding, the Company
will provide to the Holder the financial and other information described in the Loan Agreement. 
 (e) As of the date hereof, the
authorized capital stock of the Company consists of (i) 18,500,000 shares of Common Stock, of which 1,003,427 shares are issued and outstanding, 2,996,573 shares are reserved for issuance upon the exercise of options issued pursuant to the
Company’s 2002 Stock Plan and 46,176 shares are reserved for issuance upon the exercise of warrant, (ii) 6,000,000 shares of Series A Preferred Stock, of which 6,000,000 are issued and outstanding shares, and (iii) 8,101,102 shares of
Series B Redeemable Preferred Stock, of which 8,101,101 are issued and outstanding shares. Attached hereto as Exhibit B is a capitalization table summarizing the capitalization of the Company. At Holder’s request, not more than
once per calendar quarter, the Company will provide Holder with a current capitalization table indicating changes, if any, to the number of outstanding shares of common stock and preferred stock. 
 15. Amendment. The terms of this Warrant may be amended, modified or waived only with the written consent of the Holder and the Company.

 16. Representations and Covenants of the Holder. This Common Stock Purchase Warrant has been entered into by the Company in
reliance upon the following representations, warranties and covenants of the Holder, which by its execution hereof each Holder hereby confirms: 
 (a) Investment Purpose. The right to acquire Common Stock contained herein will be acquired for investment and not with a view to the sale or distribution of any part thereof, and the Holder has no present intention of selling or
engaging in any public distribution of the same except pursuant to a registration or exemption. 
  

 5 

 (b) Accredited Investor. Holder is an “accredited investor” within the meaning of the
Securities and Exchange Rule 501 of Regulation D, as presently in effect. 
 (c) Private Issue. The Holder understands (i) that
the Common Stock issuable upon exercise of the Holder’s rights contained herein is not registered under the 1933 Act or qualified under applicable state securities laws on the ground that the issuance contemplated by this Warrant will be exempt
from the registration and qualifications requirements thereof, and (ii) that the Company’s reliance on such exemption is predicated on the representations set forth in this Section 16. 
 (d) Financial Risk. The Holder has such knowledge and experience in financial and business matters as to be capable of evaluating the merits and
risks of its investment and has the ability to bear the economic risks of its investment. 
 17. Notices, Transfers, Etc. 

(a) Any notice or written communication required or permitted to be given to the Holder may be given by certified mail or delivered to the
Holder at the address most recently provided by the Holder to the Company. 
 (b) Subject to compliance with applicable federal and
state securities laws, this Warrant may be transferred by the Holder with respect to any or all of the shares purchasable hereunder. Upon surrender of this Warrant to the Company, together with the assignment notice annexed hereto duly executed, for
transfer of this Warrant as an entirety by the Holder, the Company shall issue a new warrant of the same denomination to the assignee. Upon surrender of this Warrant to the Company, together with the assignment hereof properly endorsed, by the
Holder for transfer with respect to a portion of the shares of Common Stock purchasable hereunder, the Company shall issue a new warrant to the assignee, in such denomination as shall be requested by the Holder hereof, and shall issue to such Holder
a new warrant covering the number of shares in respect of which this Warrant shall not have been transferred. 
 (c) In case this
Warrant shall be mutilated, lost, stolen or destroyed, the Company shall issue a new warrant of like tenor and denomination and deliver the same (i) in exchange and substitution for and upon surrender and cancellation of any mutilated Warrant,
or (ii) in lieu of any Warrant lost, stolen or destroyed, upon receipt of an affidavit of the Holder or other evidence reasonably satisfactory to the Company of the loss, theft or destruction of such Warrant. 
 18. No Impairment. The Company will not, by amendment of its Articles or through any reclassification, capital reorganization, consolidation,
merger, sale or conveyance of assets, dissolution, liquidation, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance of performance of any of the terms of this Warrant, but will at all times in good faith
assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the Holder. 
  

 6 

 19. Governing Law. The provisions and terms of this Warrant shall be governed by and construed in
accordance with the internal laws of the State of California. 
 20. Successors and Assigns. This Warrant shall be binding upon the
Company’s successors and assigns and shall inure to the benefit of the Holder’s successors, legal representatives and permitted assigns. 
 21. Business Days. If the last or appointed day for the taking of any action required of the expiration of any rights granted herein shall be a Saturday or Sunday or a legal holiday in California, then such action may be taken or
right may be exercised on the next succeeding day which is not a Saturday or Sunday or such a legal holiday. 
 22. Value. The Company
and the Holder agree that the value of this Warrant on the date of grant is $50. 
  

			
	CODEXIS, INC.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

  

 7 

 Subscription 
  

									
	To:	 	  
	 		 	Date:	 	  

 The undersigned hereby subscribes for
                     shares of Common Stock covered by this Warrant. The certificate(s) for such shares shall be issued in the name of the
undersigned or as otherwise indicated below: 
  

	
	  

	Signature
	
	  

	Name for Registration
	
	  

	Mailing Address

 Net Issue Election Notice 
  

									
	To:	 	  
	 		 	Date:	 	  

 The undersigned hereby elects under Section 4 to surrender the right to purchase
                     shares of Common Stock pursuant to this Warrant. The certificate(s) for such shares issuable upon such net issue election
shall be issued in the name of the undersigned or as otherwise indicated below: 
  

	
	  

	Signature
	
	  

	Name for Registration
	
	  

	Mailing Address

 Assignment 
 For value received _______________________________________ hereby sells, assigns and transfers unto _______________ 
 __________________________________________________________________________________________________________ 
 __________________________________________________________________________________________________________ 
 [Please print or typewrite name and
address of Assignee] 
 the within Warrant, and does hereby irrevocably constitute and appoint _________________________________________________ 

its attorney to transfer the within Warrant on the books of the within named Company with full power of substitution on the premises. 
  

			
	Dated:	 	  

	
	In the Presence of:

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00140-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00140-of-00352.parquet"}]]