TENDER AND SUPPORT AGREEMENT This TENDER AND SUPPORT AGREEMENT (this Agreement ) is entered into as of

TENDER AND SUPPORT AGREEMENT

This TENDER AND SUPPORT AGREEMENT (this Agreement ) is entered into as of August 10, 2020, by and among Ligand

Pharmaceuticals Incorporated, a Delaware corporation ( Parent ), Pelican Acquisition Sub, Inc., a Delaware corporation and wholly owned subsidiary of Parent ( Acquisition Sub ), and certain stockholders of Pfenex

Inc., a Delaware corporation (the Company ), listed on Annex A (each, a Stockholder ), each an owner of Company Common Stock.

W I T N E S S E T H:

WHEREAS, as of the date hereof, each Stockholder on Annex A is a holder of record and the beneficial owner (within

the meaning of Rule 13d-3 under the Securities Exchange Act of 1934, as amended (the Exchange Act )) of the Company Common Stock, Company Preferred Stock, and Company Options set forth

opposite such Stockholder s name (all such Company Preferred Stock, Company Common Stock, and Company Options that are outstanding as of the date hereof, together with any Company Preferred Stock, Company Common Stock, and Company Options that

are hereafter issued to or otherwise directly or indirectly acquired or beneficially owned by such Stockholder prior to the termination of this Agreement, including pursuant to any purchase right under the Company ESPP, exercise of Company Options,

acquisition by purchase, or stock dividend, distribution, split-up, recapitalization, combination or similar transaction, collectively, the Subject Securities );

WHEREAS, Parent, Acquisition Sub and the Company are entering into an Agreement and Plan of Merger of even date herewith (the Merger

Agreement ) which provides, among other things, for Acquisition Sub to commence a tender offer (the Offer ) for all of the issued and outstanding shares of Company Common Stock and following the consummation of the Offer,

the merger of Acquisition Sub with and into the Company, with the Company continuing as the surviving corporation and as a wholly owned subsidiary of Parent (the Merger ), upon the terms and subject to the conditions set forth in

the Merger Agreement;

WHEREAS, capitalized terms used but not otherwise defined herein shall have the respective meanings ascribed to

such terms in the Merger Agreement, and the other definitional and interpretative provisions set forth in 9.1 of the Merger Agreement shall apply hereto as if such provisions were set forth herein; and

WHEREAS, as a condition to the willingness of Parent and Acquisition Sub to enter into the Merger Agreement and as an inducement in

consideration therefor, each Stockholder has agreed to enter into this Agreement and tender and vote such Stockholder s Subject Securities as described herein.

this Agreement, intending to be legally bound, agree as follows:

SECTION 1. CERTAIN DEFINITIONS

For purposes of this Agreement:

(a) A Stockholder is deemed to own or to have acquired ownership of a security if

such Stockholder: (i) is the record owner of such security; or (ii) is the beneficial owner (within the meaning of Rule 13d-3 under the Exchange Act) of such security.

(b) Termination Date means the earliest of (i) the date upon which the Merger Agreement

is validly terminated in accordance with Section 8.1 of the Merger Agreement, (ii) the Effective Time, (iii) the date of entry, without the prior written consent of such Stockholder, into any amendment or modification to the Merger

Agreement or any waiver of any of the Company s rights under the Merger Agreement, in each case, that reduces

the amount, changes the form of, or otherwise reduces the consideration payable to such Stockholder under the Merger Agreement as in effect on the date hereof and (iv) the mutual written

consent of Parent, Acquisition Sub and Stockholders holding a majority of the Subject Securities.

(c) Support Period means the period commencing on (and including) the date of this Agreement and

ending on (and including) the Termination Date.

(d) A Person is deemed to have a effected a

Transfer of a security if such Person directly or indirectly: (i) sells, pledges, encumbers, grants an option with respect to, transfers or disposes of such security or any interest in such security to any Person other than

Parent or Acquisition Sub; (ii) enters into an agreement or commitment contemplating the possible sale of, pledge of, Lien of, grant of an option with respect to, transfer of or disposition of such security or any interest therein to any Person

other than Parent or Acquisition Sub; or (iii) reduces such Person s beneficial ownership of or interest in such security.

OF SUBJECT SECURITIES

2.1 Tender of Subject Securities. Unless this Agreement shall have been terminated

in accordance with its terms or the Offer expires or is terminated or withdrawn, in each case, in accordance with the terms of the Merger Agreement and the terms of the Offer and the Offer Documents, such Stockholder hereby agrees to tender the

Subject Securities or cause such Stockholder s Subject Securities to be tendered, free and clear of all Liens, into the Offer promptly following, and in any event no later than the tenth

(10th) Business Day following the commencement of the Offer and the Offer Documents being made publicly available on the SEC s EDGAR database (the Deadline ). Without

limiting the generality of the foregoing, such Stockholder shall (a) deliver pursuant to the terms of the Offer (i) a letter of transmittal with respect to such Stockholder s Subject Securities complying with the terms of the Offer

and the Offer Documents, (ii) a certificate (or affidavits of loss in lieu thereof and such other documentation that may be reasonably requested by the Payment Agent) representing such Subject Securities or an agent s message

(or such other evidence, if any, of transfer as the Payment Agent may reasonably request) in the case of Uncertificated Shares, and (iii) all other documents or instruments required to be delivered by stockholders of the Company pursuant to the

terms of the Offer and the Offer Documents or (b) instruct such Stockholder s broker or such other Person that is the holder of record of any Subject Securities beneficially owned by such Stockholder to tender such Subject Securities

pursuant to and in accordance with clause (a) of this Section 2.1 and the terms of the Offer and the Offer Documents. If such Stockholder acquires Subject Securities after the Deadline, unless this Agreement shall have

been terminated in accordance with its terms or the Offer expires or is terminated or withdrawn, in each case, in accordance with the terms of the Merger Agreement, such Stockholder shall promptly tender or cause to be tendered such Subject

Securities prior to the earlier of (x) three (3) Business Days following the date that the Stockholder acquires such Subject Securities and (y) the Expiration Time. Unless this Agreement shall have been terminated in accordance with its

terms or the Offer expires or is terminated or withdrawn, in each case, in accordance with the terms of the Merger Agreement, such Stockholder will not withdraw the Subject Securities, or cause the Subject Securities to be withdrawn, from the Offer

at any time. For purposes of this Section 2.1, Subject Securities shall not include any Company Options that are not exercised during the Support Period.

2.2 No Obligation to Exercise. Notwithstanding anything to the contrary in this Agreement, nothing in this

Agreement shall obligate any Stockholder to exercise any Company Option or any other right to acquire any shares of Company Common Stock.

2.3 Return of Subject Securities. If (a) the Offer is terminated or withdrawn by Parent and Acquisition Sub

or (b) this Agreement is terminated prior to the purchase of the Subject Securities in the Offer, Parent and Acquisition Sub shall promptly return, and shall cause any depository acting on behalf of Parent and Acquisition Sub to return, all

Subject Securities tendered by such Stockholder in the Offer to such Stockholder.

SECTION 3. VOTING OF SHARES; PROXY

3.1 Voting of Shares. For so long as Stockholder is obligated to tender any Subject Securities in accordance with

Section 2.1 and such Subject Securities have not been returned to Stockholder in accordance with Section 2.3, each Stockholder hereby irrevocably and unconditionally agrees that, during the Support

Period, at any meeting of the stockholders of the Company, however called, including any adjournment or postponement thereof, and in any action by written consent of stockholders of the Company, unless otherwise directed in writing by Parent,

Stockholder shall cause the Subject Securities (other than Company Options that are not exercised during the Support Period) to be counted as present thereat for purposes of establishing a quorum at any such meeting and to be voted:

(a) if any vote is required by the Company s stockholders pursuant to the DGCL, in favor of (i) the Merger,

the execution and delivery by the Company of the Merger Agreement and the adoption and approval of the Merger Agreement and the terms thereof; (ii) each of the other transactions contemplated thereby; (iii) any other transaction pursuant

to which Parent or any subsidiary thereof proposes to acquire the Company (whether by tender offer or merger) in which the stockholders of the Company would receive aggregate consideration per share of Company Common Stock equal to or greater than

the consideration to be received by such stockholders in the Offer and the Merger; (iv) any proposal to adjourn or postpone the meeting to a later date, if there are not sufficient votes for (A)] the approval and adoption of the Merger

Agreement and the other transactions contemplated thereby or (B) such other transactions as specified in clause (iii) above, in each case, on the date on which such meeting is held; and/or (v) in favor of any other matter necessary

for consummation of the transactions contemplated by the Merger Agreement, which is considered at any such meeting of the Company s stockholders.

(b) against (i) any action or agreement which is intended or would reasonably be expected to impede, delay,

postpone, interfere with, nullify or prevent, in each case, in any material respect, the Offer or the Merger, including, but not limited to, any other extraordinary corporate transaction, including, a merger, acquisition, sale, consolidation,

reorganization, recapitalization, extraordinary dividend or liquidation involving the Company and any Person (other than Parent, Acquisition Sub or their Affiliates), or any other proposal of any Person (other than Parent, Acquisition Sub or their

Affiliates) to acquire the Company or all or substantially all of the assets thereof; (ii) any amendment to the certificate of incorporation or bylaws of the Company; (iii) any material change to the capitalization of the Company;

(iv) any change in a majority of the directors of the Company Board; and/or (v) any action, proposal, transaction or agreement that would reasonably be expected to result in the occurrence of any condition set forth in Section 1.1(b)

to the Merger Agreement or result in a breach of any covenant, representation or warranty or any other obligation or agreement of such Stockholder under this Agreement;

(c) against any action or agreement that would reasonably be expected to result in a breach of Section 5.2 of the

Merger Agreement; and

(d) against any Acquisition Proposal and any action in furtherance of any Acquisition

Proposal, in each case, other than the Merger, the Merger Agreement, the transactions contemplated thereby and any action in furtherance thereof.

3.2 Grant of Proxy. During the Support Period, each Stockholder hereby shall revoke or cause to be revoked any

proxies that such Stockholder has heretofore granted with respect to the Subject Securities. Solely with respect to the matters described in Section 3.1, during the Support Period, such Stockholder hereby irrevocably grants

to, and appoints, Parent, the Chief Executive Officer of Parent and any designee thereof, as such Stockholder s proxy and attorney-in-fact, for and in the name,

place and stead of such Stockholder, to (i) attend any meeting of the stockholders of the Company on behalf of such Stockholder with respect to the matters set forth in Section 3.1, (ii) cause such Stockholder s

Subject Securities to be counted as present for purposes of establishing a quorum at any such meeting, and (iii) vote all Subject Securities, or grant or withhold

a consent or approval in respect of the Subject Securities, or issue instructions to the record holder of such Stockholder s Subject Securities to do any of the foregoing, in connection with

any meeting of the stockholders of the Company or any action by written consent in lieu of a meeting of the stockholders of the Company with respect to the matters set forth in Section 3.1, in a manner consistent with the

provisions of Section 3.1. During the Support Period, such Stockholder authorizes Parent, the Chief Executive Officer of Parent and any designee thereof, as proxy and attorney-in-fact, to substitute any other Person to act hereunder, to revoke any substitution and to file this proxy and any substitution or revocation with the Secretary of the Company. Such Stockholder

hereby affirms that the irrevocable proxy set forth in this Section 3.2 is given in connection with the execution of the Merger Agreement and granted in consideration of and as an inducement to Parent and Acquisition sub to

enter into the Merger Agreement, and that such irrevocable proxy is given to secure the performance of the duties of such Stockholder under this Agreement, subject to the termination of this Agreement pursuant to

Section 8.13; provided that such irrevocable proxy set forth in this Section 3.2 shall only be granted if such Stockholder fails to vote in accordance with

Section 3.1 herein. Each Stockholder hereby further affirms that the proxy set forth in this Section 3.2 is coupled with an interest, is intended to be irrevocable (and as such shall survive and

shall not be affected by the death, incapacity, mental illness or insanity of such Stockholder, as applicable), subject, however, to its automatic termination upon the termination of this Agreement pursuant to Section 8.13.

Parent agrees not to exercise the proxy granted herein for any purpose other than the purposes described in this Agreement.

3.3 Retention of Voting Power. During the Support Period, each Stockholder shall not enter into any agreement or

understanding with any Peron to vote or give instructions in a manner inconsistent with the obligations set forth in Section 3.1 of this Agreement. Such Stockholder shall retain at all times the right to vote all Subject

Securities in such Stockholder s sole discretion, on any matters other than those set forth in Section 3.1 of this Agreement that are presented for consideration to the Company s stockholders generally.

SECTION 4. WAIVER OF APPRAISAL RIGHTS

Such Stockholder hereby (a) irrevocably and unconditionally waives, and agrees not to exercise or assert, on its own behalf or on behalf

of any other holder of Company Common Stock, any rights of appraisal, any dissenters rights or any similar rights relating to the Merger that such Stockholder may have by virtue of, or with respect to, the Subject Securities and

(b) agrees not to commence or join in, and agrees to take all actions necessary to opt out of any class in any class action with respect to, any claim, derivative or otherwise, against Parent, Acquisition Sub, the Company or any of their

respective successors (x) challenging the validity of, or seeking to enjoin the operation of, any provision of this Agreement or (y) alleging breach of any fiduciary duty of any Person in connection with the negotiation and entry into the

SECTION 5. REPRESENTATIONS AND WARRANTIES OF STOCKHOLDER

Each Stockholder hereby represents and warrants (severally and not jointly) to each of Parent and Acquisition Sub as follows:

5.1 Authorization, etc. Such Stockholder has the right, authority and legal capacity to execute and deliver this

Agreement and to perform such Stockholder s obligations hereunder. This Agreement has been executed and delivered by such Stockholder and, assuming due authorization, execution and delivery by Parent and Acquisition Sub, constitutes the legal,