Document:

Warrant Exchange Agreement, dated as of May 17, 2009

 EXHIBIT 4.1 
 WARRANT EXCHANGE AGREEMENT 
 This Warrant Exchange Agreement (this “Agreement”) is
dated as of May 17, 2009, among Cell Genesys, Inc. a Delaware corporation (the “Company”), and Capital Ventures International (the “Holder”). 
 WHEREAS, the Holder is the holder of a Warrant, dated as of May 14, 2008, exercisable for 8,530,806 shares of the Company’s Common Stock
at an exercise price of $10.00 per share (the “Existing Warrant”). 
 WHEREAS, in connection with a Fundamental
Change (as defined in the Existing Warrant), Holder may be entitled to receive a cash payment equal to the Black Scholes Value (as defined in the Existing Warrant) at Holder’s election by surrendering the unexercised portion of the Existing
Warrant. 
 WHEREAS, the Black Scholes Value is subject to substantial fluctuation and may limit the Company’s ability to pursue
a Fundamental Transaction at any point in the future. 
 WHEREAS, subject to the terms and conditions set forth in this Agreement and
pursuant to Section 3(a)(9) of the Securities Act of 1933, as amended (the “Securities Act”), (i) the Company desires to exchange the Existing Warrant with the Holder, and the Holder desires to exchange the Existing
Warrant with the Company, for the Initial Exchanged Shares (as defined below) and the Remainder Warrant (as defined below), and (ii) each of the Company and the Holder shall have the right or obligation, as applicable, during the periods set
forth below, to exchange the Remainder Warrant, for the applicable consideration specified below. 
 NOW, THEREFORE, in consideration
of the mutual covenants contained in this Agreement, and for other good and valuable consideration the receipt and adequacy of which are hereby acknowledged, the Company and the Holder agree as follows (with capitalized terms used here in and not
otherwise defined having the meanings set forth in the Remainder Warrant): 
 1. Initial Exchange of the Existing Warrant for the New
Warrant. On the terms and subject to the conditions set forth herein, as of the date hereof (the “Closing”), the Holder hereby sells, assigns, delivers and transfers to the Company all of its right, title and interest in
and to warrants to purchase 8,530,806 shares of Common Stock (the “Initial Exchange”) in exchange for 4,000,000 freely tradable shares of the Company’s Common Stock (the “Initial Exchanged Shares”) and a new
warrant to purchase 4,265,403 shares of the Company’s Common Stock (the “Remainder Warrant”), substantially in the form of Exhibit A hereto. 
 2. Company Call Right and Purchase Obligation. 
 (a) In the event that during the period beginning on the date hereof and ending one hundred twenty (120) days from the date hereof
(the “Company Call Period”), the Company publicly announces that it has entered into a definitive agreement relating to a Fundamental Transaction (as defined in the Existing Warrant) (such public announcement being referred to as a
“Call Event”), the Company shall be obligated to purchase from the Holder, and 

 
the Holder shall be obligated to sell, assign, deliver and transfer to the Company all but not less than all, of the remaining portion of the Remainder
Warrant for a purchase price of $2,000,000 in cash (the “Company Call Consideration”) upon consummation of the Fundamental Transaction (the “Fundamental Transaction Closing Date”). In the event that the Holder has
not exchanged any of the Remainder Warrant prior to the payment of the Company Call Consideration, the aggregate Company Call Consideration shall be equal to $2,000,000 in cash. Upon the occurrence of a Call Event during the Company Call Period, the
Company Call Period shall be extended until the Fundamental Transaction Closing Date. The Company will provide written notice to the Holder of (i) the occurrence of a Call Event (the “Call Event Notice”) within one
(1) Business Day (as defined in the Remainder Warrant) following the occurrence of a Call Event and (ii) the anticipated Fundamental Transaction Closing Date; such notice to be provided at least fifteen (15) Business Days prior to the
Fundamental Transaction Closing Date. The Holder shall continue to have the right to exchange all or any portion of the Remainder Warrant pursuant to Section 3 below, and the portion of the Remainder Warrant not so exchanged shall remain
outstanding, in each case, until payment in full of the Company Call Consideration; provided, however, that in the event that the Company specifies a fixed Fundamental Transaction Closing Date in the Call Notice, which date is not less than fifteen
(15) Business Days from the Holder’s receipt of the Call Notice; the Holder shall not be permitted to exchange all or any portion of the Remainder Warrant during the period beginning five (5) Business Days prior to the Fundamental
Transaction Closing Date specified in the Call Notice (the “Exchange Limitation Period”). In the event that Fundamental Transaction Closing Date does not occur prior to the expiration of the Exchange Limitation Period, the Holder
shall thereafter continue to have the right to exchange all or any unexercised portion of the Remainder Warrant until receipt of payment in full of the Company Call Consideration. The failure of the Company to send the Call Notice within the
specified time frames shall not affect the Company’s obligation to purchase the Remainder Warrant from the Holder for the Company Call Consideration upon the consummation of the Fundamental Transaction. 
 (b) To the extent not previously exchanged by the Holder, on the Fundamental Transaction Closing Date (even if such date is later, or with
the consent of the Holder, earlier than the anticipated Fundamental Transaction Closing Date specified in the Call Notice), or such earlier time as may be agreed by the parties, the Company shall pay to the Holder the Company Call Consideration by
wire transfer of immediately available funds in accordance with the instructions set forth on Schedule A hereto. Within three (3) Business Days following receipt of the Company Call Consideration, the Holder shall remit the Remainder
Warrant to the Company for cancellation. 
 3. Holder Remainder Warrant Exchange Right. 
 (a) For a period beginning on the date hereof and ending on the expiration of the Company Call Period (as the same may be extended
pursuant to Section 2(a) hereof), from time to time the Holder shall have the right, by providing written notice to the Company (the “Put Notice”, and the date of such notice being the “Put Notice Date”) to put
the Remainder Warrant to the Company to be exchanged for a total number of freely tradable shares of the Company’s Common Stock equal to (i) $2,000,000, divided by (ii) the Market Price (as defined below) of the Company’s Common
Stock on the Put Notice Date (the “Subsequent Exchanged Shares”, and together with the Initial Exchanged Shares, the “Exchanged Shares”). The Holder 

  

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shall have the right to partially exchange the Remainder Warrant at multiple increments and in the event that the Holder elects to exchange less than all the
Remainder Warrant on any Put Notice Date, the number of Subsequent Exchanged Shares to be delivered in connection with any such exchange shall be adjusted proportionately and remaining portion of the Remainder Warrant not so exchanged shall remain
outstanding and continue to be subject to future exchange pursuant to this Section 3 and the Company call right and purchase obligation pursuant to Section 2 of this Agreement. Any Put Notice provided by the Holder shall provide for the
exchange of not less than the lesser of (x) 500,000 shares of the Company’s Common Stock then underlying the Remainder Warrant and (y) all shares of the Company’s Common Stock then underlying the Remainder Warrant then
outstanding, at any one time. Provided that the Equity Conditions (as defined below) are satisfied from the date of the Call Notice until the beginning of the Exchange Limitation Period, the Holder agrees to exchange an amount of the Remainder
Warrant such that the Company Call Consideration payable to the Holder pursuant to Section 2(a) hereof shall not exceed $1,500,000. For purposes hereof, “Market Price” shall mean the arithmetic average of the Weighted Average
Price (as defined in the Existing Warrant) for the Company’s Common Stock on each of the five (5) trading days ending on the date immediately preceding the Put Notice Date, but in no event greater than (A) the Weighted Average Price
of Common Stock on the day immediately preceding the Put Notice Date or (B) $0.50 per share. For purposes hereof, “Equity Conditions” shall mean (i) all Subsequent Exchanged Shares shall be eligible for sale without
restriction and without the need for registration under any applicable federal or state securities laws; (ii) the Common Stock is listed or designated for quotation on the principal market on which the Company’s Common Stock is then listed
or quoted (the”Principal Market”), (iii) the Weighted Average Price of the Common Stock is not less than $0.15, (iv) the minimum aggregate dollar volume (i.e. the Weighted Average Price multiplied by the daily volume) of
the Common Stock is not less than $350,000 and (v) the Company shall not have previously failed to timely deliver any Subsequent Exchanged Shares. 
 (b) On or before the first (1st) Business Day following the date on which the Company has received the Put Notice, the Company shall transmit by facsimile an acknowledgment of confirmation of receipt of the
Put Notice to the Holder and the Company’s transfer agent (the “Transfer Agent”). On or before the third (3rd) Business
Day following the date on which the Company has received the Put Notice (the “Share Delivery Date”), the Company shall credit such aggregate number of Subsequent Exchanged Shares to which the Holder is entitled to the Holder’s
balance account with DTC in accordance with the instructions on Schedule A hereto. If by the third (3rd) trading day from the Put Notice
Date the Company shall fail for any reason or for no reason to issue to the Holder the Subsequent Exchanged Shares by electronic delivery at the applicable balance account at DTC, and if on or after such Trading Day the Holder purchases (in an open
market transaction or otherwise) shares of Common Stock to deliver in satisfaction of a sale by the Holder of such Subsequent Exchanged Shares that the Holder anticipated receiving from the Company (a “Buy-In”), then the Company
shall, within three (3) Business Days after the Holder’s request and in the Holder’s discretion, either (i) pay cash to the Holder in an amount equal to the holder’s total purchase price (including brokerage commissions, if
any) for the shares of Common Stock so purchased (the “Buy-In Price”), at which point the Company’s obligation to deliver the Subsequent Exchanged Shares shall terminate, or (ii) promptly honor its obligation to deliver to
the Holder such Subsequent Exchanged Shares as provided above and pay cash to the Holder in an amount equal to the excess (if any) of the Buy-In Price over the product of (A) such number of shares of Common Stock, times (B) the lesser of
(i) Closing Bid Price on the Put Notice Date and (ii) the Closing Bid Price on the Share Delivery Date. 
  

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 4. Closing Deliveries. On the date hereof, the Company shall deliver to the Holder
(a) the Initial Exchanged Shares by electronic delivery at the applicable balance account at the Depositary Trust Company (“DTC”) in accordance with the instructions set forth on Schedule A hereto and (b) the
Remainder Warrant. The Holder shall deliver the Existing Warrant to the Company within three (3) Business Days from of the Closing. 
 5. Representations and Warranties. 
 (a) Mutual Representations and
Warranties. Each party hereto hereby makes the following representations and warranties to the other party hereto: 
 i. It is duly organized and validly existing, in good standing under the laws of its jurisdiction of incorporation or organization. 
 ii. (A) It has full power and authority to enter into this Agreement and to consummate the transactions contemplated hereby, and (B) the person who has executed this Agreement on its behalf is duly authorized to
do so and thereby bind the party on whose behalf he or she is purporting to act. 
 iii. This Agreement is its valid and
binding agreement, enforceable against it in accordance with its terms, except as may be limited by bankruptcy, insolvency, reorganization, moratorium or similar laws relating to or affecting creditors’ rights generally (including, without
limitation, fraudulent conveyance laws) and by general principles of equity, including, without limitation, concepts of materiality, reasonableness, good faith and fair dealing, and the possible unavailability of specific performance or injunctive
relief, regardless of whatever consideration in a proceeding in equity or at law. 
 iv. Neither the execution and delivery of
this Agreement, nor the consummation of the transactions contemplated hereby, will violate, result in a breach of any of the terms or provisions of, constitute a default (or any event that, with the giving of notice or the passage of time or both
would constitute a default) under, accelerate any obligations under, or conflict with, (i) its charter, articles or certificate of incorporation, partnership agreement or bylaws (or other organizational documents), if applicable, or any
agreement, indenture or other instrument to which it is a party or by which it or its properties are bound, (ii) any judgment, decree, order or award or any court, governmental body or arbitrator to which it is subject or (iii) any law,
rule or regulation applicable to it. 
 v. Neither party is consummating this Exchange “on the basis
of” (as defined in Rule 10b5-1 of the Exchange Act) any material, non-public information about the Company; provided, however, that the Holder acknowledges that, as disclosed in the Company’s filings with the SEC, the Company is
currently exploring its strategic alternatives, including without limitation, merger with or acquisition by another company and liquidation. The Holder further acknowledges that the ability of the Company to enter into or close a strategic
transaction, and the timing of any such transaction are uncertain 
  

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 (b) Representations, Warranties and Covenants of the Company. The Company hereby
represents, warrants and covenants to the Holder that: 
 i. The Exchanged Shares are duly and validly authorized and when
issued in accordance with the terms hereof, will be fully paid and nonassessable, and the Holder will acquire such Exchanged Shares free and clear of any liens, encumbrances, pledges, security interest or other restrictions or claims of third
parties, except, in each case, as may result from any actions or failures of Holder. Other than such filings as may be required to be made with the Principle Market, the Company is not required to obtain any consent, authorization or order of, or
make any filing or registration with, any court, governmental agency or any regulatory or self-regulatory agency or any other person, including, without limitation, any other security holders of the Company, in order for it to execute, deliver or
perform any of its obligations under or contemplated by this Agreement. All consents, authorizations, orders, filings and registrations which the Company is required to obtain pursuant to the preceding sentence have been obtained or effected on or
prior to the date hereof. The Company is not in violation of the listing requirements of the Principal Market and has no knowledge of any facts that would reasonably lead to delisting or suspension of the Common Stock prior to December 31,
2009. 
 ii. The exchange of the Warrant for the Exchanged Shares is being consummated pursuant to Sections 3(a)(9) and Rule
149 of the Securities Act. The Company has not engaged in any general solicitation or engaged or agreed to compensate any broker or agent in connection with the transactions contemplated by this Agreement. None of the Company, its subsidiaries, any
of their affiliates, and any person acting on their behalf has, directly or indirectly, made any offers or sales of any security or solicited any offers to buy any security, under circumstances that would require registration of any of the Exchanged
Shares under the Securities Act or cause this Exchange to be integrated with prior offerings by the Company for purposes of Securities Act or any applicable stockholder approval provisions, including, without limitation, under the rules and
regulations of any exchange or automated quotation system on which any of the securities of the Company are listed or designated. None of the Company, its subsidiaries, their affiliates and any person acting on their behalf will take any action or
steps referred to in the preceding sentence that would require registration of any of the Exchanged Shares under the Securities Act or cause the Exchange of the Exchanged Shares to be integrated with other offerings. 
 iii. The Company is current in its filings of all reports, schedules, forms, statements and other documents required to be filed by it
with the SEC pursuant to the reporting requirements of the Securities Exchange Act of 1934, as amended. Upon issuance, the Exchanged Shares are eligible for sale by the Holder to the public without registration under the Securities Act. 

iv. The Company or its counsel have previously or the Company will or will cause its counsel to, in connection with the execution of
this Agreement, deliver to the transfer agent any required legal opinions, if any, or documentation necessary to effect the delivery of the freely tradable Exchanged Shares to the Holder as required by this Agreement. The Company shall be
responsible for the fees of its transfer agent and all DTC fees associated with the issuance of the Exchanged Shares hereunder. 
  

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 v. The Company confirms that neither it nor any other person acting on its behalf has
provided the Holder or their agent or counsel with any information that constitutes or could reasonably be expected to constitute material, nonpublic information about the Company. 
 vi. The Company agrees that before the market open on May 18, 2009, the Company shall file a Current Report on Form 8-K with the
Securities and Exchange Commission announcing the Exchange and disclosing all material information regarding the Exchange in connection with the Closing. 
 vii. The Company shall not consummate a Fundamental Transaction unless (A) the Company shall have previously paid to the Holder the Company Call Consideration, or (B) the Successor Entity (which may be the
Company, in the event the surviving entity in any such Fundamental Transaction) assumes this Agreement, including, without limitation, the obligation to make payment of the Company Call Consideration in accordance with the provisions of this
Agreement. 
 (c) Representations, Warranties and Covenants of the Holder. The Holder hereby represents and warrants to
the Company that the Holder: (i) is the sole legal record, and beneficial owner of the Warrant free and clear of any liens, encumbrances, pledges, security interests or other restrictions or claims of third parties, (ii) is an
“accredited investor” (as defined in Regulation D under the Securities Act) and is acquiring the Exchanged Shares for its own account and not with a view to any distribution thereof except in compliance with the Securities Act;
(iii) is not an “affiliate” of the Company (as defined in Rule 144), (iv) has made all investigations that it deems necessary or desirable in connection with the transactions contemplated by this Agreement and has had an
opportunity to ask questions of and receive answers from the Company, and (v) has such knowledge and experience in financial and business matters as to be capable of evaluating the merits and risks of its investment in the Exchanged Shares. It
is currently the Holder’s intention during the Company Call Period to vote any Exchanged Shares it may own in favor of any Fundamental Transaction. 
 (d) All representations, warranties and agreements of each party hereto shall survive the Closing. 
 6. Exchange Limitations. 
 (a) Beneficial Ownership. The Company shall not effect the
exchange any of the Remainder Warrant, and the Holder shall not have the right to exchange any of the Remainder Warrant, to the extent that after giving effect to such exercise, such Person (together with such Person’s affiliates) would
beneficially own (as determined in accordance with this paragraph) in excess of 9.99% (the “Maximum Percentage”) of the shares of the Company’s Common Stock outstanding immediately after giving effect to such exchange. For
purposes of the foregoing sentence, the aggregate number of shares of the Company’s Common Stock beneficially owned by such Person and its affiliates shall include the number of shares of the Company’s Common Stock issuable upon exchange
of the Remainder Warrant with respect to which the determination of such sentence is being made, but shall exclude shares of the Company’s Common Stock which would be issuable upon (i) exchange of the remaining, unexchanged portion of the
Remainder Warrant beneficially owned by such Person and its 

  

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affiliates and (ii) exercise or conversion of the unexercised or unconverted portion of any other securities of the Company beneficially owned by such
Person and its affiliates (including, without limitation, any convertible notes or convertible preferred stock or warrants) subject to a limitation on conversion or exercise analogous to the limitation contained herein. Except as set forth in the
preceding sentence, for purposes of this paragraph, beneficial ownership shall be calculated in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended. For purposes of this Agreement, in determining the number of
outstanding shares of Common Stock, the Holder may rely on the number of outstanding shares of Common Stock as reflected in (1) the Company’s most recent Form 10-K, Form 10-Q, Current Report on Form 8-K or other public filing with the
Securities and Exchange Commission, as the case may be, (2) a more recent public announcement by the Company or (3) any other notice by the Company or the Transfer Agent setting forth the number of shares of Common Stock outstanding. For
any reason at any time, upon the written or oral request of the Holder, the Company shall within two (2) Business Days confirm orally and in writing to the Holder the number of shares of Common Stock then outstanding. In any case, the number of
outstanding shares of Common Stock shall be determined after giving effect to the exercise or exchange of securities of the Company, including the Warrant, by the Holder and its affiliates since the date as of which such number of outstanding shares
of Common Stock was reported. By written notice to the Company, the Holder may from time to time increase or decrease the Maximum Percentage to any other percentage not in excess of 9.99% specified in such notice; provided that (i) any
such increase will not be effective until the sixty-first (61st) day after such notice is delivered to the Company, and (ii) any such
increase or decrease will apply only to the Holder. The provisions of this paragraph shall be construed and implemented in a manner otherwise than in strict conformity with the terms of this Section 6(a) to correct this paragraph (or any
portion hereof) which may be defective or inconsistent with the intended beneficial ownership limitation herein contained or to make changes or supplements necessary or desirable to properly give effect to such limitation. 
 (b) Principal Market Regulation. The Company shall not be obligated to issue any Subsequent Exchanged Shares upon the exchange of
any of the Remainder Warrant and the Holder shall not have the right to receive upon exchange of any of the Remainder Warrant any Subsequent Exchanged Shares, if the issuance of such Subsequent Exchanged Shares would exceed the aggregate number of
shares of Common Stock which the Company may issue upon exchange of the Warrant without breaching the Company’s obligations under the rules or regulations of the Principal Market (the “Exchange Cap”), except that such
limitation shall not apply in the event that the Company (A) obtains the approval of its stockholders as required by the applicable rules of the Principal Market for issuances of shares of Common Stock in excess of such amount or
(B) obtains a written opinion from outside counsel to the Company that such approval is not required, which opinion shall be reasonably satisfactory to the Holders. Until such approval or written opinion is obtained, no Holder shall be issued a
number of Subsequent Exchanged Shares in an amount greater than the Exchange Cap. 
 7. Miscellaneous. 
 (a) Further Assurances. Each party hereto shall promptly execute and deliver such further agreements and instruments, and take such
further actions, as the other party may reasonably request in order to carry out the purpose and intent of this Agreement. 
  

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 (b) Notices. All notices, requests, demands and other communications hereunder
shall be in writing and shall be deemed given if delivered personally or by facsimile transmission (with subsequent letter confirmation by mail) or two days after being mailed by certified or registered mail, postage prepaid, return receipt
requested, to the parties, their successors in interest or their assignees at the following addresses, or at such other addresses as the parties may designate by written notice in the manner aforesaid: 
 If to the Holder: 
 Capital Ventures International 
 c/o Heights Capital Management, Inc. 
 101 California Street, Suite 3250 
 San Francisco, CA 94111 
 Attn: Martin Kobinger 
 Fax: 415-403-6525 
 If to the Company: 
 Cell Genesys, Inc. 
 500 Forbes Blvd. 
 South San Francisco, CA 94080 
 Attention: Chief Financial Officer 
 Facsimile: 650-266-3000 
 (c) Governing Law; Jurisdiction; Jury Trial. All questions concerning the construction, validity, enforcement and interpretation of this Agreement shall be governed by the internal laws of the State of New
York, without giving effect to any choice of law or conflict of law provision or rule (whether of the State of New York or any other jurisdictions) that would cause the application of the laws of any jurisdictions other than the State of New York.
Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts sitting in the City of New York, Borough of Manhattan for the adjudication of any dispute hereunder or in connection herewith or with any transaction
contemplated hereby or discussed herein, and hereby irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not personally subject to the jurisdiction of any such court, that such suit, action or
proceeding is brought in an inconvenient forum or that the venue of such suit, action or proceeding is improper. Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or
proceeding by mailing a copy thereof to such party at the address for such notices to it under this Agreement and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be
deemed to limit in any way any right to serve process in any manner permitted by law. EACH PARTY HEREBY IRREVOCABLY WAIVES ANY RIGHT IT MAY HAVE, AND AGREES NOT TO REQUEST, A JURY TRIAL FOR THE ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN
CONNECTION WITH OR ARISING OUT OF THIS AGREEMENT OR ANY TRANSACTION CONTEMPLATED HEREBY.  
  

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 (d) Disputes. In the case of a dispute as to the determination of the Market Price
or the arithmetic calculation of the Subsequent Exchanged Shares, the Company shall promptly issue to the Holder the number of Subsequent Exchanged Shares that are not disputed. In the case of a dispute as to the determination of the Market Price or
the arithmetic calculation of the Subsequent Exchanged Shares, the Company shall submit the disputed determinations or arithmetic calculations via facsimile within two (2) Business Days of receipt of the Put Notice giving rise to such dispute,
as the case may be, to the Holder. If the Holder and the Company are unable to agree upon such determination or calculation of the Market Price or the Subsequent Exchanged Shares within three Business Days of such disputed determination or
arithmetic calculation being submitted to the Holder, then the Company shall, within two (2) Business Days submit via facsimile the disputed determination of the Market Price to an independent, reputable investment bank selected by the Company
and approved by the Holder. The Company shall cause at its expense the investment bank to perform the determinations or calculations and notify the Company and the Holder of the results no later than ten Business Days from the time it receives the
disputed determinations or calculations. Such investment bank’s determination shall be binding upon all parties absent demonstrable error. 
 (e) Counterparts. This Agreement may be executed in several counterparts, each of which shall be deemed an original, but all of which shall constitute one and the same instrument. 
 (f) Complete Agreement; Amendments. This Agreement is an integrated agreement containing the entire agreement between the parties
hereto with respect to the subject matter hereof and shall supersede all previous, and all contemporaneous oral or written negotiations, commitments or understandings. No provision of this Agreement may be amended other than by an instrument in
writing signed by the Company and the Holder. 
 (g) Expenses. Except as specifically set forth herein, each party
hereto shall bear its own costs and expenses, including, without limitation, attorneys’ fees, incurred in connection with this Agreement and the transactions contemplated hereby. 
 (h) Remedies. The Holder and the Company shall be entitled to enforce their respective rights under this Agreement specifically
(without posting a bond or other security), to recover damages by reason of any breach of any provision of this Agreement and to exercise all other rights granted by law. Furthermore, recognizes that in the event that it fails to perform, observe,
or discharge any or all of its obligations under this Agreement, any remedy at law may prove to be inadequate relief to the Holder or the Company. The Company and the Holder therefore agree that the other party shall be entitled to seek temporary
and permanent injunctive relief in any such case without the necessity of proving actual damages and without posting a bond or other security. 
 (i) Payment Set Aside. To the extent that the Company makes a payment or payments to the Holder hereunder or the Holder enforces or exercises its rights hereunder or thereunder, and such payment or payments or
the proceeds of such enforcement or exercise or any part thereof are subsequently invalidated, declared to be fraudulent or preferential, set aside, recovered from, disgorged by or are required to be refunded, repaid or otherwise restored to the
Company, a trustee, receiver or any other Person under any law (including, without limitation, any bankruptcy law, foreign, state or federal law, common law or equitable cause of action), then to the extent of any such restoration the obligation or
part thereof originally intended to be satisfied shall be revived and continued in full force and effect as if such payment had not been made or such enforcement or setoff had not occurred. 
 [Signature Page Follows] 
  

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 IN WITNESS WHEREOF, each of the Holder and the Company have caused its respective signature page
to this Agreement to be duly executed as of the date first written above. 
  

			
	CELL GENESYS, INC.
		
	By:	 	/s/    Stephen A. Sherwin
		
	Name:	 	Stephen A. Sherwin
		
	Title:	 	Chairman and CEO
	
	CAPITAL VENTURES INTERNATIONAL
		
	By:	 	/s/    Martin Kobinger
		
	Name:	 	Martin Kobinger
		
	Title:	 	Investment Manager

  

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 Schedule A 
 DTC INSTRUCTIONS 
 TIN# 51-0395477 

	Address:	Capital Ventures International c/o Heights Capital Management Inc. 

	    	101 California St. 

	    	Suite 3250 

	    	San Francisco, CA 94111 

 Broker: Merrill Lynch 
 Broker Account #: 2US01600 
 DTC# 5198 (fop) 
 Contact at Merrill Lynch: 
 Krista Santangelo-Gough 
 (212) 670-3447 
 Krista_Santangelo@ml.com 
 WIRE INSTRUCTIONS 
 Chase Manhattan Bank, New York 
 Swift: CHASUS33 
 ABA: 021 000 021 
 A/c Merrill Lynch International EFG 
 A/c number: 066612489 
  

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 APPENDIX A 
 Form of WarrantAmended and Restated Warrant to Purchase Common Stock, dated as of May 17, 2009

 EXHIBIT 4.2 
 CELL GENESYS, INC. 
 AMENDED AND RESTATED
WARRANT TO PURCHASE COMMON STOCK 
 Warrant No.: 1A 

Number of Shares of Common Stock: 4,265,403 
 Date of Original Issuance:
May 14, 2008 (“Issuance Date”) 
 Cell Genesys, Inc., a Delaware corporation (the “Company”), hereby
certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Capital Ventures International, the registered holder hereof or its permitted assigns (the “Holder”), is entitled,
subject to the terms set forth below, to purchase from the Company, at the Exercise Price (as defined below) then in effect, upon surrender of this Amended and Restated Warrant to Purchase Common Stock (including any Warrants to Purchase Common
Stock issued in exchange, transfer or replacement hereof, the or this “Warrant”), at any time or times on or after the date six (6) months from the date hereof (the “Exercisability Date”), but not after 11:59
p.m., New York time, on the Expiration Date (as defined below), Four Million Two Hundred Sixty-Five Thousand Four Hundred and Three (4,265,403) fully paid nonassessable shares of Common Stock (as defined below) (the “Warrant
Shares”). Except as otherwise defined herein, capitalized terms in this Warrant shall have the meanings set forth in Section 15. This Warrant is the Warrant to purchase Common Stock issued pursuant to (i) Section 2 of that
certain Subscription Agreement (the “Subscription Agreement”), dated as of May 9, 2008 (the “Subscription Date”), by and between the Company and the Holder (the “Subscription Agreement”) and
(ii) the Company’s Registration Statement on Form S-3 (File number 333-142482) (the “Registration Statement”), such Warrant as amended and restated on May 18, 2009. 
 1. EXERCISE OF WARRANT. 
 (a) Mechanics of Exercise. Subject to the terms and conditions hereof, this
Warrant may be exercised by the Holder on any day on or after the Exercisability Date, in whole or in part, by delivery of a written notice, in the form attached hereto as Exhibit A (the “Exercise Notice”), of the
Holder’s election to exercise this Warrant. The Holder shall not be required to deliver the original Warrant in order to effect an exercise hereunder. Execution and delivery of the Exercise Notice with respect to less than all of the Warrant
Shares shall have the same effect as cancellation of the original Warrant and issuance of a new Warrant evidencing the right to purchase the remaining number of Warrant Shares. On or before the second (2nd) Business Day following the date on which the Company has received each of the Exercise Notice (the “Exercise Delivery Documents”), the Company shall transmit
by facsimile an acknowledgment of confirmation of receipt of the Exercise Delivery Documents to the Holder and the Company’s transfer agent (the “Transfer Agent”). On or before the third (3rd) Business Day following the date on which the Company has received all of the Exercise Delivery Documents (the “Share Delivery Date”), the Company shall
(X) provided that the Transfer Agent is participating in The Depository Trust Company (“DTC”) Fast Automated Securities 

 
Transfer Program, upon the request of the Holder, credit such aggregate number of Warrant Shares to which the Holder is entitled pursuant to such exercise to
the Holder’s or its designee’s balance account with DTC through its Deposit Withdrawal Agent Commission system, or (Y) if the Transfer Agent is not participating in the DTC Fast Automated Securities Transfer Program, issue and
dispatch by overnight courier to the address as specified in the Exercise Notice, a certificate, registered in the Company’s share register in the name of the Holder or its designee, for the number of shares of Common Stock to which the Holder
is entitled pursuant to such exercise. Upon delivery of the Exercise Delivery Documents, the Holder shall be deemed for all corporate purposes to have become the holder of record of the Warrant Shares with respect to which this Warrant has been
exercised, irrespective of the date such Warrant Shares are credited to the Holder’s DTC account or the date of delivery of the certificates evidencing such Warrant Shares, as the case may be. If this Warrant is submitted in connection with any
exercise pursuant to this Section 1(a) and the number of Warrant Shares represented by this Warrant submitted for exercise is greater than the number of Warrant Shares being acquired upon an exercise, then the Company shall as soon as
practicable and in no event later than three Business Days after any exercise and at its own expense, issue a new Warrant (in accordance with Section 7(d)) representing the right to purchase the number of Warrant Shares purchasable immediately
prior to such exercise under this Warrant, less the number of Warrant Shares with respect to which this Warrant is exercised. No fractional shares of Common Stock are to be issued upon the exercise of this Warrant, but rather the number of shares of
Common Stock to be issued shall be rounded up to the nearest whole number. The Company shall pay any and all taxes which may be payable with respect to the issuance and delivery of Warrant Shares upon exercise of this Warrant. 
 (b) Exercise Price. For purposes of this Warrant, “Exercise Price” means $10.00, subject to adjustment as provided
herein. 
 (c) Company’s Failure to Timely Deliver Securities. If the Company shall fail for any reason or for no
reason to issue to the Holder within three (3) Business Days of receipt of the Exercise Delivery Documents in compliance with the terms of this Section 1, a certificate for the number of shares of Common Stock to which the Holder is
entitled and register such shares of Common Stock on the Company’s share register or to credit the Holder’s balance account with DTC for such number of shares of Common Stock to which the Holder is entitled upon the Holder’s exercise
of this Warrant, and if on or after such Trading Day the Holder purchases (in an open market transaction or otherwise) shares of Common Stock to deliver in satisfaction of a sale by the Holder of shares of Common Stock issuable upon such exercise
that the Holder anticipated receiving from the Company (a “Buy-In”), then the Company shall, within three (3) Business Days after the Holder’s request and in the Holder’s discretion, either (i) pay cash to the
Holder in an amount equal to the Holder’s total purchase price (including brokerage commissions, if any) for the shares of Common Stock so purchased (the “Buy-In Price”), at which point the Company’s obligation to deliver
such certificate (and to issue such Warrant Shares) shall terminate, or (ii) promptly honor its obligation to deliver to the Holder a certificate or certificates representing such Warrant Shares and pay cash to the Holder in an amount equal to
the excess (if any) of the Buy-In Price over the product of (A) such number of shares of Common Stock, times (B) the Closing Bid Price on the date of exercise. 
  

 2 

 (d) Cashless Exercise. Upon exercise of this Warrant, in whole or in part, the
Holder shall receive upon such exercise the “Net Number” of shares of Common Stock determined according to the following formula (a “Cashless Exercise”): 
  

							
		  	Net Number =	 	(A x B) - (A x C)	  	
		  		 	B	  	

 For purposes of the foregoing formula: 
  

					
		 	A=	  	the total number of shares with respect to which this Warrant is then being exercised.
			
		 	B=	  	the arithmetic average of the Closing Sale Prices of the shares of Common Stock for the five (5) consecutive Trading Days ending on the date immediately preceding the date of the
Exercise Notice.
			
		 	C=	  	the Exercise Price then in effect for the applicable Warrant Shares at the time of such exercise.

 (e) Rule 144. For purposes of Rule 144(d) promulgated under the Securities
Act, as in effect on the date hereof, it is intended that the Warrant Shares issued in a Cashless Exercise shall be deemed to have been acquired by the Holder, and the holding period for the Warrant Shares shall be deemed to have commenced, on the
date this Warrant was originally issued pursuant to the Subscription Agreement. 
 (f) Disputes. In the case of a
dispute as to the determination of the Exercise Price or the arithmetic calculation of the Warrant Shares, the Company shall promptly issue to the Holder the number of Warrant Shares that are not disputed. 
 (g) Beneficial Ownership. The Company shall not effect the exercise of this Warrant, and the Holder shall not have the right to
exercise this Warrant, to the extent that after giving effect to such exercise, such Person (together with such Person’s affiliates) would beneficially own in excess of 9.99% (the “Maximum Percentage”) of the shares of Common
Stock outstanding immediately after giving effect to such exercise. For purposes of the foregoing sentence, the aggregate number of shares of Common Stock beneficially owned by such Person and its affiliates shall include the number of shares of
Common Stock issuable upon exercise of this Warrant with respect to which the determination of such sentence is being made, but shall exclude shares of Common Stock which would be issuable upon (i) exercise of the remaining, unexercised portion
of this Warrant beneficially owned by such Person and its affiliates and (ii) exercise or conversion of the unexercised or unconverted portion of any other securities of the Company beneficially owned by such Person and its affiliates
(including, without limitation, any convertible notes or convertible preferred stock or warrants) subject to a limitation on conversion or exercise analogous to the limitation contained herein. Except as set forth in the preceding sentence, for
purposes of this paragraph, beneficial ownership shall be calculated in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended. For purposes of this Warrant, in determining the number of outstanding shares of Common
Stock, the Holder may rely on the number of outstanding shares of Common Stock as reflected in (1) the Company’s most recent Form 10-K, Form 10-Q, Current Report on Form 8-K or other 

  

 3 

 
public filing with the Securities and Exchange Commission, as the case may be, (2) a more recent public announcement by the Company or (3) any
other notice by the Company or the Transfer Agent setting forth the number of shares of Common Stock outstanding. For any reason at any time, upon the written or oral request of the Holder, the Company shall within two (2) Business Days confirm
orally and in writing to the Holder the number of shares of Common Stock then outstanding. In any case, the number of outstanding shares of Common Stock shall be determined after giving effect to the conversion or exercise of securities of the
Company, including this Warrant, by the Holder and its affiliates since the date as of which such number of outstanding shares of Common Stock was reported. By written notice to the Company, the Holder may from time to time increase or decrease the
Maximum Percentage to any other percentage not in excess of 9.99% specified in such notice; provided that (i) any such increase will not be effective until the sixty-first (61st
) day after such notice is delivered to the Company, and (ii) any such increase or decrease will apply only to the Holder. The provisions of this paragraph shall be construed and implemented in
a manner otherwise than in strict conformity with the terms of this Section 1(h) to correct this paragraph (or any portion hereof) which may be defective or inconsistent with the intended beneficial ownership limitation herein contained or to
make changes or supplements necessary or desirable to properly give effect to such limitation. 
 2. ADJUSTMENT OF EXERCISE PRICE AND
NUMBER OF WARRANT SHARES. The Exercise Price and the number of Warrant Shares shall be adjusted from time to time as follows: 
 (a) RESERVED. 
 (b) Adjustment upon Subdivision or Combination of Common Stock. If the Company at any time on
or after the Subscription Date subdivides (by any stock split, stock dividend, recapitalization, reorganization, scheme, arrangement or otherwise) one or more classes of its outstanding shares of Common Stock into a greater number of shares, the
Exercise Price in effect immediately prior to such subdivision will be proportionately reduced and the number of Warrant Shares will be proportionately increased. If the Company at any time on or after the Subscription Date combines (by any stock
split, stock dividend, recapitalization, reorganization, scheme, arrangement or otherwise) one or more classes of its outstanding shares of Common Stock into a smaller number of shares, the Exercise Price in effect immediately prior to such
combination will be proportionately increased and the number of Warrant Shares will be proportionately decreased. Any adjustment under this Section 2(b) shall become effective at the close of business on the date the subdivision or combination
becomes effective. 
 (c) Other Events. If any event occurs of the type contemplated by the provisions of this
Section 2 but not expressly provided for by such provisions (including, without limitation, the granting of stock appreciation rights, phantom stock rights or other rights with equity features), then the Company’s Board of Directors will
make an appropriate adjustment in the Exercise Price and the number of Warrant Shares so as to protect the rights of the Holder; provided that no such adjustment pursuant to this Section 2(c) will increase the Exercise Price or decrease the
number of Warrant Shares as otherwise determined pursuant to this Section 2. 
  

 4 

 3. RIGHTS UPON DISTRIBUTION OF ASSETS. If the Company shall declare or make any dividend or other
distribution of its assets (or rights to acquire its assets) to holders of shares of Common Stock, by way of return of capital or otherwise (including, without limitation, any distribution of cash, stock or other securities, property or options by
way of a dividend, spin off, reclassification, corporate rearrangement, scheme of arrangement or other similar transaction) (a “Distribution”), at any time after the issuance of this Warrant, then, in each such case: 
 (a) any Exercise Price in effect immediately prior to the close of business on the record date fixed for the determination of holders of
shares of Common Stock entitled to receive the Distribution shall be reduced, effective as of the close of business on such record date, to a price determined by multiplying such Exercise Price by a fraction of which (i) the numerator shall be
the Closing Bid Price of the shares of Common Stock on the Trading Day immediately preceding such record date minus the value of the Distribution (as determined in good faith by the Company’s Board of Directors) applicable to one share of
Common Stock, and (ii) the denominator shall be the Closing Bid Price of the shares of Common Stock on the Trading Day immediately preceding such record date; and 
 (b) the number of Warrant Shares shall be increased to a number of shares equal to the number of shares of Common Stock obtainable
immediately prior to the close of business on the record date fixed for the determination of holders of shares of Common Stock entitled to receive the Distribution multiplied by the reciprocal of the fraction set forth in the immediately preceding
paragraph (a); provided that in the event that the Distribution is of shares of Common Stock (or common stock) (“Other Shares of Common Stock”) of a company whose common shares are traded on a national securities exchange or
a national automated quotation system, then the Holder may elect to receive a warrant to purchase Other Shares of Common Stock in lieu of an increase in the number of Warrant Shares, the terms of which shall be identical to those of this Warrant,
except that such warrant shall be exercisable into the number of shares of Other Shares of Common Stock that would have been payable to the Holder pursuant to the Distribution had the Holder exercised this Warrant immediately prior to such record
date and with an aggregate exercise price equal to the product of the amount by which the exercise price of this Warrant was decreased with respect to the Distribution pursuant to the terms of the immediately preceding paragraph (a) and the
number of Warrant Shares calculated in accordance with the first part of this paragraph (b). 
 4. PURCHASE RIGHTS; FUNDAMENTAL
TRANSACTIONS. 
 (a) Purchase Rights. In addition to any adjustments pursuant to Section 2 above, if at any
time the Company grants, issues or sells any Options, Convertible Securities or rights to purchase stock, warrants, securities or other property pro rata to the record holders of any class of shares of Common Stock (the “Purchase
Rights”), then the Holder will be entitled to acquire, upon the terms applicable to such Purchase Rights, the aggregate Purchase Rights which the Holder could have acquired if the Holder had held the number of shares of Common Stock
acquirable upon complete exercise of this Warrant (without regard to any limitations on the exercise of this Warrant) immediately before the date on which a record is taken for the grant, issuance or sale of such Purchase Rights, or, if no such
record is taken, the date as of which the record holders of shares of Common Stock are to be determined for the grant, issue or sale of such Purchase Rights. 
  

 5 

 (b) Fundamental Transactions. The Company shall not enter into or be party to a
Fundamental Transaction unless the Successor Entity assumes this Warrant in accordance with the provisions of this Section (4)(b), including agreements to deliver to each holder of Warrants in exchange for such Warrants a security of the Successor
Entity evidenced by a written instrument substantially similar in form and substance to this Warrant, including, without limitation, exercisable for, at any time after the Fundamental Transaction but prior to the Expiration Date, in lieu of the
shares of the Common Stock (or other securities, cash, assets or other property) purchasable upon the exercise of the Warrant prior to such Fundamental Transaction, such shares of stock, securities, cash, assets or any other property whatsoever
(including warrants or other purchase or subscription rights) which the Holder would have been entitled to receive upon the happening of such Fundamental Transaction had the Warrant been exercised immediately (without regard to any limitations on
the exercise of this Warrant) prior to such Fundamental Transaction, and with the Exercise Price correspondingly adjusted to give the Holder, on exercise for the same aggregate Exercise Price, such shares of stock, securities, cash, assets or any
other property whatsoever (including warrants or other purchase or subscription rights) which the Holder would have been entitled to receive upon the happening of such Fundamental Transaction had the Warrant been exercised immediately (without
regard to any limitations on the exercise of this Warrant) prior to such Fundamental Transaction, and satisfactory to the Holder. Upon the occurrence of any Fundamental Transaction, the Successor Entity shall succeed to, and be substituted for (so
that from and after the date of such Fundamental Transaction, the provisions of this Warrant referring to the “Company” shall refer instead to the Successor Entity), and may exercise every right and power of the Company and shall assume
all of the obligations of the Company under this Warrant with the same effect as if such Successor Entity had been named as the Company herein. In addition to and not in substitution for any other rights hereunder, prior to the consummation of any
Fundamental Transaction pursuant to which holders of shares of Common Stock are entitled to receive securities or other assets with respect to or in exchange for shares of Common Stock (a “Corporate Event”), the Company shall make
appropriate provision to insure that the Holder will thereafter have the right to receive upon an exercise of this Warrant at any time after the consummation of the Fundamental Transaction but prior to the Expiration Date, in lieu of the shares of
the Common Stock (or other securities, cash, assets or other property) purchasable upon the exercise of the Warrant prior to such Fundamental Transaction, such shares of stock, securities, cash, assets or any other property whatsoever (including
warrants or other purchase or subscription rights) which the Holder would have been entitled to receive upon the happening of such Fundamental Transaction had the Warrant been exercised immediately prior to such Fundamental Transaction. Provision
made pursuant to the preceding sentence shall be in a form and substance reasonably satisfactory to the Holder. The provisions of this Section shall apply similarly and equally to successive Fundamental Transactions and Corporate Events and shall be
applied without regard to any limitations on the exercise of this Warrant. 
 Notwithstanding the foregoing, in the event of a Fundamental
Transaction, at the request of the Holder delivered before the 90th day after such Fundamental Transaction, the Company (or the Successor Entity) shall purchase this Warrant from the Holder by paying to the Holder, within five Business Days after
such request (or, if later, on the effective date of the Fundamental Transaction), cash in an amount equal to the Black Scholes Value of the remaining unexercised portion of this Warrant. 
  

 6 

 5. NONCIRCUMVENTION. The Company hereby covenants and agrees that the Company will not, by
amendment of its Certificate of Incorporation, Bylaws or through any reorganization, transfer of assets, consolidation, merger, scheme of arrangement, dissolution, issue or sale of securities, or any other voluntary action, avoid or seek to avoid
the observance or performance of any of the terms of this Warrant, and will at all times in good faith carry out all the provisions of this Warrant and take all action as may be required to protect the rights of the Holder. Without limiting the
generality of the foregoing, the Company (i) shall not increase the par value of any shares of Common Stock receivable upon the exercise of this Warrant above the Exercise Price then in effect, (ii) shall take all such actions as may be
necessary or appropriate in order that the Company may validly and legally issue fully paid and nonassessable shares of Common Stock upon the exercise of this Warrant, and (iii) shall, so long as this Warrant is outstanding, take all action
necessary to reserve and keep available out of its authorized and unissued shares of Common Stock, solely for the purpose of effecting the exercise of this Warrant, 100% of the number of shares of Common Stock issuable upon exercise of this Warrant
then outstanding (without regard to any limitations on exercise). 
 6. WARRANT HOLDER NOT DEEMED A STOCKHOLDER. Except as otherwise
specifically provided herein, the Holder, solely in such Person’s capacity as a holder of this Warrant, shall not be entitled to vote or receive dividends or be deemed the holder of share capital of the Company for any purpose, nor shall
anything contained in this Warrant be construed to confer upon the Holder, solely in such Person’s capacity as the Holder of this Warrant, any of the rights of a stockholder of the Company or any right to vote, give or withhold consent to any
corporate action (whether any reorganization, issue of stock, reclassification of stock, consolidation, merger, conveyance or otherwise), receive notice of meetings, receive dividends or subscription rights, or otherwise, prior to the issuance to
the Holder of the Warrant Shares which such Person is then entitled to receive upon the due exercise of this Warrant. In addition, nothing contained in this Warrant shall be construed as imposing any liabilities on the Holder to purchase any
securities (upon exercise of this Warrant or otherwise) or as a stockholder of the Company, whether such liabilities are asserted by the Company or by creditors of the Company. 
 7. REISSUANCE OF WARRANTS. 
 (a) Transfer of Warrant. If this Warrant is to be transferred, the Holder shall surrender this Warrant to the Company, whereupon the Company will forthwith issue and deliver upon the order of the Holder a new Warrant (in accordance
with Section 7(d)), registered as the Holder may request, representing the right to purchase the number of Warrant Shares being transferred by the Holder and, if less then the total number of Warrant Shares then underlying this Warrant is being
transferred, a new Warrant (in accordance with Section 7(d)) to the Holder representing the right to purchase the number of Warrant Shares not being transferred. 
 (b) Lost, Stolen or Mutilated Warrant. Upon receipt by the Company of evidence reasonably satisfactory to the Company of the loss,
theft, destruction or mutilation of this Warrant, and, in the case of loss, theft or destruction, of any indemnification undertaking by the Holder to the Company in customary form and, in the case of mutilation, upon surrender and cancellation of
this Warrant, the Company shall execute and deliver to the Holder a new Warrant (in accordance with Section 7(d)) representing the right to purchase the Warrant Shares then underlying this Warrant. 
  

 7 

 (c) Exchangeable for Multiple Warrants. This Warrant is exchangeable, upon the
surrender hereof by the Holder at the principal office of the Company, for a new Warrant or Warrants (in accordance with Section 7(d)) representing in the aggregate the right to purchase the number of Warrant Shares then underlying this
Warrant, and each such new Warrant will represent the right to purchase such portion of such Warrant Shares as is designated by the Holder at the time of such surrender; provided, however, that no Warrants for fractional shares of Common Stock shall
be given. 
 (d) Issuance of New Warrants. Whenever the Company is required to issue a new Warrant pursuant to the
terms of this Warrant, such new Warrant (i) shall be of like tenor with this Warrant, (ii) shall represent, as indicated on the face of such new Warrant, the right to purchase the Warrant Shares then underlying this Warrant (or in the case
of a new Warrant being issued pursuant to Section 7(a) or Section 7(c), the Warrant Shares designated by the Holder which, when added to the number of shares of Common Stock underlying the other new Warrants issued in connection with such
issuance, does not exceed the number of Warrant Shares then underlying this Warrant), (iii) shall have an issuance date, as indicated on the face of such new Warrant which is the same as the Issuance Date, and (iv) shall have the same
rights and conditions as this Warrant. 
 8. NOTICES. Whenever notice is required to be given under this Warrant, unless otherwise
provided herein, such notice shall be given in accordance with Section 7 of Annex I to the Subscription Agreement. The Company shall provide the Holder with prompt written notice of all actions taken pursuant to this Warrant, including in
reasonable detail a description of such action and the reason therefore. 
 9. AMENDMENT AND WAIVER. Except as otherwise provided
herein, the provisions of this Warrant may be amended and the Company may take any action herein prohibited, or omit to perform any act herein required to be performed by it, only if the Company has obtained the written consent of the Holder.

 10. GOVERNING LAW. This Warrant shall be governed by and construed and enforced in accordance with, and all questions concerning
the construction, validity, interpretation and performance of this Warrant shall be governed by, the internal laws of the State of New York, without giving effect to any choice of law or conflict of law provision or rule (whether of the State of New
York or any other jurisdictions) that would cause the application of the laws of any jurisdictions other than the State of New York. 
 11.
CONSTRUCTION; HEADINGS. This Warrant shall be deemed to be jointly drafted by the Company and the Holder and shall not be construed against any person as the drafter hereof. The headings of this Warrant are for convenience of reference and
shall not form part of, or affect the interpretation of, this Warrant. 
  

 8 

 12. DISPUTE RESOLUTION. In the case of a dispute as to the determination of the Exercise Price or
the arithmetic calculation of the Warrant Shares, the Company shall submit the disputed determinations or arithmetic calculations via facsimile within two (2) Business Days of receipt of the Exercise Notice giving rise to such dispute, as the
case may be, to the Holder. If the Holder and the Company are unable to agree upon such determination or calculation of the Exercise Price or the Warrant Shares within three Business Days of such disputed determination or arithmetic calculation
being submitted to the Holder, then the Company shall, within two (2) Business Days submit via facsimile (a) the disputed determination of the Exercise Price to an independent, reputable investment bank selected by the Company and approved
by the Holder or (b) the disputed arithmetic calculation of the Warrant Shares to the Company’s independent, outside accountant. The Company shall cause at its expense the investment bank or the accountant, as the case may be, to perform
the determinations or calculations and notify the Company and the Holder of the results no later than ten Business Days from the time it receives the disputed determinations or calculations. Such investment bank’s or accountant’s
determination or calculation, as the case may be, shall be binding upon all parties absent demonstrable error. 
 13. REMEDIES, OTHER
OBLIGATIONS, BREACHES AND INJUNCTIVE RELIEF. The remedies provided in this Warrant shall be cumulative and in addition to all other remedies available under this Warrant, at law or in equity (including a decree of specific performance and/or
other injunctive relief), and nothing herein shall limit the right of the Holder to pursue actual damages for any failure by the Company to comply with the terms of this Warrant. 
 14. TRANSFER. This Warrant may be offered for sale, sold, transferred or assigned without the consent of the Company. 
 15. CERTAIN DEFINITIONS. For purposes of this Warrant, the following terms shall have the following meanings: 
 (a) “Black Scholes Value” means the value of this Warrant based on the Black and Scholes Option Pricing Model obtained
from the “OV” function on Bloomberg determined as of the day immediately following the first public announcement of the applicable Fundamental Transaction or of a transaction if consummated would constitute the applicable Fundamental
Transaction and reflecting (i) a risk-free interest rate corresponding to the U.S. Treasury rate for a period equal to the remaining term of this Warrant as of such date of request and (ii) an expected volatility equal to the 30 day
volatility obtained from the HVT function on Bloomberg for the period ending as of the end of the day immediately following the first such public announcement of the applicable Fundamental Transaction. 
 (b) “Bloomberg” means Bloomberg Financial Markets. 
 (c) “Business Day” means any day other than Saturday, Sunday or other day on which commercial banks in The City of New
York are authorized or required by law to remain closed. 
 (d) “Change of Control” means any Fundamental
Transaction other than (A) any reorganization, recapitalization or reclassification of the Common Stock, in which holders of the Company’s voting power immediately prior to such reorganization, 

  

 9 

 
recapitalization or reclassification continue after such reorganization, recapitalization or reclassification to hold publicly traded securities and,
directly or indirectly, the voting power of the surviving entity or entities necessary to elect a majority of the members of the board of directors (or their equivalent if other than a corporation) of such entity or entities, or (B) pursuant to
a migratory merger effected solely for the purpose of changing the jurisdiction of incorporation of the Company. 
 (e)
“Closing Bid Price” and “Closing Sale Price” means, for any security as of any date, the last closing bid price and last closing trade price, respectively, for such security on the Principal Market, as reported by
Bloomberg, or, if the Principal Market begins to operate on an extended hours basis and does not designate the closing bid price or the closing trade price, as the case may be, then the last bid price or the last trade price, respectively, of such
security prior to 4:00:00 p.m., New York time, as reported by Bloomberg, or, if the Principal Market is not the principal securities exchange or trading market for such security, the last closing bid price or last trade price, respectively, of such
security on the principal securities exchange or trading market where such security is listed or traded as reported by Bloomberg, or if the foregoing do not apply, the last closing bid price or last trade price, respectively, of such security in the
over-the-counter market on the electronic bulletin board for such security as reported by Bloomberg, or, if no closing bid price or last trade price, respectively, is reported for such security by Bloomberg, the average of the bid prices, or the ask
prices, respectively, of any market makers for such security as reported in the “pink sheets” by Pink Sheets LLC (formerly the National Quotation Bureau, Inc.). If the Closing Bid Price or the Closing Sale Price cannot be calculated for a
security on a particular date on any of the foregoing bases, the Closing Bid Price or the Closing Sale Price, as the case may be, of such security on such date shall be the fair market value as mutually determined by the Company and the Holder. All
such determinations to be appropriately adjusted for any stock dividend, stock split, stock combination or other similar transaction during the applicable calculation period. 
 (f) “Common Stock” means (i) the Company’s shares of Common Stock, par value $0.001 per share, and
(ii) any share capital into which such Common Stock shall have been changed or any share capital resulting from a reclassification of such Common Stock. 
 (g) RESERVED 
 (h) “Convertible Securities” means any stock or securities (other than Options) directly or indirectly convertible into or exercisable or exchangeable for shares of Common Stock. 
 (i) “Eligible Market” means the Principal Market, The New York Stock Exchange, Inc., The American Stock Exchange, The
NASDAQ Global Select Market or The NASDAQ Capital Market. 
 (j) “Expiration Date” means November 14,
2015 or, if such date falls on a day other than a Business Day or on which trading does not take place on the Principal Market (a “Holiday”), the next date that is not a Holiday. 
  

 10 

 (k) “Fundamental Transaction” means that the Company shall, directly or
indirectly, in one or more related transactions, (i) consolidate or merge with or into (whether or not the Company is the surviving corporation) another Person, or (ii) sell, assign, transfer, convey or otherwise dispose of all or
substantially all of the properties or assets of the Company to another Person, or (iii) allow another Person to make a purchase, tender or exchange offer that is accepted by the holders of more than the 50% of the outstanding shares of Common
Stock (not including any shares of Common Stock held by the Person or Persons making or party to, or associated or affiliated with the Persons making or party to, such purchase, tender or exchange offer), or (iv) consummate a stock purchase
agreement or other business combination (including, without limitation, a reorganization, recapitalization, spin-off or scheme of arrangement) with another Person whereby such other Person acquires more than the 50% of the outstanding shares of
Common Stock (not including any shares of Common Stock held by the other Person or other Persons making or party to, or associated or affiliated with the other Persons making or party to, such stock purchase agreement or other business combination),
(v) reorganize, recapitalize or reclassify its Common Stock, or (vi) any “person” or “group” (as these terms are used for purposes of Sections 13(d) and 14(d) of the Exchange Act) is or shall become the “beneficial
owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of 50% of the aggregate ordinary voting power represented by issued and outstanding Common Stock. 
 (l) “Options” means any rights, warrants or options to subscribe for or purchase shares of Common Stock or Convertible
Securities. 
 (m) “Parent Entity” of a Person means an entity that, directly or indirectly, controls the
applicable Person and whose common stock or equivalent equity security is quoted or listed on an Eligible Market, or, if there is more than one such Person or Parent Entity, the Person or Parent Entity with the largest public market capitalization
as of the date of consummation of the Fundamental Transaction. 
 (n) “Person” means an individual, a limited
liability company, a partnership, a joint venture, a corporation, a trust, an unincorporated organization, any other entity and a government or any department or agency thereof. 
 (o) “Principal Market” means The NASDAQ Global Market. 
 (p) RESERVED 
 (q) RESERVED 
 (r) “Successor Entity” means the Person (or, if so elected by the Holder, the
Parent Entity) formed by, resulting from or surviving any Fundamental Transaction or the Person (or, if so elected by the Holder, the Parent Entity) with which such Fundamental Transaction shall have been entered into. 
 (s) “Trading Day” means any day on which the Common Stock are traded on the Principal Market, or, if the Principal Market
is not the principal trading market for the Common Stock, then on the principal securities exchange or securities market on which the Common Stock are then traded; provided that “Trading Day” shall not include any day on which the
Common Stock are scheduled to trade on such exchange or market for less than 4.5 hours or 

  

 11 

 
any day that the Common Stock are suspended from trading during the final hour of trading on such exchange or market (or if such exchange or market does not
designate in advance the closing time of trading on such exchange or market, then during the hour ending at 4:00:00 p.m., New York time). 
 (t) RESERVED 
 [Signature Page Follows] 
  

 12 

 IN WITNESS WHEREOF, the Company has caused this Warrant to Purchase Common Stock to be duly
executed as of the Issuance Date set out above. 
  

			
	CELL GENESYS, INC.
		
	By:	 	/s/    Stephen A. Sherwin
	Name:	 	Stephen A. Sherwin
	Title:	 	Chairman and CEO

 (Signature Page to Warrant) 

 EXHIBIT A 
 EXERCISE NOTICE 
 TO BE EXECUTED BY THE REGISTERED HOLDER TO EXERCISE THIS 
 WARRANT TO PURCHASE COMMON STOCK 
 CELL GENESYS, INC. 
 The undersigned holder hereby exercises the right to purchase
                     of the shares of Common Stock (“Warrant Shares”) of CELL GENESYS, INC, a Delaware corporation
(the “Company”), evidenced by the attached Warrant to Purchase Common Stock (the “Warrant”). Capitalized terms used herein and not otherwise defined shall have the respective meanings set forth in the Warrant.

 1. Form of Exercise Price. The Holder intends that payment of the Exercise Price shall be made as: 
                  a “Cashless
Exercise” with respect to                      Warrant Shares. 
 2. Delivery of Warrant Shares. The Company shall deliver to the holder
                 Warrant Shares in accordance with the terms of the Warrant. 
 Date:                      ,              
  

			
	
	 
	Name of Registered Holder
		
	By:	 	 
		 	Name:
		 	Title:

  

 A-1 

 ACKNOWLEDGMENT 
 The Company hereby acknowledges this Exercise Notice and hereby directs [INSERT NAME OF TRANSFER AGENT] to issue the above indicated number of shares of Common Stock in accordance with the Transfer Agent Instructions
dated May     , 2008 from the Company and acknowledged and agreed to by [INSERT NAME OF TRANSFER AGENT]. 
  

			
	CELL GENESYS, INC.
		
	By:	 	 
		 	Name:
		 	Title:

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