EXHIBIT 10.1

STOCK PURCHASE AGREEMENT

THIS STOCK PURCHASE AGREEMENT (this “Agreement”) is executed and effective as of
April 8, 2009 by and between Cell Genesys, Inc., a Delaware corp oration (the
“Company”), and BioMed Realty, L.P., a Maryland limited partnership (“BioMed”).

RECITALS

WHEREAS, pursuant to the terms of that certain Agreement for Termination of
Lease and Voluntary Surrender of Premises between the Company and BMR-Bridgeview
Technology Park II LLC, a Delaware limited liability company (the “Landlord”),
dated as of March 6, 2009 (the “Termination Agreement”), the Company and the
Landlord terminated the Lease Agreement dated as of January 7, 2002 between the
Landlord (as successor in interest to F & S Hayward II, LLC, a Delaware limited
liability company) and the Company, subject to the satisfaction of certain
Termination Conditions, as defined in the Termination Agreement; and

WHEREAS, in accordance with Section 4 of the Termination Agreement, the Company
and BioMed, the sole member of Landlord, enter into this Agreement pursuant to
which the Company shall issue to BioMed, and BioMed acquire from the Company, an
aggregate of One Million (1,000,000) shares (the “Shares”) of the Company’s
Common Stock, par value $0.001 per share (the “Common Stock”), on the terms and
subject to the conditions specified herein.

NOW, THEREFORE, in consideration of the premises and mutual covenants contained
herein, the parties hereto hereby agree as follows:

1. Issuance of Shares.

1.1 Issuance of Shares. On the date hereof and subject to the terms and
conditions of this Agreement, in consideration of entering into the Termination
Agreement and for other good and valuable consideration the sufficiency of which
is hereby recognized, the Company agrees to issue to BioMed, and BioMed agrees
to acquire from the Company, the Shares.

1.2 Delivery of Shares. No later than two (2) business days following the date
hereof, the Company shall deliver to BioMed or cause to be delivered to BioMed,
a share certificate registered in BioMed’s name representing the Shares that
BioMed is to receive from the Company.

2. Representations and Warranties of the Company. The Company hereby represents
and warrants to BioMed as of the date hereof, and with respect to Sections 2.7,
2.8, 2.9 and 2.10 for so long as BioMed holds the Shares, as follows:

2.1 Organization; Good Standing. The Company is a corporation duly organized,
validly existing and in good standing under the laws of the State of Delaware
and has all requisite corporate power and authority to carry on its business as
presently conducted and as proposed to be conducted, and is qualified to do
business as a foreign corporation in good standing in all other jurisdictions in
which the conduct of its business requires such qualification.

--------------------------------------------------------------------------------

2.2 Authorization. All corporate action on the part of the Company, its
respective officers, directors and shareholders necessary for the authorization,
execution and delivery of this Agreement, the performance of all obligations of
the Company hereunder, and the authorization, issuance and delivery of the
Shares has been taken, and this Agreement constitutes a valid and legally
binding obligation of the Company, enforceable in accordance with its terms,
except (i) as limited by applicable bankruptcy, insolvency, reorganization,
moratorium, and other laws of general application affecting enforcement of
creditors’ rights generally and (ii) as limited by laws relating to the
availability of specific performance, injunctive relief, or other equitable
remedies. The Shares being purchased by BioMed hereunder, when issued, sold and
delivered in accordance with the terms of this Agreement for the consideration
expressed herein, will be duly and validly issued, fully paid and nonassessable,
and not subject to preemptive or other similar rights of the Company’s
stockholders or others.

2.3 Percentage of Outstanding Stock. The Shares represent less than five percent
(5.0%) of the voting interest and less than five percent (5.0%) of the value of
the outstanding stock of the Company.

2.4 Securities Laws. Subject to the accuracy of the representations and
warranties of BioMed set forth in Section 3 below, the offering, issuance and
sale of the Shares to BioMed is exempt from the registration requirements of
Section 5 of the Securities Act of 1933, as amended (“Securities Act”) by virtue
of Rule 506 of Regulation D promulgated by the Securities Act, and no consent,
approval, qualification, registration or filing under any federal or state
securities law is required in connection therewith, except for the filing of a
Form D, which shall be filed with the Securities and Exchange Commission after
the Shares are issued and which the Company agrees to file in a timely manner
whenever required. Rule 506 of Regulation D is available to the offering,
issuance, sale and delivery of the Shares to BioMed because, among other things,
(1) there has been no general solicitation or general advertisement in
connection with such offering, issuance and sale to BioMed, and (2) there are no
other offerings of securities of the Company which could be integrated with the
offering, issuance and sale of the Shares contemplated by this Agreement.

2.5 Restrictions. The Shares will be free of restrictions on transfer other than
restrictions on transfer set forth in this Agreement.

2.6 No Violation. Neither the execution, delivery and performance of this
Agreement by the Company nor the issuance, sale and delivery of the Shares
contemplated hereby will violate, conflict with or result in any breach of any
of the terms, conditions or provisions of, constitute a default under, or
require any consent not obtained as of the date hereof under, (1) the
certificate of incorporation or by-laws of the Company, (2) any agreement,
contract, arrangement or understanding to which the Company is a party
(including, but not limited to, any shareholders’ or similar agreements), or
(3) any statute or any rule, regulation, order, judgment or decree of any court
or other governmental body applicable to the Company.

2.7 Health Care / Lodging Facilities. The Company does not operate or manage any
health care facilities (including a congregate care facility or assisted living
facility) or lodging facilities or provide any person, under a franchise,
license or otherwise, rights to any brand name under which any lodging facility
or health care facility is operated.

 

-2-

--------------------------------------------------------------------------------

2.8 Annual Reports. The Company shall furnish to BioMed, as soon as practicable
and in any event within 90 days after the end of each fiscal year of the
Company, audited, consolidated annual financial statements certified by an
independent certified public accountant and prepared in accordance with U.S.
GAAP; provided, however, that so long as the Company remains subject to the
reporting requirements of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), the Company may satisfy this requirement by the timely filing
of such financial statements with the Securities and Exchange Commission.

2.9 Quarterly Information. The Company shall furnish to BioMed, as soon as
practicable and in any event within 15 days after the end of each calendar
quarter, (i) a capitalization table setting forth all of the capital stock
issued and outstanding or issuable by the Company, including the value of such
capital stock, the voting power of such capital stock and the rights of such
capital stock to appoint directors of the Company; provided, however, that so
long as the Company remains subject to the reporting requirements of the
Exchange Act, the Company may satisfy this requirement by timely filing its
quarterly reports on Form 10-Q and annual report on Form 10-K with the
Securities and Exchange Commission; and (ii) such other information as is
reasonably requested by BioMed to be necessary or helpful to monitor BioMed’s
compliance with the requirements relating to the status of BioMed or its
affiliates as a real estate investment trust for federal income tax purposes.

2.10 Notification. In the event that the Company becomes aware of any event
which has resulted or which may result in the Shares held by BioMed constituting
greater than five percent (5.0%) of the voting interest and/or greater than five
percent (5.0%) of the value of the outstanding stock of the Company, the Company
shall immediately notify BioMed, and in no event later than five (5) days after
the occurrence of such event.

3. Representations and Warranties of BioMed to the Company. BioMed hereby
represents and warrants to the Company as of the date hereof that:

3.1 Authorization. All corporate action on the part of BioMed, its respective
officers, directors, members and shareholders necessary for the authorization,
execution and delivery of this Agreement, and the performance of all obligations
of BioMed hereunder, has been taken, and such Agreement constitutes a valid and
legally binding obligation of BioMed, enforceable in accordance with its terms
except (i) as limited by applicable bankruptcy, insolvency, reorganization,
moratorium and other laws of general application affecting enforcement of
creditors’ rights generally, and (ii) as limited by laws relating to the
availability or specific performance, injunctive relief, or other equitable
remedies.

3.2 No Violation. Neither the execution, delivery and performance of this
Agreement by BioMed nor the acquisition by BioMed of the Shares will violate,
conflict with or result in any breach of any of the terms, conditions or
provisions of, constitute a default under, or require any consent not obtained
as of the date hereof under, (1) the certificate of incorporation or by-laws of
BioMed, (2) any agreement, contract, arrangement or understanding to which
BioMed is a party (including, but not limited to, any shareholders’ or similar
agreements), or (3) any statute or any rule, regulation, order, judgment or
decree of any court or other governmental body applicable to BioMed.

 

-3-

--------------------------------------------------------------------------------

3.3 Purchase Entirely for Own Account. This Agreement is made with BioMed in
reliance upon BioMed’s representation to the Company, which by BioMed’s
execution of this Agreement BioMed hereby confirms, that the Shares to be
received by BioMed will be acquired for investment for BioMed’s own account, not
as a nominee or agent, and not with a view to the resale or distribution of any
part thereof, and that BioMed has no present intention of selling, granting any
participation in, or otherwise distributing the same. By executing this
Agreement, BioMed further represents that BioMed does not have any contract,
undertaking, agreement or arrangement with any person to sell, transfer or grant
participation to such person or to any third person, with respect to any of the
Shares.

3.4 Investment Experience. BioMed is an “accredited investor” within the meaning
of Rule 501 of Regulation D under the Securities Act. BioMed acknowledges that
it can bear the economic risk of its investment, and has such knowledge and
experience in financial or business matters that it is capable of evaluating the
merits and risks of the investment in the Shares. BioMed also represents it has
not been organized solely for the purpose of acquiring the Shares.

3.5 Restricted Securities. BioMed understands that the Shares it is purchasing
are characterized as “restricted securities” under the Securities Act inasmuch
as they are being acquired from the Company in a transaction not involving a
public offering and that under such laws and applicable regulations such
securities may be resold without registration under the Securities Act only in
certain limited circumstances. In addition, BioMed represents that it is
familiar with Rule 144 under the Securities Act, as presently in effect, and
understands the resale limitations imposed thereby and by the Securities Act.

3.6 Legends. It is understood that the certificate(s) evidencing the Shares
shall bear the following legend:

THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). SUCH SHARES MAY NOT BE SOLD OR
TRANSFERRED IN THE ABSENCE OF SUCH REGISTRATION UNLESS THE COMPANY RECEIVES AN
OPINION OF COUNSEL REASONABLY ACCEPTABLE TO IT STATING THAT SUCH SALE OR
TRANSFER IS EXEMPT FROM THE REGISTRATION AND PROSPECTUS DELIVERY REQUIREMENTS OF
SAID ACT OR UNLESS SOLD PURSUANT TO RULE 144 OF THE ACT.

4. Notification. BioMed agrees to promptly notify the Company after it disposes
of all of the Shares issued to BioMed hereunder.

5. Lock-Up. BioMed will not, during the period ending 90 days after the date
of issuance of the Shares, (i) offer, pledge, announce the intention to sell,
sell, contract to sell, sell any option or contract to purchase, purchase any
option or contract to sell, grant any option, right or warrant to purchase, or
otherwise transfer or dispose of, directly or indirectly, any of the Shares, or
any securities convertible into or exercisable or exchangeable for the Shares or
(ii) enter into any swap or other agreement that transfers, in whole or in part,
any of the economic consequences of ownership of the Shares, whether any such
transaction described in clause (i) or (ii) above is to be settled by delivery
of the Shares or such other securities, in cash or otherwise. In furtherance of
the foregoing, the Company and any duly appointed transfer agent for the
registration or transfer of the securities described herein are hereby
authorized to decline to make any transfer of securities if such transfer would
constitute a violation or breach of this Agreement.

 

-4-

--------------------------------------------------------------------------------

6. Piggyback Registration. If at any time prior to 90 days after the date of
issuance of the Shares (but without any obligation to do so) the Company
proposes to register any additional shares of its Common Stock or other
securities under the Securities Act in connection with the public offering of
such securities (other than (a) a registration statement relating to the sale of
securities to employees of the Company pursuant to a stock option, stock
purchase or similar plan, (b) a registration statement on Form S-4, or (c) a
registration statement on a form not available for registering the Shares), the
Company shall, at such time, promptly give BioMed written notice of such
registration. Upon the written request of BioMed given within five (5) days
after mailing of such notice by the Company, the Company shall use its
commercially reasonable efforts to cause to be registered under the Securities
Act all of the Shares that BioMed has requested to be registered (subject to any
limitations or cutbacks that may be required by an underwriter if such public
offering is an underwritten public offering); provided, however, that the
Company shall have the right to postpone or withdraw any registration statement
pursuant to this Section 6 without obligation to BioMed.

7. Miscellaneous.

7.1 Successors and Assigns. Except as otherwise provided herein, the terms and
conditions of this Agreement shall inure to the benefit of and be binding upon
the respective successors and assigns of the parties. Nothing in this Agreement,
express or implied, is intended to confer upon any party other than the parties
hereto or their respective successors and assigns any rights, remedies,
obligations, or liabilities under or by reason of this Agreement, except as
expressly provided in this Agreement.

7.2 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.

7.3 Counterparts. This Agreement may be executed in counterparts, each of which
shall be deemed an original, but all of which together shall constitute one and
the same instrument.

7.4 Titles and Subtitles. The titles and subtitles used in this Agreement are
used for convenience only and are not to be considered in construing or
interpreting this Agreement.

7.5 Notices. All notices and other communications required or permitted
hereunder shall be in writing, shall be effective when given, and shall in any
event be deemed to be given upon receipt or, if earlier, (a) five (5) days after
deposit with the U.S. Postal Service or other applicable postal service, if
delivered by first class mail, postage prepaid, (b) upon delivery, if delivered
by hand, (c) one (1) business day after the business day of deposit with Federal
Express or similar overnight courier, freight prepaid or (d) one (1) business
day after the business day of facsimile transmission (with confirmation), if
delivered by facsimile transmission with copy by first class mail, postage
prepaid, and shall be addressed (i) if to BioMed, at 17190 Bernardo Center
Drive, San Diego, CA 92128, Attn: General Counsel/Corporate Legal; and (ii) if
to the Company, at the address or facsimile number of the Company’s principal
corporate offices, or at such other address as a party may designate by ten
days’ advance written notice to the other party pursuant to the provisions
above.

 

-5-

--------------------------------------------------------------------------------

7.6 Costs and Expenses. Each party shall pay its respective expenses in
connection with the preparation, execution and delivery of this Agreement and
the transactions contemplated hereby, including the fees and out-of-pocket
expenses of legal counsel.

7.7 Amendment and Waivers. Any term of this Agreement may be amended and the
severance of any term of this Agreement may be waived (either generally or in a
particular instance and either retroactively or prospectively) only with the
written consent of the parties hereto.

7.8 Severability. If one or more provisions of this Agreement are held to be
unenforceable under applicable law, such provision shall be excluded from this
Agreement and the balance of the Agreement shall be interpreted as if such
provision were so excluded and shall be enforceable in accordance with its
terms.

7.9 Entire Agreement. This Agreement and the documents referred to herein
constitute the entire agreement among the parties and no party shall be liable
or bound to any other party in any manner by any warranties, representations, or
covenants except as specifically set forth herein or therein.

[Remainder of page intentionally left blank.]

 

-6-

--------------------------------------------------------------------------------

The parties have executed this Stock Purchase Agreement as of the date first
above written.

 

CELL GENESYS, INC. By:   /s/ Sharon E. Tetlow Name:   Sharon E. Tetlow Title:  
Chief Financial Officer BIOMED REALTY, L.P. By:   /s/ Kent Griffin Name:   Kent
Griffin Title:   President

[SIGNATURE PAGE TO STOCK PURCHASE AGREEMENT]

 

-7-