Document:

EX-10.69

SUBSCRIPTION AGREEMENT

Cytokinetics, Incorporated

280 East Grand Avenue

South San Francisco, California 94080

Gentlemen:

The undersigned (the “Investor”) hereby confirms its agreement with Cytokinetics,
Incorporated, a Delaware corporation (the “Company”), as follows:

1. This Subscription Agreement, including the Terms and Conditions for Purchase of Units
attached hereto as Annex I (collectively, this “Agreement”) is made as of the date set
forth below between the Company and the Investor.

2. The Company has authorized the sale and issuance to certain investors of up to an aggregate
of 7,106,600 units (the “Units”), subject to adjustment by the Company’s Board of Directors or a
committee thereof, with each Unit consisting of (i) one share (the “Share,” collectively, the
“Shares”) of its common stock, par value $0.001 per share (the “Common Stock”), and (ii) one
warrant (the “Warrant,” collectively, the “Warrants”) to purchase 0.50 shares of Common Stock (and
the fractional amount being the “Warrant Ratio”), in substantially the form attached hereto as
Exhibit B, for a purchase price of $1.97 per Unit (the “Purchase Price”). Units will not
be issued or certificated. The Shares and Warrants are immediately separable and will be issued
separately. The shares of Common Stock issuable upon exercise of the Warrants are referred to
herein as the “Warrant Shares” and, together with the Units, the Shares and the Warrants, are
referred to herein as the “Securities”).

3. The offering and sale of the Units (the “Offering”) are being made pursuant to (a) an
effective Registration Statement on Form S-3, No. 333-155259 (the “Registration Statement”) filed
by the Company with the Securities and Exchange Commission (the “Commission”), including the
Prospectus contained therein (the “Base Prospectus”), (b) if applicable, certain “free writing
prospectuses” (as that term is defined in Rule 405 under the Securities Act of 1933, as amended
(the “Act”)), that have been or will be filed, if required, with the Commission and delivered to
the Investor on or prior to the date hereof (the “Issuer Free Writing Prospectus”), containing
certain supplemental information regarding the Units, the terms of the Offering and the Company and
(c) a Prospectus Supplement (the “Prospectus Supplement” and, together with the Base Prospectus,
the “Prospectus”) containing certain supplemental information regarding the Units and terms of the
Offering that will be filed with the Commission and delivered to the Investor (or made available to
the Investor by the filing by the Company of an electronic version thereof with the Commission).

4. The Company and the Investor agree that the Investor will purchase from the Company and the
Company will issue and sell to the Investor the Units set forth below for the aggregate purchase
price set forth below. The Units shall be purchased pursuant to the Terms and Conditions for
Purchase of Units attached hereto as Annex I and incorporated herein by this reference as
if fully set forth herein. The Investor acknowledges that the Offering is not being underwritten
by the placement agent (the “Placement Agent”) named in the Prospectus Supplement and that there is
no minimum offering amount.

5. The manner of settlement of the Shares included in the Units purchased by the Investor
shall be determined by such Investor as follows (check one):

	 	 	[      ] A. Delivery by crediting the account of the Investor’s prime broker (as specified by such
Investor on Exhibit A annexed hereto) with the Depository Trust Company (“DTC”)
through its Deposit/Withdrawal At Custodian (“DWAC”) system, whereby Investor’s prime broker
shall initiate a DWAC transaction on the Closing Date using its DTC participant identification
number, and released by BNY Mellon Shareowner Services, the Company’s transfer agent (the
“Transfer Agent”), at the Company’s direction. NO LATER THAN ONE (1) BUSINESS DAY AFTER THE
EXECUTION OF THIS AGREEMENT BY THE INVESTOR AND THE COMPANY, THE INVESTOR SHALL:

	 	(I)	 	DIRECT THE BROKER-DEALER AT WHICH THE ACCOUNT OR ACCOUNTS TO
BE CREDITED WITH THE SHARES ARE MAINTAINED TO SET UP A DWAC INSTRUCTING THE
TRANSFER AGENT TO CREDIT SUCH ACCOUNT OR ACCOUNTS WITH THE SHARES, AND

	 	(II)	 	REMIT BY WIRE TRANSFER THE AMOUNT OF FUNDS EQUAL TO THE
AGGREGATE PURCHASE PRICE FOR THE UNITS BEING PURCHASED BY THE INVESTOR TO THE
FOLLOWING ACCOUNT:

[Account information to be provided under separate cover]

	 	 	 
	– OR –

[      ] B.
	 	

Delivery versus payment (“DVP”) through DTC ( i.e., on the Closing

Date, the Company shall deliver the Shares registered in the

Investor’s name and address as set forth below and released by the

Transfer Agent to the Investor through DTC at the Closing directly

to the account(s) at Lazard Capital Markets LLC (“LCM”) identified

by the Investor; upon receipt of such Shares, LCM shall promptly

electronically deliver such Shares to the Investor, and

simultaneously therewith payment shall be made by LCM by wire

transfer to the Company). NO LATER THAN ONE (1) BUSINESS DAY AFTER

THE EXECUTION OF THIS AGREEMENT BY THE INVESTOR AND THE COMPANY,

THE INVESTOR SHALL:

	 	(I)	 	NOTIFY LCM OF THE ACCOUNT OR ACCOUNTS AT LCM TO BE CREDITED
WITH THE SHARES BEING PURCHASED BY SUCH INVESTOR, AND

	 	(II)	 	CONFIRM THAT THE ACCOUNT OR ACCOUNTS AT LCM TO BE CREDITED
WITH THE SHARES BEING PURCHASED BY THE INVESTOR HAVE A MINIMUM BALANCE EQUAL
TO THE AGGREGATE PURCHASE PRICE FOR THE UNITS BEING PURCHASED BY THE INVESTOR.

IT IS THE INVESTOR’S RESPONSIBILITY TO (A) MAKE THE NECESSARY WIRE TRANSFER OR CONFIRM THE
PROPER ACCOUNT BALANCE IN A TIMELY MANNER AND (B) ARRANGE FOR SETTLEMENT BY WAY OF DWAC OR DVP IN A
TIMELY MANNER. IF THE INVESTOR DOES NOT DELIVER THE AGGREGATE PURCHASE PRICE FOR THE UNITS OR DOES
NOT MAKE PROPER ARRANGEMENTS FOR SETTLEMENT IN A TIMELY MANNER, THE SHARES AND WARRANTS MAY NOT BE
DELIVERED AT CLOSING TO THE INVESTOR OR THE INVESTOR MAY BE EXCLUDED FROM THE CLOSING ALTOGETHER,
AT THE COMPANY’S DISCRETION.

6. The executed Warrant shall be delivered in accordance with the terms thereof.

7. The Investor represents that, except as set forth below, (a) it has had no position, office
or other material relationship within the past three years with the Company or persons known to it
to be affiliates of the Company, (b) it is not a member of the Financial Industry Regulatory
Authority, Inc. or an Associated Person (as such term is defined under the NASD Membership and
Registration Rules Section 1011) as of the Closing, and (c) neither the Investor nor any group of
Investors (as identified in a public filing made with the Commission) of which the Investor is a
part in connection with the Offering of the Units, acquired, or obtained the right to acquire, 20%
or more of the Common Stock (or securities convertible into or exercisable for Common Stock) or the
voting power of the Company on a post-transaction basis. Exceptions:

(If no exceptions, write “none.” If left blank, response will be deemed to be “none.”)

8. The Investor represents that it has received (or otherwise had made available to it by the
filing by the Company of an electronic version thereof with the Commission) the Base Prospectus
which is a part of the Company’s Registration Statement, the documents incorporated by reference
therein and any free writing prospectus (collectively, the “Disclosure Package”), prior to or in
connection with the receipt of this Agreement. The Investor acknowledges that, prior to the
delivery of this Agreement to the Company, the Investor will receive certain additional information
regarding the Offering, including pricing information (the “Offering Information”). Such
information may be provided to the Investor by any means permitted under the Act, including the
Prospectus Supplement, a free writing prospectus and oral communications.

9. No offer by the Investor to buy Units will be accepted and no part of the Purchase Price
will be delivered to the Company until the Investor has received the Offering Information and the
Company has accepted such offer by countersigning a copy of this Agreement, and any such offer may
be withdrawn or revoked, without obligation or commitment of any kind, at any time prior to the
Company (or Placement Agent on behalf of the Company) sending (orally, in writing or by electronic
mail) notice of its acceptance of such offer. An indication of interest will involve no obligation
or commitment of any kind until the Investor has been delivered the Offering Information and this
Agreement is accepted and countersigned by or on behalf of the Company. The Investor understands
and agrees that the Company, in its sole discretion, reserves the right to accept or reject this
subscription for Units, in whole or in part.

10. The Company acknowledges that the only material, non-public information relating to the
Company it has provided to the Investor in connection with the Offering prior to the date hereof is
the existence of the Offering.

1

Number of Units:      

Purchase Price Per Unit: $1.97

Aggregate Purchase Price: $     

Please confirm that the foregoing correctly sets forth the agreement between us by signing in
the space provided below for that purpose.

Dated as of: May      , 2009

INVESTOR

By:       

Print Name:       

Title:       

Address:       

      

      

Agreed and Accepted

this        day of May, 2009:

CYTOKINETICS, INCORPORATED

By: Sharon Barbari

Title:       Sr. Vice President, Finance & CFO       

ANNEX I

TERMS AND CONDITIONS FOR PURCHASE OF UNITS

1. Authorization and Sale of the Units. Subject to the terms and conditions of this
Agreement, the Company has authorized the sale of the Units.

2. Agreement to Sell and Purchase the Units; Placement Agent.

2.1 At the Closing (as defined in Section 3.1), the Company will sell to the Investor,
and the Investor will purchase from the Company, upon the terms and conditions set forth herein,
the number of Units set forth on the last page of the Agreement to which these Terms and Conditions
for Purchase of Units are attached as Annex I (the “Signature Page”) for the aggregate
purchase price therefor set forth on the Signature Page.

2.2 The Company proposes to enter into substantially this same form of Subscription Agreement
with certain other investors (the “Other Investors”) and expects to complete sales of Units to
them. The Investor and the Other Investors are hereinafter sometimes collectively referred to as
the “Investors,” and this Agreement and the Subscription Agreements executed by the Other Investors
are hereinafter sometimes collectively referred to as the “Agreements.”

2.3 Investor acknowledges that the Company has agreed to pay Lazard Capital Markets LLC (the
“Placement Agent” or “LCM”) a fee (the “Placement Fee”) in respect of the sale of Units to the
Investor.

2.4 The Company has entered into a Placement Agent Agreement, dated May      , 2009 (the
“Placement Agreement”), with the Placement Agent that contains certain representations, warranties,
covenants and agreements of the Company that may be relied upon by the Investor, which shall be a
third party beneficiary thereof.

3. Closing and Delivery of the Shares, Warrants and Funds.

3.1 Closing. The completion of the purchase and sale of the Units (the “Closing”)
shall occur at a place and time (the “Closing Date”) to be specified by the Company and the
Placement Agent, and of which the Investors will be notified in advance by the Placement Agent, in
accordance with Rule 15c6-1 promulgated under the Securities Exchange Act of 1934, as amended (the
“Exchange Act”). At the Closing, (a) the Company shall cause the Transfer Agent to deliver to the
Investor the number of Shares set forth on the Signature Page registered in the name of the
Investor or, if so indicated on the Investor Questionnaire attached hereto as Exhibit A, in
the name of a nominee designated by the Investor, (b) the Company shall cause to be delivered to
the Investor a Warrant to purchase a number of whole Warrant Shares determined by multiplying the
number of Shares set forth on the signature page by the Warrant Ratio and rounding down to the
nearest whole number and (c) the aggregate purchase price for the Units being purchased by the
Investor will be delivered by or on behalf of the Investor to the Company.

3.2 Conditions to the Obligations of the Parties.

(a) Conditions to the Company’s Obligations. The Company’s obligation to issue and
sell the Units to the Investor shall be subject to: (i) the receipt by the Company of the purchase
price for the Units being purchased hereunder as set forth on the Signature Page and (ii) the
accuracy of the representations and warranties made by the Investor and the fulfillment of those
undertakings of the Investor to be fulfilled prior to the Closing Date.

(b) Conditions to the Investor’s Obligations. The Investor’s obligation to purchase
the Units will be subject to the accuracy of the representations and warranties made by the Company
and the fulfillment of those undertakings of the Company to be fulfilled prior to the Closing Date,
including without limitation, those contained in the Placement Agreement, and to the condition that
the Placement Agent shall not have: (i) terminated the Placement Agreement pursuant to the terms
thereof or (ii) determined that the conditions to the closing in the Placement Agreement have not
been satisfied. The Investor’s obligations are expressly not conditioned on the purchase by any or
all of the Other Investors of the Units that they have agreed to purchase from the Company. The
Investor understands and agrees that, in the event that the Placement Agent in its sole discretion
determines that the conditions to closing in the Placement Agreement have not been satisfied or if
the Placement Agent Agreement may be terminated for any other reason permitted by such Agreement,
then the Placement Agent may, but shall not be obligated to, terminate such Agreement, which shall
have the effect of terminating this Subscription Agreement pursuant to Section 14 below.

3.3 Delivery of Funds.

(a) DWAC Delivery. If the Investor elects to settle the Shares purchased by such
Investor through DTC’s Deposit/Withdrawal at Custodian (“DWAC”) delivery system, no later than
one (1) business day after the execution of this Agreement by the Investor and the Company, the
Investor shall remit by wire transfer the amount of funds equal to the aggregate purchase price for
the Units being purchased by the Investor to the following account designated by the Company and
the Placement Agent pursuant to the terms of that certain Escrow Agreement (the “Escrow Agreement”)
dated as of the date hereof, by and among the Company, the Placement Agent and JPMorgan Chase Bank,
N.A. ( (the “Escrow Agent”):

[Account information to be provided under separate cover]

Such funds shall be held in escrow until the Closing and delivered by the Escrow Agent on
behalf of the Investors to the Company upon the satisfaction, in the sole judgment of the Placement
Agent, of the conditions set forth in Section 3.2(b) hereof. The Placement Agent shall
have no rights in or to any of the escrowed funds, unless the Placement Agent and the Escrow Agent
are notified in writing by the Company in connection with the Closing that a portion of the
escrowed funds shall be applied to the Placement Fee. The Company agrees to indemnify and hold the
Escrow Agent harmless from and against any and all losses, costs, damages, expenses and claims
(including, without limitation, court costs and reasonable attorneys fees) (“Losses”) arising under
this Section 3.3 or otherwise with respect to the funds held in escrow pursuant hereto or
arising under the Escrow Agreement, except to the extent that it is finally, judicially determined
that such Losses resulted from the willful misconduct or gross negligence of the Escrow Agent.
Anything in this Agreement to the contrary notwithstanding, in no event shall the Escrow Agent be
liable for any special, indirect or consequential loss or damage of any kind whatsoever (including
but not limited to lost profits), even if the Escrow Agent has been advised of the likelihood of
such loss or damage and regardless of the form of action.

(b) Delivery Versus Payment through The Depository Trust Company. If the Investor
elects to settle the Shares purchased by such Investor by delivery versus payment through DTC,
no later than one (1) business day after the execution of this Agreement by the Investor and
the Company, the Investor shall confirm that the account or accounts at the Placement Agent to
be credited with the Units being purchased by the Investor have a minimum balance equal to the
aggregate purchase price for the Units being purchased by the Investor.

3.4 Delivery of Shares.

(a) DWAC Delivery. If the Investor elects to settle the Shares purchased by such
Investor through DTC’s DWAC delivery system, no later than one (1) business day after the
execution of this Agreement by the Investor and the Company, the Investor shall direct the
broker-dealer at which the account or accounts to be credited with the Shares being purchased by
such Investor are maintained, which broker/dealer shall be a DTC participant, to set up a DWAC
instructing BNY Mellon Shareowner Services, the Company’s “Transfer Agent”, to credit such account
or accounts with the Shares. Such DWAC instruction shall indicate the settlement date for the
deposit of the Shares, which date shall be provided to the Investor by LCM. Simultaneously with
the delivery to the Company by the Escrow Agent of the funds held in escrow pursuant to
Section 3.3 above, the Company shall direct the Transfer Agent to credit the Investor’s
account or accounts with the Shares pursuant to the information contained in the DWAC.

(b) Delivery Versus Payment through The Depository Trust Company. If the Investor
elects to settle the Shares purchased by such Investor by delivery versus payment through DTC, no
later than one (1) business day after the execution of this Agreement by the Investor and the
Company, the Investor shall notify LCM of the account or accounts at LCM to be credited with the
Shares being purchased by such Investor. On the Closing Date, the Company shall deliver the Shares
to the Investor through DTC directly to the account(s) at LCM identified by Investor and
simultaneously therewith payment shall be made by LCM by wire transfer to the Company.

4. Representations, Warranties and Covenants of the Investor.

The Investor acknowledges, represents and warrants to, and agrees with, the Company and the
Placement Agent that:

4.1 The Investor (a) is knowledgeable, sophisticated and experienced in making, and is
qualified to make decisions with respect to, investments in shares presenting an investment
decision like that involved in the purchase of the Units, including investments in securities
issued by the Company and investments in comparable companies, (b) has answered all questions on
the Signature Page and the Investor Questionnaire and the answers thereto are true and correct as
of the date hereof and will be true and correct as of the Closing Date and (c) in connection with
its decision to purchase the number of Units set forth on the Signature Page, has received and is
relying only upon the Disclosure Package and the documents incorporated by reference therein and
the Offering Information.

4.2 (a) No action has been or will be taken in any jurisdiction outside the United States by
the Company or the Placement Agent that would permit an offering of the Units, or possession or
distribution of offering materials in connection with the issue of the Securities in any
jurisdiction outside the United States where action for that purpose is required, (b) if the
Investor is outside the United States, it will comply with all applicable laws and regulations in
each foreign jurisdiction in which it purchases, offers, sells or delivers Securities or has in its
possession or distributes any offering material, in all cases at its own expense and (c) the
Placement Agent is not authorized to make and has not made any representation, disclosure or use of
any information in connection with the issue, placement, purchase and sale of the Units, except as
set forth or incorporated by reference in the Base Prospectus or the Prospectus Supplement or any
free writing prospectus.

4.3 (a) The Investor has full right, power, authority and capacity to enter into this
Agreement and to consummate the transactions contemplated hereby and has taken all necessary action
to authorize the execution, delivery and performance of this Agreement, and (b) this Agreement
constitutes a valid and binding obligation of the Investor enforceable against the Investor in
accordance with its terms, except as enforceability may be limited by applicable bankruptcy,
insolvency, reorganization, moratorium or similar laws affecting creditors’ and contracting
parties’ rights generally and except as enforceability may be subject to general principles of
equity (regardless of whether such enforceability is considered in a proceeding in equity or at
law) and except as to the enforceability of any rights to indemnification or contribution that may
be violative of the public policy underlying any law, rule or regulation (including any federal or
state securities law, rule or regulation).

4.4 The Investor understands that nothing in this Agreement, the Prospectus, the Disclosure
Package, the Offering Information or any other materials presented to the Investor in connection
with the purchase and sale of the Units constitutes legal, tax or investment advice. The Investor
has consulted such legal, tax and investment advisors and made such investigation as it, in its
sole discretion, has deemed necessary or appropriate in connection with its purchase of Units. The
Investor also understands that there is no established public trading market for the Warrants being
offered in the Offering, and that the Company does not expect such a market to develop. In
addition, the Company does not intend to apply for listing the Warrants on any securities exchange.
Without an active market, the liquidity of the Warrants will be limited.

4.5 Since the date on which the Placement Agent first contacted the Investor about the
Offering, the Investor has not disclosed any information regarding the Offering to any third
parties (other than its legal, accounting and other advisors) and has not engaged in any purchases
or sales involving the securities of the Company (including, without limitation, any Short Sales
involving the Company’s securities). The Investor covenants that it will not engage in any
purchases or sales involving the securities of the Company (including Short Sales) prior to the
time that the transactions contemplated by this Agreement are publicly disclosed. The Investor
agrees that it will not use any of the Securities acquired pursuant to this Agreement to cover any
short position in the Common Stock if doing so would be in violation of applicable securities laws.
For purposes hereof, “Short Sales” include, without limitation, all “short sales” as defined in
Rule 200 promulgated under Regulation SHO under the Exchange Act, whether or not against the box,
and all types of direct and indirect stock pledges, forward sales contracts, options, puts, calls,
short sales, swaps, “put equivalent positions” (as defined in Rule 16a-1(h) under the Exchange Act)
and similar arrangements (including on a total return basis), and sales and other transactions
through non-US broker dealers or foreign regulated brokers.

4.6 The Investor understands that there is significant uncertainty whether or not Amgen Inc.
(“Amgen”) will acquire an exclusive worldwide (excluding Japan) license to develop and
commercialize CK-1827452 pursuant to the rights granted it under that certain Collaboration and
Option Agreement between the Company and Amgen dated December 29, 2006, as amended from time to
time by the parties.

5. Survival of Representations, Warranties and Agreements; Third Party Beneficiary.
Notwithstanding any investigation made by any party to this Agreement or by the Placement Agent,
all covenants, agreements, representations and warranties made by the Company and the Investor
herein will survive the execution of this Agreement, the delivery to the Investor of the Shares and
Warrants being purchased and the payment therefor. The Placement Agent and Lazard Fréres & Co.
shall be third party beneficiaries with respect to the representations, warranties and agreements
of the Investor in Section 4 hereof.

6. Notices. All notices, requests, consents and other communications hereunder will be in
writing, will be mailed (a) if within the domestic United States by first-class registered or
certified airmail, or nationally recognized overnight express courier, postage prepaid, or by
facsimile or (b) if delivered from outside the United States, by International Federal Express or
facsimile, and (c) will be deemed given (i) if delivered by first-class registered or certified
mail domestic, three business days after so mailed, (ii) if delivered by nationally recognized
overnight carrier, one business day after so mailed, (iii) if delivered by International Federal
Express, two business days after so mailed and (iv) if delivered by facsimile, upon electronic
confirmation of receipt and will be delivered and addressed as follows:

(a) if to the Company, to:

Cytokinetics, Incorporated

280 East Grand Avenue

South San Francisco, California 94080

Attention: General Counsel

Facsimile: (650) 624-3010

with copies to:

Wilson Sonsini Goodrich and Rosati, PC

650 Page Mill Road

Palo Alto, California 94304

Attention: Michael O’Donnell

Facsimile: (650) 493-6811

	 	(b)	 	if to the Investor, at its address on the
Signature Page hereto, or at such other address or addresses as may have
been furnished to the Company in writing.

7. Changes. This Agreement may not be modified or amended except pursuant to an instrument in
writing signed by the Company and the Investor.

8. Headings. The headings of the various sections of this Agreement have been inserted for
convenience of reference only and will not be deemed to be part of this Agreement.

9. Severability. In case any provision contained in this Agreement should be invalid, illegal
or unenforceable in any respect, the validity, legality and enforceability of the remaining
provisions contained herein will not in any way be affected or impaired thereby.

10. Governing Law. This Agreement will be governed by, and construed in accordance with, the
internal laws of the State of New York, without giving effect to the principles of conflicts of law
that would require the application of the laws of any other jurisdiction.

11. Counterparts. This Agreement may be executed in two or more counterparts, each of which
will constitute an original, but all of which, when taken together, will constitute but one
instrument, and will become effective when one or more counterparts have been signed by each party
hereto and delivered to the other parties. The Company and the Investor acknowledge and agree that
the Company shall deliver its counterpart to the Investor along with the Prospectus Supplement (or
the filing by the Company of an electronic version thereof with the Commission).

12. Confirmation of Sale. The Investor acknowledges and agrees that such Investor’s receipt
of the Company’s signed counterpart to this Agreement, together with the Prospectus Supplement (or
the filing by the Company of an electronic version thereof with the Commission), shall constitute
written confirmation of the Company’s sale of the Units to such Investor.

13. Press Release. The Company and the Investor agree that the Company shall, prior to the
opening of the financial markets in New York City on the business day immediately after the date
hereof, (a) issue a press release announcing the Offering and disclosing all material information
regarding the Offering and (b) file a Current Report on Form 8-K with the Securities and Exchange
Commission including a form of this Agreement and a form of Warrant as exhibits thereto.

14. Termination. In the event that the Placement Agreement is terminated by the Placement Agent

pursuant to the terms thereof, this Agreement shall terminate without any further action on the

part of the parties hereto.EXHIBIT A

CYTOKINETICS, INCORPORATED

INVESTOR QUESTIONNAIRE

Pursuant to Section 3 of Annex I to the Agreement, please provide us with the
following information:

	 
	1. The exact name that your Shares and Warrants are to be registered in. You

may use a nominee name if appropriate:

	2. The relationship between the Investor and the registered holder listed in

response to item 1 above:

	3. The mailing address of the registered holder listed in response to item 1

above:

	4. The Social Security Number or Tax Identification Number of the registered

holder listed in the response to item 1 above:

	5. Name of DTC Participant (broker-dealer at which the account or accounts to

be credited with the Shares are maintained):

	6. DTC Participant Number:

	7. Name of Account at DTC Participant being credited with the Shares:

	8. Account Number at DTC Participant being credited with the Shares:

2EX-10.70

CYTOKINETICS, INCORPORATED

WARRANT TO PURCHASE COMMON STOCK

Warrant No.: [      ]

Number of Shares of Common Stock: [      ]

Date of Issuance: [     , 2009] (“Issuance Date”)

Cytokinetics, Incorporated, a Delaware corporation (the “Company”), hereby certifies that, for
good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged,
[      ], 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) in effect at the time of exercise, upon surrender of this Warrant to Purchase
Common Stock (including any Warrants to Purchase Common Stock issued in exchange, transfer or
replacement hereof, the “Warrant”), at any time or times on or after the date hereof, but not after
11:59 p.m., New York time, on the Expiration Date (as defined below), [     
(      )]1 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. As used herein, the “Exercise Period”
means the period beginning on the Issuance Date and ending at 11:59 p.m., New York time, on the
Expiration Date. This Warrant is the Warrant to purchase Common Stock issued pursuant to Section 2
of that certain Subscription Agreement (the “Subscription Agreement”), dated as of [     , 2009]
(the “Subscription Date”), by and between the Company and the Holder (the “Subscription
Agreement”), and is issued pursuant to the Company’s Registration Statement on Form S-3 (File
number 333-155259) (the “Registration Statement”).

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 Business Day during the Exercise Period, in whole or in part,
by (i) delivery in accordance with Section 8 of a written notice, in the form attached
hereto as Exhibit A (the “Exercise Notice”), of the Holder’s election to exercise this
Warrant accompanied by the Warrant (collectively, the “Exercise Documents”); and (ii) (A) payment
to the Company of an amount equal to the Exercise Price in effect at the time of exercise
multiplied by the number of Warrant Shares as to which this Warrant is being exercised (the
“Aggregate Exercise Price”) in cash or by wire transfer of immediately available funds, or (B) by
notifying the Company in accordance with Section 8 that this Warrant is being exercised
pursuant to a Cashless Exercise (as defined in Section 1(e)) (a “Cashless Exercise
Notice”). Notwithstanding Section 1(a)(ii)(A), at any time, upon receipt of an Exercise
Notice, the Company may, in its sole discretion, require that the Holder exercise this Warrant on a
Cashless Exercise basis; in such event, if the Holder has exercised the Warrant by payment of the
Aggregate Exercise Price pursuant to Section 1(a)(ii)(A), then the Company shall promptly
return such funds to an account designated by the Holder, and the Holder shall, for all purposes
hereunder, be deemed to have delivered a notice of Cashless Exercise with respect to such exercise
on the date on which the Exercise Notice was delivered, or alternatively, at the Holder’s election,
the Exercise Notice shall be null and void. The “Exercise Date” shall mean (a) the first
(1st) Business Day following the date of the Company’s or its designated agent’s receipt
of the Exercise Documents and either the Aggregate Exercise Price or a Cashless Exercise Notice, if
received prior to 7 p.m. Eastern Time, or (b) the second (2nd) Business Day following
the date of the Company’s or its designated agent’s receipt of the Exercise Documents and either
the Aggregate Exercise Price or a Cashless Exercise Notice, if received on or after 7 p.m. Eastern
Time. The Holder shall not be required to deliver the original Warrant in order to effect an
exercise hereunder, but shall deliver the original Warrant within five (5) Business Days
thereafter.

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
first (1st) Business Day following the Exercise Date, the Company shall transmit by facsimile an
acknowledgment of confirmation of receipt of the Exercise Delivery Documents and the Aggregate
Exercise Price or a Cashless Exercise Notice to the Holder and the Company’s transfer agent (the
“Transfer Agent”). On or before the third (3rd) Business Day following the Exercise Date (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, make available 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 At Custodian system, or (Y) if the Transfer Agent is not
participating in the DTC Fast Automated Securities Transfer Program, process the issuance of a
certificate, 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 the Exercise Date, 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 two Business Days after receipt by
the Company, following an exercise of the Warrant, of the original Warrant, 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 under this Warrant after giving effect to such exercise of
the Warrant. 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 transfer taxes which may be payable with
respect to the issuance and delivery of Warrant Shares upon exercise of this Warrant by the Holder
of this Warrant.

(b) Exercise Price. For purposes of this Warrant, “Exercise Price” initially means
$2.75, subject to adjustment as provided herein. In the event that, during the Exercise Period,
Amgen Inc. (“Amgen”) does not acquire an exclusive worldwide (excluding Japan) license to develop
and commercialize CK-1827452 pursuant to the rights granted it under that certain Collaboration and
Option Agreement between the Company and Amgen dated December 29, 2006, as amended from time to
time by the parties, (the “Decision”) by June 30, 2009 (the “Assessment Date”), then the Exercise
Price shall be changed to be the Market Price on June 30, 2009, subject to adjustment as provided
herein; provided, however, that in no event shall the Exercise Price (i) exceed
$2.75 or (ii) be less than $1.50, in each case subject to appropriate adjustment in the event of
any stock dividend, stock split, combination or other similar recapitalization with respect to the
Common Stock. If Amgen does acquire an exclusive worldwide (excluding Japan) license to develop
and commercialize CK-1827452 pursuant to the rights granted it under that certain Collaboration and
Option Agreement between the Company and Amgen dated December 29, 2006, as amended from time to
time by the parties, by the Assessment Date, then the Exercise Price will not change.

(c) Market Price. For purposes of this Warrant, “Market Price” means the Weighted
Average Price for the Common Stock for the five (5) Trading Days immediately preceding the
Assessment Date.

(d) Company’s Failure to Timely Deliver Securities. If the Company fails for any
reason within its control to issue to the Holder within three (3) Business Days following the
Exercise Date 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 make
available 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 the fifth
(5th) Trading Day following the Exercise Date 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 (and, if the Transfer Agent delivers
such Warrant Shares thereafter, the Holder will promptly work with the Transfer Agent, at the
Company’s expense, to return such Warrant Shares), 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 Sale Price on the date of exercise. If for
any other reason the Company fails to issue to the Holder within three (3) Business Days following
the Exercise Date 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 make
available 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, then the Company’s sole
obligation shall be to allow the Holder to rescind the Warrant exercise, in which case the Company
shall promptly return to the Warrant to the Holder and refund to the Holder the Aggregate Exercise
Price (if actually paid by the Holder). In the event the Company does not have an effective
registration statement, there is no circumstance that would require the Company to net cash settle
the Warrant.

(e) Cashless Exercise. Upon the election of a Holder pursuant to Section 1(a)(ii)(B)
or an election by the Company to require that this Warrant be exercised on a Cashless Exercise
basis pursuant to the proviso in the first sentence of Section 1(a), this Warrant shall be
exercised by the Holder hereof, in whole or in part and, in lieu of making a cash payment otherwise
contemplated to be made to the Company upon such exercise in payment of the Aggregate Exercise
Price, by the Holder’s receiving 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 Exercise Date; provided, however, that if the Company requires
that this Warrant be exercised on a Cashless Exercise basis pursuant to the proviso
in the first sentence of Section 1(a), “B” shall instead equal the greater of
(i) 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 Exercise Date and (ii) the Closing Sale Price on the Exercise Date.

C= the Exercise Price then in effect for the applicable Warrant Shares at the time of
such exercise.

(f) Rule 144. For purposes of Rule 144(d) promulgated under the Securities Act, as in
effect on the date hereof, assuming the Holder is not an affiliate of the Company, 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.

(g) 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, if any, that are not disputed.

(h) Beneficial Ownership. The Holder shall not have the right to exercise this
Warrant to the extent that after giving effect to such exercise, the Holder (together with the
Holder’s affiliates) would beneficially own in excess of [     %] (the “Maximum Percentage”) of the
shares of Common Stock outstanding immediately after giving effect to such exercise, except as the
Company may otherwise agree in writing in its sole and absolute discretion, and subject to
Section 14. If the Holder has delivered an Exercise Notice, the Company shall be entitled
to assume that such exercise will not result in the Holder exceeding the Maximum Percentage as a
result of the exercise contemplated by such Exercise Notice. For purposes of the foregoing
sentence, the aggregate number of shares of Common Stock beneficially owned by such Holder 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 immediately
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 the most recent of (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 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. 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
and reasonably 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) 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. For the avoidance of doubt, if the
Exercise Price is adjusted as a result of the occurrence of the Decision, then the Exercise Price
so adjusted shall be in effect, without regard to any adjustment as a result of any subdivision or
combination of the Common Stock described in this Section 2(a) that may have occurred prior
to the date on which the adjustment resulting from the occurrence of the Decision occurs, but the
Exercise Price shall thereafter be adjusted to reflect any subdivision or combination of the Common
Stock described in this Section 2(a) that may occur on or after the date on which the
adjustment resulting from the occurrence of the Decision occurs.

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).

For the avoidance of doubt, if the Exercise Price is adjusted as a result of the occurrence of a
Distribution, then the Exercise Price so adjusted shall be in effect, without regard to any
adjustment as a result of a Distribution that may have occurred prior to the date on which the
adjustment resulting from the occurrence of the Decision occurs, but the Exercise Price shall
thereafter be adjusted to reflect any Distribution that may occur on or after the date on which the
adjustment resulting from the occurrence of the Decision occurs.

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”) (and not, for the avoidance of doubt,
equity awards to employees, directors or consultants), 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.

(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) and delivers to each holder of Warrants in exchange for
such Warrants, promptly following consummation of such Fundamental Transaction, a new Warrant
substantially similar in form and substance to this Warrant reflecting any modification in the
terms of the Warrant pursuant to this Section 4(b). If, at any time prior to the
Expiration Date, the Company enters into or is a party to a Fundamental Transaction pursuant to
which holders of shares of Common Stock are entitled or required to receive securities issued by
another company or cash or other assets with respect to or in exchange for shares of Common Stock
(a “Corporate Event”), the Holder shall thereafter have the right to receive upon an exercise of
this Warrant for each Warrant Share that would have been issuable upon exercise of this Warrant
prior to consummation of such Corporate Event, 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 Corporate Event, 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 consummation of such Corporate Event had the Warrant been
exercised for one Warrant Share immediately prior to consummation of such Corporate Event. If
holders of Common Stock are given any choice as to the securities, cash or property to be received
in a Corporate Event, then the Holder shall be given the same choice as to the consideration it
receives upon any exercise of this Warrant following consummation of such Corporate Event. The
provisions of this Section 4(b) 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 in Section 1(h). Notwithstanding the foregoing, in the event of a
Fundamental Transaction, at the request of the Holder delivered before the 15th calendar day after
consummation of such Fundamental Transaction, the Company (or the Successor Entity) shall purchase
this Warrant from the Holder by paying to the Holder, within five (5) Business Days after such
request (or, if later, within one Business Day after the effective date of such Corporate Event),
cash in an amount equal to the Black Scholes Value of the remaining unexercised portion of this
Warrant on the date of consummation of such Fundamental Transaction. In the event a Corporate
Event is consummated before the Assessment Date, then the Exercise Price hereunder shall for all
purposes thereafter be the Weighted Average Price for the Common Stock for the five (5) Trading
Days immediately preceding the first public announcement of such Corporate Event; provided,
however, that in no event shall the Exercise Price determined in accordance with this
sentence (i) exceed $2.75 or (ii) be less than $1.50, in each case subject to appropriate
adjustment in the event of any stock dividend, stock split, combination or other similar
recapitalization with respect to the Common Stock.

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 comply with all the
provisions of this Warrant. 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, then as a condition
precedent to such transfer becoming effective, Holder shall surrender the original Warrant to the
Company in accordance with Section 8, whereupon the Company will forthwith issue and
deliver upon a new Warrant (in accordance with Section 7(d)), registered to such Person 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. For each
Warrant so transferred, the Maximum Percentage shall be 4.99%, except as the Company may otherwise
agree in writing in its sole and absolute discretion.

(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.

(c) Exchangeable for Multiple Warrants. This Warrant is exchangeable, upon the
surrender of the original Warrant by the Holder at the principal office of the Company in
accordance with Section 8, for a new Warrant or Warrants (in accordance with
Section 7(c)) 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.
Notwithstanding anything to the contrary herein, in no event shall this Warrant be subdivided into
more than 20 separate Warrants.

(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 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,
subject to Section 7(a).

8. NOTICES. All notices, requests, consents and other communications under this
Warrant will be in writing, will be mailed (a) if within the domestic United States by first-class
registered or certified airmail, or nationally recognized overnight express courier, postage
prepaid, or by facsimile or (b) if delivered from outside the United States, by International
Federal Express, and (c) will be deemed delivered upon the Business Day received:

(i) if to the Company, to:

Cytokinetics, Incorporated

280 East Grand Avenue

South San Francisco, California 94080

Attention: Stock Administrator

with an electronic copy (for informational purposes only) to:

stockadministrator@cytokinetics.com

(ii) if to the Holder, to its principal place of business, or at such other address or
addresses as may have been furnished to the Company in writing in accordance with this Section
8.

Either party may change its notice information by written notice to the other party given in
accordance with this Section 8.

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.

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
its receipt of written notice from the Holder that such dispute has arisen 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
thereafter 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, which
approval shall not be unreasonably withheld 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 (10) 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. Subject to applicable law, this Warrant may be offered for sale, sold,
transferred or assigned without the consent of the Company, provided that any purported sale,
transfer or assignment of this Warrant shall be null, void and of no legal effect unless the
Holder has first surrendered the original Warrant to the Company in accordance with Section
7(a).

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 using (i) a price per share of
Common Stock equal to the Weighted Average Price of the Common Stock for the Trading Day
immediately preceding the date of consummation of the applicable Fundamental Transaction, (ii) 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 the date of consummation of the applicable Fundamental Transaction and
(iii) an expected volatility equal to the lesser of 50% and the 30-day volatility obtained from the
HVT function on Bloomberg determined as of the Trading Day immediately following the 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) “Closing Sale Price” means, for any security as of any date, the last closing trade price
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 trade price, 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 trade price 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 trade price 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 trade price 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 Sale Price cannot be calculated for a security on a particular date
on any of the foregoing bases, the Closing Sale Price of such security on such date shall be the
fair market value as mutually determined by the Company and the Holder. If the Company and the
Holder are unable to agree upon the fair market value of such security, then such dispute shall be
resolved pursuant to Section 12 with the term “Closing Sale Price” being substituted for
the term “Exercise Price.” All such determinations to be appropriately adjusted for any stock
dividend, stock split, stock combination or other similar transaction during the applicable
calculation period.

(e) “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.

(f) “Convertible Securities” means any stock or securities (other than Options) directly or
indirectly convertible into or exercisable or exchangeable for shares of Common Stock.

(g) “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.

(h) “Expiration Date” means the thirty (30) month anniversary of the Issuance Date.

(i) “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 sell, assign, transfer, convey or otherwise dispose of
all or substantially all of the properties or assets of the Company to another Person, or
(ii) 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 (iii) 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), or (iv) 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.

(j) “Options” means any rights, warrants or options to subscribe for or purchase shares of
Common Stock or Convertible Securities.

(k) “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.

(l) “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.

(m) “Principal Market” means The NASDAQ Global Market.

(n) “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.

(o) “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 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).

(p) “Weighted Average Price” means, for any security as of any date, the dollar
volume-weighted average price for such security on the Principal Market during the period beginning
at 9:30:01 a.m., New York City time, and ending at 4:00:00 p.m., New York City time, as reported by
Bloomberg through its “Volume at Price” function or, if the foregoing does not apply, the dollar
volume-weighted average price of such security in the over-the-counter market on the electronic
bulletin board for such security during the period beginning at 9:30:01 a.m., New York City time,
and ending at 4:00:00 p.m., New York City time, as reported by Bloomberg, or, if no dollar
volume-weighted average price is reported for such security by Bloomberg for such hours, the
average of the highest closing bid price and the lowest closing ask price of any of the market
makers for such security as reported in the “pink sheets” by Pink Sheets LLC (formerly the National
Quotation Bureau, Inc.). If the Weighted Average Price cannot be calculated for such security on
such date on any of the foregoing bases, the Weighted Average Price of such security on such date
shall be the fair market value as mutually determined by the Company and the Holder. If the
Company and the Holder are unable to agree upon the fair market value of such security, then such
dispute shall be resolved pursuant to Section 12 with the term “Weighted Average Price”
being substituted for the term “Exercise Price.” All such determinations shall be appropriately
adjusted for any share dividend, share split or other similar transaction during such period.

[Signature Page Follows]

	1	 	Insert a number of shares equal to 50% of the
number of shares of Common Stock purchased under the Subscription Agreement.

1

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.

CYTOKINETICS, INCORPORATED

By:

Name:

Title:

EXHIBIT A

EXERCISE NOTICE

TO BE EXECUTED BY THE REGISTERED HOLDER TO EXERCISE THIS

WARRANT TO PURCHASE COMMON STOCK

CYTOKINETICS, INCORPORATED

The undersigned holder hereby exercises the right to purchase        of the shares
of Common Stock (“Warrant Shares”) of CYTOKINETICS, INCORPORATED, 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. The terms of this Exercise Notice are subject to adjustment as a result of
the Company’s right pursuant to Section 1(a) to require that an exercise be on a Cashless
Exercise Basis.

1. Form of Exercise Price. The Holder intends that payment of the Exercise Price
shall be made as:

       a “Cash Exercise” with respect to        Warrant Shares;
and/or

       a “Cashless Exercise” with respect to        Warrant Shares.

2. Payment of Exercise Price. In the event that the holder has elected a Cash
Exercise with respect to some or all of the Warrant Shares to be issued pursuant hereto, the holder
shall pay the Aggregate Exercise Price in the sum of $        to the Company in
accordance with the terms of the Warrant.

3. 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:

ACKNOWLEDGMENT

The Company hereby acknowledges this Exercise Notice and hereby directs BNY Mellon Shareowner
Services to issue the above indicated number of shares of Common Stock in accordance with the
Transfer Agent Instructions dated [     , 2009] from the Company and acknowledged and agreed to by
BNY Mellon Shareowner Services.

CYTOKINETICS, INCORPORATED

By:

Name:

Title:

2

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