Document:

EX-4.5

Exhibit 4.5

CYTOKINETICS, INCORPORATED

CERTIFICATE OF DESIGNATION OF PREFERENCES,

RIGHTS AND LIMITATIONS

OF

SERIES A CONVERTIBLE PREFERRED STOCK

PURSUANT TO SECTION 151 OF THE

DELAWARE GENERAL CORPORATION LAW

CYTOKINETICS, INCORPORATED, a Delaware corporation (the “Corporation”), in accordance
with the provisions of Section 103 of the Delaware General Corporation Law (the “DGCL”) does hereby
certify that, in accordance with Sections 141(c) and 151 of the DGCL, the following resolution was
duly adopted by the Board of Directors of the Corporation as of April 14, 2011:

RESOLVED, that the Board of Directors of the Corporation pursuant to authority expressly
vesting in it by the provisions of the Certificate of Incorporation of the Corporation, hereby
authorizes the issuance of a series of Preferred Stock designated as the Series A Convertible
Preferred Stock, par value $0.001 per share, of the Corporation and hereby fixes the designation,
number of shares, powers, preferences, rights, qualifications, limitations and restrictions thereof
(in addition to any provisions set forth in the Certificate of Incorporation of the Corporation
which are applicable to the Preferred Stock of all classes and series) as follows:

SERIES A CONVERTIBLE PREFERRED STOCK

Section 1. Definitions. For the purposes hereof, the following terms shall
have the following meanings:

“Affiliate” means any person or entity that, directly or indirectly through one or
more intermediaries, controls or is controlled by or is under common control with a person
or entity, as such terms are used in and construed under Rule 144 under the Securities Act .
With respect to a Holder, any investment fund or managed account that is managed on a
discretionary basis by the same investment manager as such Holder will be deemed to be an
Affiliate of such Holder.

“Alternate Consideration” shall have the meaning set forth in Section 7(b).

“Beneficial Ownership Limitation” shall have the meaning set forth in Section 6(c).

“Business Day” means any day except Saturday, Sunday, any day which shall be a
federal legal holiday in the United States or any day on which banking institutions in the
State of New York are authorized or required by law or other governmental action to close.

“Buy-In” shall have the meaning set forth in Section 6(d)(iii).

“Closing Sale Price” means, for any security as of any date, the last closing trade
price for such security prior to 4:00 p.m., New York City time, on the principal securities
exchange or trading market where such security is listed or traded, as reported by
Bloomberg, L.P. (or an equivalent, reliable reporting service mutually acceptable to and
hereafter designated by Holders of a majority of the then-outstanding Series A Preferred
Stock and the Corporation), or if the foregoing do not apply, the last trade price of such
security in the over-the-counter market on the electronic bulletin board for such security
as reported by Bloomberg, L.P., or, if no last trade price is reported for such security by
Bloomberg, L.P., the average of the bid prices of any market makers for such security as
reported on the OTC Pink Market by OTC Markets Group, 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 determined in
good faith by the Board of Directors of the Corporation.

“Commission” means the Securities and Exchange Commission.

“Common Stock” means the Corporation’s common stock, par value $0.001 per share, and
stock of any other class of securities into which such securities may hereafter be
reclassified or changed into.

“Common Stock Equivalents” means any securities of the Corporation or the
Subsidiaries which would entitle the holder thereof to acquire at any time Common Stock,
including, without limitation, any debt, preferred stock, rights, options, warrants or other
instrument that is at any time convertible into or exchangeable for, or otherwise entitles
the holder thereof to receive, Common Stock.

“Conversion Date” shall have the meaning set forth in Section 6(a).

“Conversion Price” shall mean $1.50, as adjusted pursuant to paragraph 7 hereof.

“Conversion Ratio” shall have the meaning set forth in Section 6(b).

“Conversion Shares” means, collectively, the shares of Common Stock issuable upon
conversion of the shares of Series A Preferred Stock in accordance with the terms hereof.

“Daily Failure Amount” means the product of (x) .005 multiplied by (y) the Closing
Sale Price of the Common Stock on the applicable Share Delivery Date.

“DGCL” shall mean the Delaware General Corporation Law.

“Distributions” shall have the meaning set forth in Section 5(a).

“DWAC Delivery” shall have the meaning set forth in Section 6(a).

“Exchange Act” means the Securities Exchange Act of 1934, as amended, and the rules
and regulations promulgated thereunder.

“Fundamental Transaction” shall have the meaning set forth in Section 7(b).

“Holder” means any holder of Series A Preferred Stock.

“Issuance Date” means the date of the “Closing” as defined in that certain
Securities Purchase Agreement, dated April 18, 2011, by and among the Corporation and the
“Investors” named therein (the “Securities Purchase Agreement”).

“Investors” shall have the meaning given to such term in the Securities Purchase
Agreement.

“Junior Securities” shall have the meaning set forth in Section 5(a).

“Notice of Conversion” shall have the meaning set forth in Section 6(a).

“Parity Securities” shall have the meaning set forth in Section 5(a).

“Person” means any individual or corporation, partnership, trust, incorporated or
unincorporated association, joint venture, limited liability company, joint stock company,
government (or an agency or subdivision thereof) or other entity of any kind.

“Securities Act” means the Securities Act of 1933, as amended, and the rules and
regulations promulgated thereunder.

“Senior Securities” shall have the meaning set forth in Section 5(a).

“Series A Preferred Stock Register” shall have the meaning set forth in Section
2(b).

“Share Delivery Date” shall have the meaning set forth in Section 6(d).

“Stated Value” shall mean $1,500.00.

“Trading Day” means a day on which the Common Sock is traded for any period on the
principal securities exchange or if the Common Stock is not traded on a principal securities
exchange, on a day that the Common Stock is traded on another securities market on which the
Common Stock is then being traded.

Section 2. Designation, Amount and Par Value; Assignment.

a) The series of preferred stock designated by this Certificate shall be designated as
the Corporation’s Series A Convertible Preferred Stock (the “Series A Preferred
Stock”) and the number of shares so designated shall be 8,070 (which shall not be
subject to increase without the written consent of the Holders of a majority of the issued
and outstanding Series A Preferred Stock). Each share of Series A Preferred Stock shall have
a par value of $0.001 per share.

b) The Corporation shall register shares of the Series A Preferred Stock, upon records
to be maintained by the Corporation for that purpose (the “Series A Preferred Stock
Register”), in the name of the Holders thereof from time to time. The Corporation may
deem and treat the registered Holder of shares of Series A Preferred Stock as the absolute
owner thereof for the purpose of any conversion thereof and for all other purposes. The
Corporation shall register the transfer of any shares of Series A Preferred Stock in the
Series A Preferred Stock Register, upon surrender of the certificates evidencing such shares
to be transferred, duly endorsed by the Holder thereof, to the Corporation at its address
specified herein. Upon any such registration or transfer, a new certificate evidencing the
            shares of Series A Preferred Stock so transferred shall be issued to the transferee and a
new certificate evidencing the remaining portion of the shares not so transferred, if any,
shall be issued to the transferring Holder, in each case, within three Business Days. The
provisions of this Certificate are intended to be for the benefit of all Holders from time
to time and shall be enforceable by any such Holder.

 

Section 3. Dividends. Holders shall not be
entitled to receive any dividends in respect of the Series A Preferred Stock, unless and until
specifically declared by the Board of Directors of the Corporation to be payable to the Holders of
the Series A Preferred Stock.

Section 4. Voting Rights. Except as otherwise provided herein or as otherwise
required by the DGCL, the Series A Preferred Stock shall have no voting rights. However, as long as
any shares of Series A Preferred Stock are outstanding, the Corporation shall not, without the
affirmative vote of the Holders of a majority of the then outstanding shares of the Series A
Preferred Stock, (a) alter or change adversely the powers, preferences or rights given to the
Series A Preferred Stock or alter or amend this Certificate, (b) increase the number of authorized
shares of Series A Preferred Stock, or (c) enter into any agreement with respect to any of the
foregoing.

Section 5. Rank; Liquidation.

a) The Series A Preferred Stock shall rank (i) senior to all of the Common Stock; (ii)
senior to any class or series of capital stock of the Corporation hereafter created
specifically ranking by its terms junior to any Series A Preferred Stock (“Junior
Securities”); (iii) on parity with any class or series of capital stock of the
Corporation hereafter created specifically ranking by its terms on parity with the Series A
Preferred Stock (“Parity Securities”); and (iv) junior to any class or series of
capital stock of the Corporation hereafter created specifically ranking by its terms senior
to any Series A Preferred Stock (“Senior Securities”), in each case, as to
distributions of assets upon liquidation, dissolution or winding up of the Corporation,
whether voluntarily or involuntarily (all such distributions being referred to collectively
as “Distributions”).

b) Subject to the prior and superior rights of the holders of any Senior Securities of
the Corporation, upon liquidation, dissolution or winding up of the Corporation, whether
voluntary or involuntary, each holder of shares of Series A Preferred Stock shall be
entitled to receive, in preference to any distributions of any of the assets or surplus
funds of the Corporation to the holders of the Common Stock and Junior Securities and pari
passu with any distribution to the holders of Parity Securities, an amount equal to $0.001
per share of Series A Preferred Stock, plus an additional amount equal to any dividends
declared but unpaid on such shares, before any payments shall be made or any assets
distributed to holders of any class of Common Stock or Junior Securities. If, upon any such
liquidation, dissolution or winding up of the Corporation, the assets of the Corporation
shall be insufficient to pay the holders of shares of the Series A Preferred Stock the
amount required under the preceding sentence, then all remaining assets of the Corporation
shall be distributed ratably to holders of the shares of the Series A Preferred Stock and
Parity Securities.

Section 6. Conversion.

a) Conversions at Option of Holder. Each share of Series A Preferred Stock
shall be convertible, at any time and from time to time from and after the Issuance Date, at
the option of the Holder thereof, into a number of shares of Common Stock equal to the
Conversion Ratio. Holders shall effect conversions by providing the Corporation with the
form of conversion notice attached hereto as Annex A (a “Notice of
Conversion”), duly completed and executed. Other than a conversion following a
Fundamental Transaction or following a notice provided for under Section 7(d)(ii) hereof,
the Notice of Conversion must specify at least a number of shares of Series A Preferred
Stock to be converted equal to the lesser of (x) 100 shares (such number subject to
appropriate adjustment following the occurrence of an event specified in Section 7(a)
hereof) and (y) the number of shares of Series A Preferred Stock then held by the Holder.
Provided the Corporation’s transfer agent is participating in the Depository Trust Company
(“DTC”) Fast Automated Securities Transfer program, the Notice of Conversion may
specify, at the Holder’s election, whether the applicable Conversion Shares shall be
credited to the account of the Holder’s prime broker with DTC through its Deposit Withdrawal
Agent Commission system (a “DWAC Delivery”). The “Conversion Date”, or the
date on which a conversion shall be deemed effective, shall be defined as the Trading Day
that the Notice of Conversion, completed and executed, is sent by facsimile to, and received
during regular business hours by, the Corporation; provided that the original certificate(s)
representing such shares of Series A Preferred Stock being converted, duly endorsed, and the
accompanying Notice of Conversion, are received by the Corporation within two (2) Trading
Days thereafter. In all other cases, the Conversion Date shall be defined as the Trading
Day on which the original shares of Series A Preferred Stock being converted, duly endorsed,
and the accompanying Notice of Conversion, are received by the Corporation. The
calculations set forth in the Notice of Conversion shall control in the absence of manifest
or mathematical error.

b) Conversion Ratio. The “Conversion Ratio” for each share of Series A
Preferred Stock shall be equal to the Stated Value divided by the Conversion Price.

c) Beneficial Ownership Limitation. Notwithstanding anything herein to the
contrary, the Corporation shall not effect any conversion of the Series A Preferred Stock,
and a Holder shall not have the right to convert any portion of the Series A Preferred
Stock, to the extent that, after giving effect to an attempted conversion set forth on an
applicable Notice of Conversion, such Holder (together with such Holder’s Affiliates, and
any other Person whose beneficial ownership of Common Stock would be aggregated with the
Holder’s for purposes of Section 13(d) of the Exchange Act and the applicable regulations of
the Commission, including any “group” of which the Holder is a member) would beneficially
own a number of shares of Common Stock in excess of the Beneficial Ownership Limitation (as
defined below).  For purposes of the foregoing sentence, the 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 conversion of the Series A Preferred Stock subject to
the Notice of Conversion with respect to which such determination is being made, but shall
exclude the number of shares of Common Stock which are issuable upon (A) conversion of the
remaining, unconverted Series A Preferred Stock beneficially owned by such Holder or any of
its Affiliates, and (B) exercise or conversion of the unexercised or unconverted portion of
any other securities of the Corporation (including any warrants) beneficially owned by such
Holder or any of its Affiliates that are subject to a limitation on conversion or exercise
similar to the limitation contained herein.  Except as set forth in the preceding sentence,
for purposes of this Section 6(c), beneficial ownership shall be calculated in accordance
with Section 13(d) of the Exchange Act and the applicable regulations of the Commission. In
addition, for purposes hereof, “group” has the meaning set forth in Section 13(d) of the
Exchange Act and the applicable regulations of the Commission. For purposes of this Section
6(c), it is understood that the number of shares of Common Stock beneficially owned by each
Investor shall be aggregated with each other Investor for purposes of Section 13(d) of the
Exchange Act. For purposes of this Section 6(c), in determining the number of outstanding
            shares of Common Stock, a Holder may rely on the number of outstanding shares of Common
Stock as stated in the most recent of the following: (A) the Corporation’s most recent
periodic or annual filing with the Commission, as the case may be, (B) a more recent public
announcement by the Corporation that is filed with the Commission or (C) a more recent
notice by the Corporation or the Corporation’s transfer agent to the Holder setting forth
the number of shares of Common Stock then outstanding.  Upon the written request of a Holder
(which may be by email), the Corporation shall, within three (3) Trading Days thereof,
confirm in writing to such Holder (which may be via email) 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 any actual conversion or exercise of securities of the
Corporation, including shares of Series A Preferred Stock, by such Holder or its Affiliates
since the date as of which such number of outstanding shares of Common Stock was last
publicly reported or confirmed to the Holder. The “Beneficial Ownership Limitation”
shall be 9.98% of the number of shares of the Common Stock outstanding immediately after
giving effect to the issuance of shares of Common Stock pursuant to such Notice of
Conversion (to the extent permitted pursuant to this Section 6(c)). The Corporation shall
be entitled to rely on representations made to it by the Holder in any Notice of Conversion
regarding its Beneficial Ownership Limitation.

d) Mechanics of Conversion

i. Delivery of Certificate or Electronic Issuance Upon Conversion. Not
later than three Trading Days after the applicable Conversion Date, or if the Holder
requests the issuance of physical certificate(s), two Trading Days after receipt by
the Corporation of the original certificate(s) representing such shares of Series A
Preferred Stock being converted, duly endorsed, and the accompanying Notice of
Conversion (the “Share Delivery Date”), the Corporation shall (a) deliver,
or cause to be delivered, to the converting Holder a physical certificate or
certificates representing the number of Conversion Shares being acquired upon the
conversion of shares of Series A Preferred Stock or (b) in the case of a DWAC
Delivery, electronically transfer such Conversion Shares by crediting the account of
the Holder’s prime broker with DTC through its DWAC system. If in the case of any
Notice of Conversion such certificate or certificates are not delivered to or as
directed by or, in the case of a DWAC Delivery, such shares are not electronically
delivered to or as directed by, the applicable Holder by the Share Delivery Date,
the applicable Holder shall be entitled to elect to rescind such Conversion Notice
by written notice to the Corporation at any time on or before its receipt of such
certificate or certificates for Conversion Shares or electronic receipt of such
            shares, as applicable, in which event the Corporation shall promptly return to such
Holder any original Series A Preferred Stock certificate delivered to the
Corporation and such Holder shall promptly return to the Corporation any Common
Stock certificates or otherwise direct the return of any shares of Common Stock
delivered to the Holder through the DWAC system, representing the shares of Series A
Preferred Stock unsuccessfully tendered for conversion to the Corporation.

 

ii. Obligation Absolute. Subject to Section 6(c) hereof and subject to
Holder’s right to rescind a Conversion Notice pursuant to Section 6(d)(i) above, the
Corporation’s obligation to issue and deliver the Conversion Shares upon conversion
of Series A Preferred Stock in accordance with the terms hereof are absolute and
unconditional, irrespective of any action or inaction by a Holder to enforce the
same, any waiver or consent with respect to any provision hereof, the recovery of
any judgment against any Person or any action to enforce the same, or any setoff,
counterclaim, recoupment, limitation or termination, or any breach or alleged breach
by such Holder or any other Person of any obligation to the Corporation or any
violation or alleged violation of law by such Holder or any other Person, and
irrespective of any other circumstance which might otherwise limit such obligation
of the Corporation to such Holder in connection with the issuance of such Conversion
Shares. Subject to Section 6(c) hereof and subject to Holder’s right to rescind a
Conversion Notice pursuant to Section 6(d)(i) above, in the event a Holder shall
elect to convert any or all of its Series A Preferred Stock, the Corporation may not
refuse conversion based on any claim that such Holder or any one associated or
affiliated with such Holder has been engaged in any violation of law, agreement or
for any other reason, unless an injunction from a court, on notice to Holder,
restraining and/or enjoining conversion of all or part of the Series A Preferred
Stock of such Holder shall have been sought and obtained by the Corporation, and the
Corporation posts a surety bond for the benefit of such Holder in the amount of 150%
of the value of the Conversion Shares into which would be converted the Series A
Preferred Stock which is subject to such injunction, which bond shall remain in
effect until the completion of arbitration/litigation of the underlying dispute and
the proceeds of which shall be payable to such Holder to the extent it obtains
judgment. In the absence of such injunction, the Corporation shall, subject to
Section 6(c) hereof and subject to Holder’s right to rescind a Conversion Notice
pursuant to Section 6(d)(i) above, issue Conversion Shares upon a properly noticed
conversion. If the Corporation fails to deliver to a Holder such certificate or
certificates, or electronically deliver (or cause its transfer agent to
electronically deliver) such shares in the case of a DWAC Delivery, pursuant to
Section 6(d)(i) on or prior to the fifth (5th) Trading Day after the Share Delivery
Date applicable to such conversion (other than a failure caused by incorrect or
incomplete information provided by Holder to the Corporation), then, unless the
Holder has rescinded the applicable Conversion Notice pursuant to Section 6(d)(i)
above, the Corporation shall pay (as liquidated damages and not as a penalty) to
such Holder an amount payable, at the Corporation’s option, either (a) in cash or
(b) in shares of Common Stock that are valued for these purposes at the Closing Sale
Price on the date of such calculation, in each case equal to the product of (x) the
number of Conversion Shares required to have been issued by the Corporation on such
Share Delivery Date, (y) an amount equal to the Daily Failure Amount and (z) the
number of Trading Days actually lapsed after such fifth (5th) Trading Day after the
Share Delivery Date during which such certificates have not been delivered, or, in
the case of a DWAC Delivery, such shares have not been electronically delivered;
provided, however, the Holder shall only receive up to such amount of shares of
Common Stock such that Holder and any other persons or entities whose beneficial
ownership of Common Stock would be aggregated with the Holder’s for purposes of
Section 13(d) of the Exchange Act (including shares held by any “group” of which the
Holder is a member, but excluding shares beneficially owned by virtue of the
ownership of securities or rights to acquire securities that have limitations on the
right to convert, exercise or purchase similar to the limitation set forth herein)
shall not collectively beneficially own greater than 9.98% of the total number of
            shares of Common Stock of the Corporation then issued and outstanding. Nothing
herein shall limit a Holder’s right to pursue actual damages for the Corporation’s
failure to deliver Conversion Shares within the period specified herein and such
Holder shall have the right to pursue all remedies available to it hereunder, at law
or in equity including, without limitation, a decree of specific performance and/or
injunctive relief; provided that Holder shall not receive duplicate damages for the
Corporation’s failure to deliver Conversion Shares within the period specified
herein. The exercise of any such rights shall not prohibit a Holder from seeking to
enforce damages pursuant to any other Section hereof or under applicable law.

iii. Compensation for Buy-In on Failure to Timely Deliver Certificates Upon
Conversion. If the Corporation fails to deliver to a Holder the applicable
certificate or certificates or to effect a DWAC Delivery, as applicable, by the
Share Delivery Date pursuant to Section 6(d)(i) (other than a failure caused by
incorrect or incomplete information provided by Holder to the Corporation), and if
after such Share Delivery Date such Holder is required by its brokerage firm to
purchase (in an open market transaction or otherwise), or the Holder’s brokerage
firm otherwise purchases, shares of Common Stock to deliver in satisfaction of a
sale by such Holder of the Conversion Shares which such Holder was entitled to
receive upon the conversion relating to such Share Delivery Date (a “Buy-In”), then
the Corporation shall (A) pay in cash to such Holder (in addition to any other
remedies available to or elected by such Holder) the amount by which (x) such
Holder’s total purchase price (including any brokerage commissions) for the shares
of Common Stock so purchased exceeds (y) the product of (1) the aggregate number of
            shares of Common Stock that such Holder was entitled to receive from the conversion
at issue multiplied by (2) the actual sale price at which the sell order giving rise
to such purchase obligation was executed (including any brokerage commissions) and
(B) at the option of such Holder, either reissue (if surrendered) the shares of
Series A Preferred Stock equal to the number of shares of Series A Preferred Stock
submitted for conversion or deliver to such Holder the number of shares of Common
Stock that would have been issued if the Corporation had timely complied with its
delivery requirements under Section 6(d)(i). For example, if a Holder purchases
            shares of Common Stock having a total purchase price of $11,000 to cover a Buy-In
with respect to an attempted conversion of shares of Series A Preferred Stock with
respect to which the actual sale price (including any brokerage commissions) giving
rise to such purchase obligation was a total of $10,000 under clause (A) of the
immediately preceding sentence, the Corporation shall be required to pay such Holder
$1,000. The Holder shall provide the Corporation written notice, within three (3)
Trading Days after the occurrence of a Buy-In, indicating the amounts payable to
such Holder in respect of such Buy-In together with applicable confirmations and
other evidence reasonably requested by the Corporation. Nothing herein shall limit
a Holder’s right to pursue any other remedies available to it hereunder, at law or
in equity including, without limitation, a decree of specific performance and/or
injunctive relief with respect to the Corporation’s failure to timely deliver
certificates representing shares of Common Stock upon conversion of the shares of
Series A Preferred Stock as required pursuant to the terms hereof; provided,
however, that the Holder shall not be entitled to both (i) require the reissuance of
the shares of Series A Preferred Stock submitted for conversion for which such
conversion was not timely honored and (ii) receive the number of shares of Common
Stock that would have been issued if the Corporation had timely complied with its
delivery requirements under Section 6(d)(i).

iv. Reservation of Shares Issuable Upon Conversion. The Corporation
covenants that it will at all times reserve and keep available out of its authorized
and unissued shares of Common Stock for the sole purpose of issuance upon conversion
of the Series A Preferred Stock, free from preemptive rights or any other actual
contingent purchase rights of Persons other than the Holders of the Series A
Preferred Stock, not less than such aggregate number of shares of the Common Stock
as shall be issuable (taking into account the adjustments of Section 7) upon the
conversion of all outstanding shares of Series A Preferred Stock. The Corporation
covenants that all shares of Common Stock that shall be so issuable shall, upon
issue, be duly authorized, validly issued, fully paid and nonassessable.

v. Fractional Shares. No fractional shares or scrip representing
fractional shares of Common Stock shall be issued upon the conversion of the Series
A Preferred Stock. As to any fraction of a share which a Holder would otherwise be
entitled to receive upon such conversion, the Corporation shall at its election,
either pay a cash adjustment in respect of such final fraction in an amount equal to
such fraction multiplied by the Conversion Price or round up to the next whole
share.

vi. Transfer Taxes. The issuance of certificates for shares of the
Common Stock upon conversion of the Series A Preferred Stock shall be made without
charge to any Holder for any documentary stamp or similar taxes that may be payable
in respect of the issue or delivery of such certificates, provided that the
Corporation shall not be required to pay any tax that may be payable in respect of
any transfer involved in the issuance and delivery of any such certificate upon
conversion in a name other than that of the registered Holder(s) of such shares of
Series A Preferred Stock and the Corporation shall not be required to issue or
deliver such certificates unless or until the Person or Persons requesting the
issuance thereof shall have paid to the Corporation the amount of such tax or shall
have established to the satisfaction of the Corporation that such tax has been paid.

e) Status as Stockholder. Upon each Conversion Date, (i) the shares of Series
A Preferred Stock being converted shall be deemed converted into shares of Common Stock and
(ii) the Holder’s rights as a holder of such converted shares of Series A Preferred Stock
shall cease and terminate, excepting only the right to receive certificates for such shares
of Common Stock and to any remedies provided herein or otherwise available at law or in
equity to such Holder because of a failure by the Corporation to comply with the terms of
this Certificate of Designation. In all cases, the holder shall retain all of its rights
and remedies for the Corporation’s failure to convert Series A Preferred Stock.

Section 7. Certain Adjustments.

a) Stock Dividends and Stock Splits. If the Corporation, at any time while
this Series A Preferred Stock is outstanding: (A) pays a stock dividend or otherwise makes a
distribution or distributions payable in shares of Common Stock (which, for avoidance of
doubt, shall not include any shares of Common Stock issued by the Corporation upon
conversion of this Series A Preferred Stock) with respect to the then outstanding shares of
Common Stock; (B) subdivides outstanding shares of Common Stock into a larger number of
            shares; or (C) combines (including by way of a reverse stock split) outstanding shares of
Common Stock into a smaller number of shares, then the Conversion Price shall be multiplied
by a fraction of which the numerator shall be the number of shares of Common Stock
(excluding any treasury shares of the Corporation) outstanding immediately before such event
and of which the denominator shall be the number of shares of Common Stock outstanding
immediately after such event (excluding any treasury shares of the Corporation). Any
adjustment made pursuant to this Section 7(a) shall become effective immediately after the
record date for the determination of stockholders entitled to receive such dividend or
distribution and shall become effective immediately after the effective date in the case of
a subdivision or combination.

 

b) Fundamental Transaction. If, at any time while this Series A Preferred Stock
is outstanding, (A) the Corporation effects any merger or consolidation of the Corporation
with or into another Person (other than a merger in which the Corporation is the surviving
or continuing entity and its Common Stock is not exchanged for or converted into other
securities, cash or property), (B) the Corporation effects any sale of all or substantially
all of its assets in one transaction or a series of related transactions, (C) any tender
offer or exchange offer (whether by the Corporation or another Person) is completed pursuant
to which all of the Common Stock is exchanged for or converted into other securities, cash
or property, or (D) the Corporation effects any reclassification of the Common Stock or any
compulsory share exchange pursuant (other than as a result of a dividend, subdivision or
combination covered by Section 7(a) above) to which the Common Stock is effectively
converted into or exchanged for other securities, cash or property (in any such case, a
“Fundamental Transaction”), then, upon any subsequent conversion of this Series A
Preferred Stock the Holders shall have the right to receive, in lieu of the right to receive
Conversion Shares, for each Conversion Share that would have been issuable upon such
conversion immediately prior to the occurrence of such Fundamental Transaction, the same
kind and amount of securities, cash or property as it would have been entitled to receive
upon the occurrence of such Fundamental Transaction if it had been, immediately prior to
such Fundamental Transaction, the holder of one share of Common Stock (the “Alternate
Consideration”). For purposes of any such subsequent conversion, the determination of
the Conversion Ratio shall be appropriately adjusted to apply to such Alternate
Consideration based on the amount of Alternate Consideration issuable in respect of one
share of Common Stock in such Fundamental Transaction, and the Corporation shall adjust the
Conversion Ratio in a reasonable manner reflecting the relative value of any different
components of the Alternate Consideration. If holders of Common Stock are given any choice
as to the securities, cash or property to be received in a Fundamental Transaction, then the
Holders shall be given the same choice as to the Alternate Consideration it receives upon
any conversion of this Series A Preferred Stock following such Fundamental Transaction. To
the extent necessary to effectuate the foregoing provisions, any successor to the
Corporation or surviving entity in such Fundamental Transaction shall file a new Certificate
of Designation with the same terms and conditions and issue to the Holders new preferred
stock consistent with the foregoing provisions and evidencing the Holders’ right to convert
such preferred stock into Alternate Consideration. The terms of any agreement to which the
Corporation is a party and pursuant to which a Fundamental Transaction is effected shall
include terms requiring any such successor or surviving entity to comply with the provisions
of this Section 7(b) and insuring that this Series A Preferred Stock (or any such
replacement security) will be similarly adjusted upon any subsequent transaction analogous
to a Fundamental Transaction. The Corporation shall cause to be delivered to each Holder,
at its last address as it shall appear upon the stock books of the Corporation, written
notice of any Fundamental Transaction at least 20 calendar days prior to the date on which
such Fundamental Transaction is expected to become effective or close.

 

c) Calculations. All calculations under this Section 7 shall be made to the
nearest cent or the nearest 1/100th of a share, as the case may be. For purposes of this
Section 7, the number of shares of Common Stock deemed to be issued and outstanding as of a
given date shall be the sum of the number of shares of Common Stock (excluding any treasury
            shares of the Corporation) issued and outstanding.

d) Notice to the Holders.

i. Adjustment to Conversion Price. Whenever the Conversion Price is
adjusted pursuant to any provision of this Section 7, the Corporation shall promptly
deliver to each Holder a notice setting forth the Conversion Ratio after such
adjustment and setting forth a brief statement of the facts requiring such
adjustment.

 

ii. Other Notices. If (A) the Corporation shall declare a dividend (or
any other distribution in whatever form) on the Common Stock, (B) the Corporation
shall declare a special nonrecurring cash dividend on or a redemption of the Common
Stock, (C) the Corporation shall authorize the granting to all holders of the Common
Stock of rights or warrants to subscribe for or purchase any shares of capital stock
of any class or of any rights, (D) the approval of any stockholders of the
Corporation shall be required in connection with any reclassification of the Common
Stock, any consolidation or merger to which the Corporation is a party, any sale or
transfer of all or substantially all of the assets of the Corporation, of any
compulsory share exchange whereby the Common Stock is converted into other
securities, cash or property or (E) the Corporation shall authorize the voluntary or
involuntary dissolution, liquidation or winding up of the affairs of the
Corporation, then, in each case, the Corporation shall cause to be filed at each
office or agency maintained for the purpose of conversion of this Series A Preferred
Stock, and shall cause to be delivered to each Holder at its last address as it
shall appear upon the stock books of the Corporation, at least 20 calendar days
prior to the applicable record or effective date hereinafter specified, a notice
stating (x) the date on which a record is to be taken for the purpose of such
dividend, distribution, redemption, rights or warrants, or if a record is not to be
taken, the date as of which the holders of the Common Stock of record to be entitled
to such dividend, distributions, redemption, rights or warrants are to be determined
or (y) the date on which such reclassification, consolidation, merger, sale,
transfer or share exchange is expected to become effective or close, and the date as
of which it is expected that holders of the Common Stock of record shall be entitled
to exchange their shares of the Common Stock for securities, cash or other property
deliverable upon such reclassification, consolidation, merger, sale, transfer or
share exchange, provided that the failure to deliver such notice or any defect
therein or in the delivery thereof shall not affect the validity of the corporate
action required to be specified in such notice.

Section 8. Miscellaneous.

a) Notices. Any and all notices or other communications or deliveries to be
provided by the Holders hereunder including, without limitation, any Notice of Conversion,
shall be in writing and delivered personally, by facsimile, or sent by a nationally
recognized overnight courier service, addressed to the Corporation, at 280 East Grand
Avenue, South San Francisco, California 94080, facsimile number (650) 624-3010, or such
other facsimile number or address as the Corporation may specify for such purposes by notice
to the Holders delivered in accordance with this Section. Any and all notices or other
communications or deliveries to be provided by the Corporation hereunder shall be in writing
and delivered personally, by facsimile, or sent by a nationally recognized overnight courier
service addressed to each Holder at the facsimile number or address of such Holder appearing
on the books of the Corporation, or if no such facsimile number or address appears on the
books of the Corporation, at the principal place of business of such Holder. Any notice or
other communication or deliveries hereunder shall be deemed given and effective on the
earliest of (i) the date of transmission, if such notice or communication is delivered via
facsimile at the facsimile number specified in this Section prior to 5:30 p.m. (New York
City time) on any date, (ii) the date immediately following the date of transmission, if
such notice or communication is delivered via facsimile at the facsimile number specified in
this Section between 5:30 p.m. and 11:59 p.m. (New York City time) on any date, (iii) the
second Business Day following the date of mailing, if sent by nationally recognized
overnight courier service, or (iv) upon actual receipt by the party to whom such notice is
required to be given.

 

b) [Reserved.]

c) Lost or Mutilated Series A Preferred Stock Certificate. If a Holder’s
Series A Preferred Stock certificate shall be mutilated, lost, stolen or destroyed, the
Corporation shall execute and deliver, in exchange and substitution for and upon
cancellation of a mutilated certificate, or in lieu of or in substitution for a lost, stolen
or destroyed certificate, a new certificate for the shares of Series A Preferred Stock so
mutilated, lost, stolen or destroyed, but only upon receipt of evidence of such loss, theft
or destruction of such certificate, and of the ownership thereof, reasonably satisfactory to
the Corporation and, in each case, customary and reasonable indemnity, if requested.
Applicants for a new certificate under such circumstances shall also comply with such other
reasonable regulations and procedures and pay such other reasonable third-party costs as the
Corporation may prescribe.

d) Waiver. Any waiver by the Corporation or a Holder of a breach of any
provision of this Certificate of Designation shall not operate as or be construed to be a
waiver of any other breach of such provision or of any breach of any other provision of this
Certificate of Designation or a waiver by any other Holders. The failure of the Corporation
or a Holder to insist upon strict adherence to any term of this Certificate of Designation
on one or more occasions shall not be considered a waiver or deprive that party (or any
other Holder) of the right thereafter to insist upon strict adherence to that term or any
other term of this Certificate of Designation. Any waiver by the Corporation or a Holder
must be in writing. Notwithstanding any provision in this Certificate of Designation to the
contrary, any provision contained herein and any right of the holders of Series A Preferred
Stock granted hereunder may be waived as to all shares of Series A Preferred Stock (and the
Holders thereof) upon the written consent of the Holders of not less than a majority of the
            shares of Series A Preferred Stock then outstanding, unless a higher percentage is required
by the DGCL, in which case the written consent of the holders of not less than such higher
percentage shall be required.

e) Severability. If any provision of this Certificate of Designation is
invalid, illegal or unenforceable, the balance of this Certificate of Designation shall
remain in effect, and if any provision is inapplicable to any Person or circumstance, it
shall nevertheless remain applicable to all other Persons and circumstances. If it shall be
found that any interest or other amount deemed interest due hereunder violates the
applicable law governing usury, the applicable rate of interest due hereunder shall
automatically be lowered to equal the maximum rate of interest permitted under applicable
law.

f) Next Business Day. Whenever any payment or other obligation hereunder shall
be due on a day other than a Business Day, such payment shall be made on the next succeeding
Business Day.

g) Headings. The headings contained herein are for convenience only, do not
constitute a part of this Certificate of Designation and shall not be deemed to limit or
affect any of the provisions hereof.

h) Status of Converted Series A Preferred Stock. If any shares of Series A
Preferred Stock shall be converted or reacquired by the Corporation, such shares shall
resume the status of authorized but unissued shares of preferred stock and shall no longer
be designated as Series A Preferred Stock.

********************

IN WITNESS WHEREOF, the undersigned has executed this Certificate of Designation this        day
of April 2011.

	 
	Name:

	Title:

1

ANNEX A

NOTICE OF CONVERSION

(TO BE EXECUTED BY THE REGISTERED HOLDER IN ORDER TO CONVERT SHARES OF SERIES A PREFERRED STOCK)

The undersigned Holder hereby irrevocably elects to convert the number of shares of Series A
Convertible Preferred Stock indicated below, represented by stock certificate No(s).      
(the “Preferred Stock Certificates”), into shares of common stock, par value $0.001 per
share (the “Common Stock”), of Cytokinetics, Incorporated, a Delaware corporation (the
“Corporation”), as of the date written below. If securities are to be issued in the name
of a person other than the undersigned, the undersigned will pay all transfer taxes payable with
respect thereto. Capitalized terms utilized but not defined herein shall have the meaning ascribed
to such terms in that certain Certificate of Designation of Preferences, Rights and Limitations of
Series A Convertible Preferred Stock (the “Certificate of Designation”) filed by the
Corporation on April   , 2011.

As of the date hereof, the number of shares of Common Stock beneficially owned by the undersigned
Holder (together with such Holder’s Affiliates, and any other Person whose beneficial ownership of
Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange
Act and the applicable regulations of the Commission, including any “group” of which the Holder is
a member), including the number of shares of Common Stock issuable upon conversion of the Series A
Preferred Stock subject to this Notice of Conversion, but excluding the number of shares of Common
Stock which are issuable upon (A) conversion of the remaining, unconverted Series A Preferred Stock
beneficially owned by such Holder or any of its Affiliates, and (B) exercise or conversion of the
unexercised or unconverted portion of any other securities of the Corporation (including any
warrants) beneficially owned by such Holder or any of its Affiliates that are subject to a
limitation on conversion or exercise similar to the limitation contained in Section 6(c) of the
Certificate of Designation, is       . For purposes hereof, beneficial ownership
shall be calculated in accordance with Section 13(d) of the Exchange Act and the applicable
regulations of the Commission. In addition, for purposes hereof, “group” has the meaning set forth
in Section 13(d) of the Exchange Act and the applicable regulations of the Commission.

Conversion calculations:

	 	 	 
	Date to Effect Conversion:       

	Number of shares of Series A Preferred Stock owned prior to Conversion: ________

	Number of shares of Series A Preferred Stock to be Converted: _________________

	Number of shares of Common Stock to be Issued:       

	Address for delivery of physical certificates:       

	or

	 	

	 

	 	

	for DWAC Delivery:

	 	

	DWAC Instructions:

	 	

	Broker no:      

Account no:      

	 	

	[HOLDER]

By:     

Name:

	 	

	Title:

	 	

	Date:

	 	

2EX-10.67

Exhibit 10.67

SECURITIES PURCHASE AGREEMENT

This SECURITIES PURCHASE AGREEMENT (this “Agreement”), dated as of April 18, 2011, is
by and among Cytokinetics, Incorporated (the “Company”) and Deerfield Private Design Fund
II, L.P., Deerfield Private Design International II, L.P., Deerfield Special Situations Fund, L.P.
and Deerfield Special Situations Fund International Limited (collectively the “Investors”).

RECITALS

WHEREAS, the Company has filed with the Securities and Exchange Commission (the
“Commission”) the Registration Statement (as defined below) relating to the offer and sale
from time to time of the Company’s securities, including shares of its common stock, par value
$0.001 per share (the “Common Stock”), shares of its preferred stock, par value $0.001 per
share (“Preferred Stock”) and warrants to purchase shares of Common Stock
(“Warrants”);

WHEREAS, the Board of Directors of the Company has authorized the creation of a new series of
Preferred Stock denominated as Series A Convertible Preferred Stock (“Series A Preferred
Stock”);

WHEREAS, the Company is offering for sale shares of Common Stock, Series A Preferred Stock and
Warrants (the “Offered Shares”) pursuant to the Registration Statement;

WHEREAS, the Investors desire to purchase from the Company Offered Shares on the terms and
conditions set forth herein;

NOW, THEREFORE, in consideration of the foregoing recitals (which are deemed to be a part of
this Agreement), mutual covenants, representations, warranties and agreements contained herein and
other good and valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereto agree as follows:

1. Definitions. As used herein, the following terms have the meanings indicated:

“Business Day” means any day other than Saturday, Sunday or a day on which banks in
the City of New York are authorized or required to be closed.

“Certificate of Designations” means the Certificate of Designation of Preferences,
Rights and Limitations of the Series A Convertible Preferred Stock, in the form attached hereto as
Exhibit A.

“knowledge” means with respect to any statement made to the Company’s knowledge, that
statement is based upon the actual knowledge of Robert I. Blum, the Company’s President and Chief
Executive Officer and Sharon A. Barbari, the Company’s Executive Vice President, Finance and Chief
Financial Officer.

“Loss” shall have the meaning set forth in Section 5 hereof.

“Person” shall mean any individual, partnership, limited liability company, joint
venture, firm, corporation, association, trust or other enterprise or any government or political
subdivision or any agency, department or instrumentality thereof.

“Prospectus” shall have the meaning set forth in Section 4(b)(7) hereof.

“Prospectus Supplement” shall mean the prospectus supplement filed regarding the
Investor Shares with the Commission pursuant to Rule 424(b) promulgated under the Securities Act
(“Rule 424(b)”) and deemed to be part of the Registration Statement at the time of
effectiveness.

“Registration Statement” shall mean the registration statement on Form S-3 (File No.
333-155259), including a prospectus, and including all amendments and supplements thereto
(including the Prospectus Supplement), relating to the offer and sale of certain of the Company’s
Common Stock, Preferred Stock and Warrants, including the Investor Shares (as defined below).
References herein to the term “Registration Statement” as of any date shall mean such effective
registration statement, as amended or supplemented to such date, including all information and
documents incorporated by reference therein as of such date.

“Securities Act” shall mean the Securities Act of 1933, as amended.

2. Purchase of Common Stock, Series A Preferred Stock and Warrants. Subject and
pursuant to the terms and conditions set forth in this Agreement, the Company agrees that it will
issue and sell to the Investors, and the Investors agree that they will purchase from the Company,
the number of shares of Common Stock, Series A Preferred Stock and Warrants set forth on
Schedule 1 attached hereto (the “Investor Shares”). The aggregate purchase price
for the Investor Shares (the “Aggregate Purchase Price”) is set forth on Schedule 1
hereto. The closing of the purchase and sale of the Investor Shares will take place on April 20,
2011, or such other date or time as the parties may agree upon in writing (the “Closing”).

3. Deliveries at Closing.

(a) Deliveries by the Investor. At the Closing, each Investor shall deliver to the
Company the Aggregate Purchase Price set forth next to their name on Schedule 1 hereto by
wire transfer of immediately available funds to a bank account designated in writing by the Company
to the Investors, which funds will be delivered to the Company in consideration of the Investor
Shares issued at the Closing.

(b) Deliveries by the Company. At the Closing, the Company shall

(1) cause its transfer agent to electronically transmit the shares of Common Stock purchased
by each Investor by crediting the account of each Investor’s prime broker with DTC through its
Deposit Withdrawal Agent Commission (“DWAC”) system;

(2) deliver to each Investor stock certificates in the form attached hereto as Exhibit B and
Warrants in the form attached hereto as Exhibit C registered in the name of such Investor
evidencing the number of shares of Series A Preferred Stock and Warrants purchased by each
Investor; and

(3) deliver evidence satisfactory to the Investors, that the Certificate of Designations has
been filed with the Secretary of State of Delaware and has become effective on or prior to the
Closing.

4. Representations, Warranties, Covenants and Agreements.

(a) Investor Representations, Warranties and Covenants. Each Investor represents,
warrants, covenants and agrees as follows as of the date hereof and as of the Closing:

(1) Investor has received and reviewed copies of the Registration Statement and the
Prospectus, including all documents and information incorporated by reference therein and
amendments thereto, and understands that no Person has been authorized to give any information or
to make any representations that were not contained in the Registration Statement and the
Prospectus, and Investor has not relied on any such other information or representations in making
a decision to purchase the Investor Shares. Investor hereby consents to receiving delivery of the
Registration Statement and the Prospectus, including all documents and information incorporated by
reference therein and amendments thereto, by electronic mail. Investor understands that an
investment in the Company involves a high degree of risk for the reasons, among others, set forth
under the caption “Risk Factors” in the Prospectus.

(2) Investor acknowledges that it has sole responsibility for its own due diligence
investigation and its own investment decision, and that in connection with its investigation of the
accuracy of the information contained or incorporated by reference in the Registration Statement
and the Prospectus and its investment decision, Investor has not relied on any representation or
information, as the case may be, not set forth in this Agreement, the Registration Statement or the
Prospectus, or any Person affiliated with the Company or on the fact that any other Person has
decided to purchase the Offered Shares.

(3) The execution and delivery of this Agreement by Investor and the performance of this
Agreement and the consummation by Investor of the transactions contemplated hereby have been duly
authorized by all necessary corporate or partnership action of Investor, as applicable, and this
Agreement, when duly executed and delivered by Investor, will constitute a valid and legally
binding instrument, enforceable in accordance with its terms against Investor, except as
enforcement hereof may be limited by the effect of any applicable bankruptcy, insolvency,
reorganization or similar laws or court decisions affecting enforcement of creditors’ rights
generally and except as enforcement hereof is subject to general principles of equity (regardless
of whether enforcement is considered in a proceeding in equity or at law).

(b) Company Representations, Warranties and Covenants. The Company hereby represents,
warrants, covenants and agrees as follows as of the date hereof and as of the Closing:

(1) The Company has been duly incorporated and has a valid existence and the authorization to
transact business as a corporation under the laws of the State of Delaware, with corporate power
and authority to own its properties and conduct its business as described in the Prospectus, and
has been duly qualified as a foreign corporation for the transaction of business and is in good
standing under the laws of each other jurisdiction in which it owns or leases properties or
conducts any business so as to require such qualification, except for such jurisdictions wherein
the failure to be so qualified and in good standing would not individually or in the aggregate have
a material adverse effect on the business, results of operations or financial condition of the
Company (a “Material Adverse Effect”).

(2) The Company does not have any subsidiaries.

(3) The execution, delivery and performance of this Agreement by the Company and the
consummation of the transactions contemplated hereby are within the corporate powers of the Company
and have been duly authorized by all necessary corporate action on the part of the Company and this
Agreement, when duly executed and delivered by the parties hereto, will constitute a valid and
legally binding instrument of the Company enforceable in accordance with its terms, except as
enforcement hereof may be limited by the effect of any applicable bankruptcy, insolvency,
reorganization or similar laws or court decisions affecting enforcement of creditors’ rights
generally and except as enforcement hereof is subject to general principles of equity (regardless
of whether enforcement is considered in a proceeding in equity or at law).

(4) The Investor Shares have been duly authorized by the Company, and when issued and
delivered by the Company against payment therefor as contemplated by this Agreement, the Investor
Shares will be validly issued, fully paid and nonassessable, and will conform to the description of
the Common Stock, the Series A Preferred Stock and Warrants contained in the Prospectus.

(5) The Company has reserved from its duly authorized capital stock a number of shares of
Common Stock sufficient for issuance of all shares of Common Stock issuable upon the conversion of
all shares of Series A Preferred Stock (the “Conversion Shares”) and the exercise of all of
the Warrants (the “Warrant Shares”).

(6) The execution and delivery of this Agreement do not, and the compliance by the Company
with the terms hereof will not, (i) violate the Certificate of Incorporation (as amended to date)
of the Company or the By-Laws (as amended to date) of the Company, (ii) result in a breach or
violation of any of the terms or provisions of, or constitute a material default under, any
indenture, mortgage, deed of trust, loan agreement or other agreement or instrument to which the
Company is a party or by which the Company is bound or to which any of its properties or assets are
subject, or (iii) result in a violation of, or failure to be in compliance with, any applicable
statute or any order, judgment, decree, rule or regulation of any court or governmental, regulatory
or self-regulatory agency or body having jurisdiction over the Company or any of its properties or
assets, except where such breach, violation, default or the failure to be in compliance would not
individually or in the aggregate have a Material Adverse Effect or adversely affect the ability of
the Company to issue and sell the Investor Shares; and no consent, approval, authorization, order,
registration, filing or qualification of or with any such court or governmental, regulatory or
self-regulatory agency or body is required for the valid authorization, execution, delivery and
performance by the Company of this Agreement or the issuance of the Investor Shares, except for the
filing of a Form 8-K, the filing of the Prospectus Supplement, the filing of the Certificate of
Designations (which is required to be filed and effective prior to the Closing in accordance with
Section 3(b)(3) hereof), the filing of a Notification of Listing of Additional Shares with The
NASDAQ Stock Market LLC, and for such consents, approvals, authorizations, registrations, filings
or qualifications as may be required under state securities or “blue sky” laws.

(7) The Company meets the requirements for use of Form S-3 under the Securities Act. The
Registration Statement, which covers the Investor Shares, the Conversion Shares and the Warrant
Shares, including a form of prospectus and such amendments or supplements to such Registration
Statement as may have been required prior to the date of this Agreement, has been prepared by the
Company under the provisions of the Securities Act, has been filed with the Commission, has become
effective and filed with the Commission and incorporates by reference documents which the Company
has filed in accordance with the provisions of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”). The Company has prepared a Prospectus Supplement to the prospectus
included in the Registration Statement referred to above, setting forth the terms of the offering
and sale of the Investor Shares, the Conversion Shares and the Warrant Shares and additional
information concerning the Company and its business and will promptly file the Prospectus
Supplement with the Commission pursuant to Rule 424(b). No stop order suspending the effectiveness
of the Registration Statement or any post-effective amendment thereto, or any part thereof, has
been issued and served on the Company, and no proceedings for that purpose are pending or, to the
knowledge of the Company, threatened by the Commission. The form of prospectus included in the
Registration Statement as of the date hereof, as amended or supplemented from time to time
(including the Prospectus Supplement), is referred to herein as the “Prospectus.” Any
reference herein to the Registration Statement, the Prospectus or any amendment or supplement
thereto shall be deemed to refer to and include the documents incorporated (or deemed to be
incorporated) by reference therein, and any reference herein to the terms “amend,” “amendment” or
“supplement” with respect to the Registration Statement or Prospectus shall be deemed to refer to
and include the filing after the execution hereof of any document with the Commission deemed to be
incorporated by reference therein. As of the close of business on April 15, 2011, at least a
number of shares of Common Stock, Series A Preferred Stock and Warrants equal to the number of
Investor Shares, Conversion Shares and Warrant Shares were available for issuance pursuant to the
Registration Statement, which permits the issuance of the Investor Shares, the Conversion Shares
and the Warrant Shares in the manner contemplated by this Agreement.

Each part of the Registration Statement, when such part became or becomes effective, and the
Prospectus and any amendment or supplement thereto, on the date of filing thereof with the
Commission and at the date hereof and the date of the Closing, did or will in all material respects
comply with all applicable provisions of the Securities Act and the Exchange Act. Each part of the
Registration Statement, when such part became or becomes effective, did not or will not contain any
untrue statement of a material fact or omit to state a material fact required to be stated therein
or necessary in order to make the statements therein not misleading. The Prospectus and any
amendment or supplement thereto, on the date of filing thereof with the Commission, did not or will
not contain any untrue statement of a material fact or omit to state a material fact necessary to
make the statements therein, in the light of the circumstances under which they were made, not
misleading. The foregoing representations and warranties in this Section 4(b)(6) do not
apply to any statements or omissions made in reliance on and in conformity with information
relating to the Investors furnished in writing to the Company by the Investors specifically for
inclusion in the Registration Statement or Prospectus or any amendment or supplement thereto.

(8) The consolidated financial statements and financial schedules of the Company included or
incorporated by reference in the Registration Statement and the Prospectus have been prepared in
conformity with generally accepted accounting principles (except, with respect to the unaudited
consolidated financial statements, for the footnotes and subject to customary audit adjustments)
applied on a consistent basis, are consistent in all material respects with the books and records
of the Company, and accurately present in all material respects the consolidated financial
position, results of operations and cash flow of the Company as of and for the periods covered
thereby.

(9) The Company has not sustained since the respective dates of the latest audited financial
statements included in the Registration Statement and Prospectus any material loss or interference
with its business from fire, explosion, flood or other calamity, whether or not covered by
insurance, or from any labor dispute or court or governmental action, order or decree, otherwise
than as disclosed in or contemplated by the Registration Statement and Prospectus; and, since the
respective dates as of which information is given in the Registration Statement and Prospectus,
there has not been any material change in the capital stock or long-term debt of the Company.

(10) Other than as disclosed in the Prospectus, there are no legal, governmental or regulatory
proceedings pending to which the Company is a party or of which any material property of the
Company is the subject which, taking into account the likelihood of the outcome, the damages or
other relief sought and other relevant factors, would individually or in the aggregate reasonably
be expected to have a Material Adverse Effect or adversely affect the ability of the Company to
issue and sell the Investor Shares, and no such proceedings are threatened in writing to the
Company or, to the Company’s knowledge, have been contemplated by governmental or regulatory
authorities or threatened by others.

(11) The Company has title to all the real property, and owns all other properties and assets,
reflected as owned in the financial statements included in the Registration Statement and the
Prospectus, subject to no lien, mortgage, pledge, charge or encumbrance of any kind except those,
if any, reflected in such financial statements or disclosed in the Company’s Commission filings or
exhibits thereto, or which are not material to the Company. The Company holds its respective
leased real and personal properties under valid and binding leases, except where the failure to do
so would not reasonably be expected to individually or in the aggregate have a Material Adverse
Effect.

(12) The Company has filed all necessary federal and state income and franchise tax returns
and has paid all taxes shown as due thereon or has filed all necessary extensions, and there is no
tax deficiency that has been, or to the knowledge of the Company could reasonably be expected to
be, asserted against the Company or any of its properties or assets that would in the aggregate or
individually reasonably be expected to have a Material Adverse Affect.

(13) There are no holders of securities of the Company having preemptive rights to purchase
Common Stock. There are no holders or beneficial owners of securities of the Company having rights
to registration thereof whose securities have not been previously registered or who have not waived
such rights with respect to the registration of the Company’s securities on the Registration
Statement, except where the failure to obtain such waiver would not individually or in the
aggregate reasonably be expected to have a Material Adverse Effect.

(14) The Company is not, and does not intend to conduct its business in a manner in which it
would become, an “investment company” as defined in Section 3(a) of the Investment Company Act of
1940, as amended.

5. Indemnification.

(a) Subject to the limitations and other provisions of this Section 5, the Company
covenants and agrees to indemnify, defend and hold harmless the Investors and their respective
directors, officers, partners, managers, employees and agents (each, an “Investor Party”)
from and against any and all Losses arising from claims by third parties resulting from, incurred
in connection with or arising out of (but only to the extent of) (a) any breach of any
representation, warranty or covenant of the Company contained herein, or (b) the failure of the
Company to perform any of the Company’s agreements, covenants or obligations contained herein
(other than if any such claim was a result of a breach by the Investor under this Agreement).
Subject to the limitations and other provisions of this Section 5, the Investor covenants
and agrees to indemnify, defend and hold harmless the Company from and against (but only to the
extent of) any and all Losses arising from claims by third parties resulting from, incurred in
connection with or arising out of (but only to the extent of) (a) any breach of any representation
or warranty of the Investor contained herein, or (b) the failure of the Investor to perform any of
the agreements, covenants or obligations of the Investor contained herein. The term “Loss”
or any similar term shall mean any and all damages, deficiencies, costs, claims, fines, judgments,
amounts paid in settlement, expenses of investigation, interest, penalties, taxes, assessments,
out-of-pocket expenses (including reasonable attorneys’ and auditors’ fees and disbursements,
witness fees and court costs) but specifically excluding consequential, special, punitive, multiple
and other similar damages. The party or parties being indemnified are referred to herein as the
“Indemnitee” and the indemnifying party is referred to herein as the “Indemnitor.”

(b) Indemnification Procedure.

(1) Any party who receives notice of a potential claim that may, in the judgment of such
party, result in a Loss shall use all reasonable efforts to provide the parties hereto notice
thereof within fifteen (15) days of the filing or other written assertion of any such claim against
the Indemnitee, provided that failure or delay or alleged delay in providing such notice shall not
adversely affect such party’s right to indemnification hereunder, unless and then only to the
extent that such failure or delay or alleged delay has resulted in actual prejudice to the
Indemnitor, including, without limitation, by the expiration of a statute of limitations. In the
event that any party shall incur or suffer any Losses in respect of which indemnification may be
sought by such party hereunder, the Indemnitee shall assert a claim for indemnification by written
notice (a “Notice”) to the Indemnitor stating the nature and basis of such claim.

(2) If indemnification is sought, the Indemnitor shall, if necessary, retain counsel
reasonably satisfactory to the Indemnitee, it being agreed that Cooley LLP is satisfactory, and
have the option (i) to conduct any proceedings or negotiations in connection therewith, (ii) to
take all other steps to settle or defend any such claim (provided that the Indemnitor shall not
settle any such claim without the consent of the Indemnitee which consent shall not be unreasonably
withheld or delayed) and (iii) to employ counsel to contest any such claim or liability in the name
of the Indemnitee or otherwise. In any event, the Indemnitee shall be entitled to participate at
its own expense and by its own counsel in any proceedings relating to any third party claim. The
Indemnitor shall, within fifteen (15) Business Days of receipt of the Notice, notify the Indemnitee
of its intention to assume the defense of such claim. If (i) the Indemnitor shall decline to
assume the defense of any such claim, (ii) the Indemnitor shall fail to notify the Indemnitee
within fifteen (15) Business Days after receipt of the Notice of the Indemnitor’s election to
defend such claim or (iii) in the reasonable opinion of counsel for the Indemnitee, the
representation by the same counsel of the Indemnitor and the Indemnitee would be inappropriate due
to actual or potential material differing interests between such Indemnitee and any other party
represented by such counsel in such proceeding, then in each such case the Indemnitor shall not
have the right to direct the defense of such action on behalf of the Indemnitee and the Indemnitee
shall, at the sole expense of the Indemnitor, defend against such claim; provided, that the
Indemnitee may not settle such claim without the consent of the Indemnitor (which consent will not
be unreasonably withheld or delayed). The Indemnitor shall pay for only one separate legal counsel
for the Indemnitees, and such legal counsel shall be selected by the Indemnitor. The reasonable
expenses of all proceedings, contests or lawsuits in respect of such claims shall be borne and paid
by the Indemnitor if the Indemnitee is entitled to indemnification hereunder and the Indemnitor
shall pay the Indemnitee, in immediately available funds, the amount of any Losses, within a
reasonable time of the incurrence of such Losses. Regardless of which party shall assume the
defense or negotiation of the settlement of the claim, the parties agree to cooperate fully with
one another in connection therewith. Anything in this Section 5 to the contrary
notwithstanding, the Indemnitor shall not, without the Indemnitee’s prior written consent, settle
or compromise any claim or consent to entry of any judgment in respect thereof which imposes any
future obligation on the Indemnitee or which does not include, as an unconditional term thereof,
the giving by the claimant or plaintiff to the Indemnitee, a release from all liability in respect
of such claim.

6. Conditions.

(a) The obligation of each Investor to purchase and acquire the Investor Shares hereunder
shall be subject to the conditions that:

(1) All representations and warranties of the Company herein shall be true and correct in all
material respects as of and on each of the date of this Agreement and the date of the Closing;

(2) The Company shall have performed all of its obligations hereunder; including but not
limited to delivery of the shares of Common Stock included in the Investor Shares through DWAC,
certificates for the Series A Preferred Stock and the Warrants;

(3) The Prospectus Supplement shall have been filed with the Commission pursuant to Rule
424(b) within the applicable time period prescribed for such filing, no stop order suspending the
effectiveness of the Registration Statement or any part thereof shall have been issued and no
proceeding for that purpose shall have been initiated or threatened by the Commission, and the
Investor shall have received the Prospectus in accordance with the federal securities laws; and

(4) The Investors shall have received an opinion of Cooley LLP, counsel to the Company, in the
form attached hereto as Exhibit D.

(b) The obligation of the Company to sell the Investor Shares hereunder shall be subject to
the conditions that:

(1) All representations and warranties and other statements of the Investors herein shall be
true and correct in all material respects as of and on each of the date of this Agreement and the
date of the Closing; and

(2) The Investors shall have performed all of their obligations hereunder, including but not
limited to payment of the Aggregate Purchase Price as provided herein.

7. Miscellaneous.

(a) Binding Agreement; Assignment. This Agreement shall be binding upon, and shall
inure solely to the benefit of, each of the parties hereto, and each of their respective heirs,
executors, administrators, successors and permitted assigns, and no other person shall acquire or
have any right under or by virtue of this Agreement. The Company may not assign any of its rights
or obligations hereunder to any other person or entity without the prior written consent of the
Investors.

(b) Entire Agreement. This Agreement, including the Schedules hereto, constitute the
entire understanding between the parties hereto with respect to the subject matter hereof and may
be amended only by written execution by both parties. Upon execution by the Company and the
Investors, this Agreement shall be binding on each of the parties hereto.

(c) Consent To Jurisdiction. THIS AGREEMENT SHALL BE ENFORCED, GOVERNED AND CONSTRUED
IN ALL RESPECTS IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT GIVING EFFECT TO ITS
CONFLICTS OF LAWS PRINCIPLES OTHER THAN SECTIONS 5-1401 AND 5-1402 OF THE GENERAL OBLIGATIONS LAW
OF SUCH STATE. FURTHERMORE, THE INVESTOR HEREBY IRREVOCABLY SUBMITS TO THE JURISDICTION OF THE
FEDERAL OR STATE COURTS LOCATED IN THE STATE OF NEW YORK IN ANY LEGAL PROCEEDING ARISING OUT OF OR
RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY. EACH OF THE COMPANY AND THE
INVESTORS (AND, TO THE EXTENT PERMITTED BY LAW, ON BEHALF OF ITS AND THEIR EQUITY HOLDERS AND
CREDITORS) HEREBY KNOWINGLY, VOLUNTARILY AND IRREVOCABLY WAIVES ANY RIGHT IT MAY HAVE TO A TRIAL BY
JURY IN RESPECT OF ANY CLAIM BASED UPON, ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT AND
THE TRANSACTIONS CONTEMPLATED HEREBY.

(d) Notices. Any notice, request or other communication to be given or made under
this Agreement shall be in writing. Such notice, request or other communication shall be deemed to
have been duly given or made when it shall be delivered by hand, overnight mail, international
courier (confirmed by facsimile), or facsimile (with a hard copy delivered within two (2) Business
Days) to the Party to which it is required or permitted to be given or made at such Party’s address
specified below or at such other address as such Party shall have designated by notice to the other
Parties.

For the Borrower:

Cytokinetics, Incorporated

200 East Grand Avenue

South San Francisco, CA 94080

Attention: President and Chief Executive Officer

Facsimile: (650) 624-3200

with a courtesy copy to:

Cooley LLP

3175 Hanover Street

Palo Alto, CA 94304

Facsimile: (650) 849-7400

Attention: Michael E. Tenta

For the Investors c/o:

Deerfield Private Design Fund, L.P.

780 Third Avenue, 37th Floor

New York, New York 10017

Attention: James E. Flynn

Facsimile: (212) 573-8111

with a courtesy copy to:

Katten Muchin Rosenman LLP

575 Madison Avenue

New York, New York 10022-2585

Facsimile: (212) 894-5877

Attention: Mark I. Fisher

Elliot Press

or to such other Person at such other place as the parties shall designate to one another in
writing.

(e) Counterparts. This Agreement maybe executed in any number of counterparts and by
the parties hereto in separate counterparts, each of which when so executed shall be deemed to be
an original and all of which taken together shall constitute one in the same agreement.

(f) Telecopy Execution and Delivery. A facsimile, telecopy, PDF or other reproduction
of this Agreement may be executed by one or more parties hereto, and an executed copy of this
Agreement may be delivered by one or more parties by facsimile, e-mail or similar electronic
transmission device pursuant to which the signature of or on behalf of such party can be seen, and
such execution and delivery shall be considered valid, binding and effective for all purposes. At
the request of any party, all parties agree to execute an original of this Agreement as well as any
facsimile, telecopy or reproduction thereof. The parties hereto hereby agree that neither shall
raise the execution of facsimile, telecopy, PDF or other reproduction of this Agreement, or the
fact that any signature or document was transmitted or communicated by facsimile, e-mail or similar
electronic transmission device, as a defense to the formation of this Agreement.

[Signature pages follow]IN WITNESS WHEREOF, the parties have executed this Agreement as
of the date first written above.

COMPANY:

CYTOKINETICS, INCORPORATED

By: /s/ Sharon A. Barbari

Name: Sharon A. Barbari

Title: Executive Vice President, Finance and

Chief Financial Officer

INVESTORS:

DEERFIELD PRIVATE DESIGN

FUND II, L.P.

By: Deerfield Capital, L.P., General Partner

By: J. E. Flynn Capital LLC, General Partner

By: /s/ James E. Flynn

Name: James E. Flynn

Title: President

DEERFIELD PRIVATE DESIGN INTERNATIONAL II, L.P.

By: Deerfield Capital, L.P., General Partner

By: J. E. Flynn Capital LLC, General Partner

By: /s/ James E. Flynn

Name: James E. Flynn

Title: President

DEERFIELD SPECIAL SITUATIONS FUND, L.P.

By: Deerfield Capital, L.P., General Partner

By: J. E. Flynn Capital LLC, General Partner

/s/ James E. Flynn

Name: James E. Flynn

Title: President

DEERFIELD SPECIAL SITUATIONS FUND INTERNATIONAL
LIMITED

/s/ James E. Flynn

Name: James E. Flynn

Title: Director

1

Schedule 1

	 	 	 	 	 
	Purchase Price Per Share of Common Stock:
	 	$	1.50	 
	Purchase Price Per Share of Series A Preferred Stock
	 	$	1,500	 
	Exercise Price of Warrants
	 	$	1.65	 

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	Number	 	 	 	 
	 	 	 	 	 	 	Number	 	of Shares of
	 	 	 	 	 	 	of Shares of	 	Series A
	 	 	 	 	 	 	Common Stock	 	Preferred Stock
	 	 	 	 	 	 	to be	 	to be	 	 
	 	 	 	 	 	 	Purchased	 	Purchased	 	Warrants to be
	Name of	 	Aggregate	 	by	 	by	 	Purchased by
	Investor	 	Purchase Price	 	Investor	 	Investor	 	Investor
	Deerfield Private
Design Fund II,
L.P.
	 	$	6,466,350	 	 	 	1,700,900	 	 	 	2,610	 	 	 	2,155,450	 
	Deerfield Private
Design
International II,
L.P.
	 	$	7,408,650	 	 	 	1,949,100	 	 	 	2,990	 	 	 	2,469,550	 
	Deerfield Special
Situations Fund,
L.P.
	 	$	2,409,750	 	 	 	643,500	 	 	 	963	 	 	 	803,250	 
	Deerfield Special
Situations Fund
International
Limited
	 	$	 3,770,250	 	 	 	1,006,500	 	 	 	1,507	 	 	 	1,256,750	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total:
	 	$	20,055,000	 	 	 	5,300,000	 	 	 	8,070	 	 	 	6,685,000	 

2

Exhibit A

[Certificate of Designations]

Exhibit B

[Form of Stock Certificate for Series A Preferred Stock]

	 	 	 	 	 
	P—-«Certificate#»
	 	Incorporated Under the Laws of the

State of Delaware on August 5, 1997

	 	**«#Shares»**

 CUSIP 23282W 407

CYTOKINETICS, INCORPORATED

Series A Convertible Preferred Stock

This Certifies That «Shareholder» is the record holder of «NumShares»
(«#Shares») Shares of the Series A Convertible Preferred Stock of Cytokinetics,
Incorporated, transferable only on the books of the corporation by the holder
hereof, in person or by duly authorized attorney, upon surrender of this Certificate
properly endorsed or assigned.

A statement of the rights, preferences, privileges and restrictions granted to or
imposed upon the respective classes or series of shares of stock of the Corporation and
upon holders thereof as established by the Certificate of Incorporation or by any
Certificate of Designation of Preferences, and the number of shares constituting each
series and the designations thereof, may be obtained by any shareholder upon request and
without charge at the principal office of the corporation.

In Witness Whereof, the Corporation has caused this Certificate to be
signed by its duly authorized officers this        day of April, 2011.

Secretary President

Transfer Agent and Registrar

3

Exhibit C

[Form of Warrant]

4

Exhibit D

[Form of Opinion]

	 	1.	 	The Shares have been duly authorized, and upon issuance and delivery against payment
therefor in accordance with the terms of the Purchase Agreement, the Shares will be validly
issued, fully paid and nonassessable.

	 	2.	 	The shares of Common Stock issuable upon conversion of the Preferred Shares have been
duly authorized, and when issued upon conversion in accordance with the terms of the
Preferred Shares, will be validly issued, fully paid and nonassessable.

	 	3.	 	The shares of Common Stock issuable upon exercise of the Warrants have been duly
authorized, and when issued upon exercise of the Warrants, will be validly issued, fully
paid and nonassessable.

5

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