Document:

Form of Warrant to Purchase Common Stock

 Exhibit 4.1 
 THRESHOLD PHARMACEUTICALS, INC. 
 WARRANT 

 

			
	Warrant No. 2011-«Number»	  	Dated: March 16, 2011

Threshold Pharmaceuticals, Inc., a Delaware corporation (the “Company”), hereby certifies that, for value received,
«Name_of_Investor» or its registered assigns (the “Holder”), is entitled to purchase from the Company up to a total of «Warrants» shares of common stock, $0.001 par value per share (the “Common
Stock”), of the Company (each such share, a “Warrant Share” and all such shares, the “Warrant Shares”) at an exercise price equal to $2.46 per share (as adjusted from time to time as provided in
Section 8, the “Exercise Price”), at any time and on or after the date hereof (the “Initial Exercise Date”) and through and including the date that is sixty (60) months from the date hereof (the
“Expiration Date”), subject to the following terms and conditions. This Warrant (this “Warrant”) is one of a series of similar warrants issued pursuant to the prospectus supplement dated March 11, 2011 and
accompanying prospectus (collectively, the “Prospectus”) that forms part of the Registration Statement on Form S-3 (File No. 333-169689) (the “Registration Statement”). All such warrants are referred to herein,
collectively, as the “Warrants.” 
 1. Registration of Warrant. The Company shall register this Warrant,
upon records to be maintained by the Company for that purpose (the “Warrant Register”), in the name of the record Holder hereof from time to time. The Company may deem and treat the registered Holder of record of this Warrant as the
absolute owner hereof for the purpose of any exercise hereof or any distribution to the Holder, and for all other purposes, absent actual notice to the contrary. 
 2. Registration of Transfers. The Company shall register the transfer of any portion of this Warrant in the Warrant Register, upon surrender of this Warrant, with the Form of Assignment attached
hereto duly completed and signed, to the Company at its address specified in the Prospectus. Upon any such registration of transfer, a new warrant to purchase Common Stock, in substantially the form of this Warrant (any such new warrant, a
“New Warrant”), evidencing the portion of this Warrant so transferred shall be issued to the transferee and a New Warrant evidencing the remaining portion of this Warrant not so transferred, if any, shall be issued to the
transferring Holder. The acceptance of the New Warrant by the transferee thereof shall be deemed the acceptance by such transferee of all of the rights and obligations of a holder of a Warrant. 

3. Exercise and Duration of Warrants. 
 (a) This Warrant shall be exercisable by the registered Holder at any time and from time to time on or after the Initial Exercise Date and including the Expiration Date. At 6:30 p.m., New York City time
on the Expiration Date, the portion of this Warrant not exercised prior thereto shall be and become void and of no value. 
 (b)
A Holder may exercise this Warrant by delivering to the Company (i) an exercise notice, in the form attached hereto (the “Exercise Notice”), appropriately completed and duly signed, and (ii) payment of the Exercise Price
for the number of Warrant Shares as to which this Warrant is being exercised (which may take the form of a “cashless exercise” if 

  
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permitted by Section 9 and so indicated in the Exercise Notice), and the date such items are delivered to the Company (as determined in accordance with the notice provisions hereof) is an
“Exercise Date.” The Holder shall not be required to deliver the original Warrant in order to effect an exercise hereunder. Execution and delivery of the Exercise Notice 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. 
 4. Delivery
of Warrant Shares. 
 (a) Upon exercise of this Warrant, the Company shall promptly issue or cause to be issued and cause to
be delivered to or upon the written order of the Holder and in such name or names as the Holder may designate, a certificate for the Warrant Shares issuable upon such exercise, free of restrictive legends. The Holder, or any Person so designated by
the Holder to receive Warrant Shares, shall be deemed to have become the holder of record of such Warrant Shares as of the Exercise Date. A “Person” means an individual, a limited liability company, a partnership, a joint venture, a
corporation, a trust, an unincorporated organization, a government or any department or agency thereof and any other legal entity. The Company shall, upon the written request of the Holder and provided that the Company’s transfer agent is
participating in The Depository Trust Company (“DTC”) Fast Automated Securities Transfer Program, use its commercially reasonable efforts, to credit such aggregate number of Warrant Shares to which the Holder is entitled pursuant to
such exercise to the Holder’s or its designee’s balance account with DTC through its Deposit Withdrawal Agent Commission system (“DWAC”); provided, that the Holder provides the Company the reasonably necessary
details to effect the foregoing DWAC delivery. 
 (b) This Warrant is exercisable, either in its entirety or, from time to time,
for a portion of the number of Warrant Shares. Upon surrender of this Warrant following one or more partial exercises, the Company shall issue or cause to be issued, at its expense, a New Warrant evidencing the right to purchase the remaining number
of Warrant Shares. 
 (c) The Company’s obligations to issue and deliver Warrant Shares in accordance with the terms hereof
are absolute and unconditional, irrespective of any action or inaction by the 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 the Holder or any other Person of any obligation to the Company or any violation or alleged violation of law by the Holder or any other Person,
and irrespective of any other circumstance which might otherwise limit such obligation of the Company to the Holder in connection with the issuance of Warrant Shares. The Company acknowledges that the remedy at law for a breach of its obligations
under this Section 4 may be inadequate and agrees, in the event of a breach or threatened breach by the Company of the provisions of this Section 4, that the Holder shall be entitled, in addition to all other available remedies, to an
order and/or injunction restraining any breach and requiring immediate issuance and delivery of certificates representing shares of Common Stock upon the exercise of this Warrant as required pursuant to the terms hereof without the necessity of
showing economic loss and without any bond or other security being required. 

  
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 5. Charges, Taxes and Expenses. Issuance and delivery of certificates for shares of
Common Stock upon exercise of this Warrant shall be made without charge to the Holder for any issue or transfer tax, withholding tax, transfer agent fee or other incidental tax or expense in respect of the issuance of such certificates, all of which
taxes and expenses shall be paid by the Company; provided, however, that the Company shall not be required to pay any tax which may be payable in respect of any transfer involved in the registration of any certificates for Warrant Shares or Warrants
in a name other than that of the Holder. The Holder shall be responsible for all other tax liability that may arise as a result of holding or transferring this Warrant or receiving Warrant Shares upon exercise hereof. 

6. Replacement of Warrant. If this Warrant is mutilated, lost, stolen or destroyed, the Company shall issue or cause to be issued
in exchange and substitution for and upon cancellation hereof, or in lieu of and substitution for this Warrant, a New Warrant, but only upon receipt of evidence reasonably satisfactory to the Company of such loss, theft or destruction and customary
and reasonable bond or indemnity, if requested. Applicants for a New Warrant under such circumstances shall also comply with such other reasonable regulations and procedures and pay such other reasonable third-party costs as the Company may
prescribe. 
 7. Reservation of Warrant Shares. The Company covenants that it will at all times reserve and keep
available out of the aggregate of its authorized but unissued and otherwise unreserved Common Stock, solely for the purpose of enabling it to issue Warrant Shares upon exercise of this Warrant as herein provided, the number of Warrant Shares which
are then issuable and deliverable upon the exercise of this entire Warrant, free from preemptive rights or any other contingent purchase rights of persons other than the Holder (after giving effect to the adjustments and restrictions of
Section 8, if any). The Company covenants that all Warrant Shares so issuable and deliverable shall, upon issuance and the payment of the applicable Exercise Price in accordance with the terms hereof, be duly and validly authorized, issued and
fully paid and nonassessable. The Company will take all such action as may be necessary to assure that such shares of Common Stock may be issued as provided herein without violation of any applicable law or regulation, or of any requirements of any
securities exchange or automated quotation system upon which the Common Stock may be listed. 
 8. Certain Adjustments.
The Exercise Price and number of Warrant Shares issuable upon exercise of this Warrant are subject to adjustment from time to time as set forth in this Section 8. 
 (a) Stock Dividends and Splits. If the Company, at any time while this Warrant is outstanding, (i) pays a stock dividend on its Common Stock or otherwise makes a distribution on any class of
capital stock that is payable in shares of Common Stock, (ii) subdivides outstanding shares of Common Stock into a larger number of shares, or (iii) combines outstanding shares of Common Stock into a smaller number of shares, then in each
such case the Exercise Price shall be multiplied by a fraction of which the numerator shall be the number of shares of Common Stock outstanding immediately before such event and of which the denominator shall be the number of shares of Common Stock
outstanding immediately after such event. Any adjustment made pursuant to clause (i) of this paragraph shall become effective immediately after the record date for the determination of stockholders entitled to receive such

  
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dividend or distribution, and any adjustment pursuant to clause (ii) or (iii) of this paragraph shall become effective immediately after the effective date of such subdivision or
combination. 
 (b) Pro Rata Distributions. If the Company, at any time while this Warrant is outstanding, distributes to
holders of Common Stock (i) evidences of its indebtedness, (ii) any security (other than a distribution of Common Stock covered by the preceding paragraph), (iii) rights or warrants to subscribe for or purchase any security, or
(iv) cash or any other asset (in each case, “Distributed Property”), then in each such case the Holder shall be entitled, upon exercise of this Warrant for the purchase of any or all of the Warrant Shares, to receive the amount
of Distributed Property which would have been payable to the Holder had such Holder been the holder of such Warrant Shares on the record date for the determination of stockholders entitled to such Distributed Property. The Company will at all times
set aside in escrow and keep available for distribution to such holder upon exercise of this Warrant a portion of the Distributed Property to satisfy the distribution to which such Holder is entitled pursuant to the preceding sentence. 

(c) Fundamental Transactions. If, at any time while this Warrant is outstanding, (i) the Company effects any merger or
consolidation of the Company with or into another Person, (ii) the Company effects any sale of all or substantially all of its assets in one or a series of related transactions, (iii) any tender offer or exchange offer (whether by the
Company or another Person) is completed pursuant to which holders of Common Stock owning more than 50% of the outstanding shares of Common Stock (not including any shares of Common Stock held by the Person or Persons making or affiliated with the
Persons making the tender or exchange offer) tender or exchange their shares for other securities, cash or property, or (iv) the Company effects any reclassification of the Common Stock or any compulsory share exchange pursuant to which the
Common Stock is effectively converted into or exchanged for other securities, cash or property (other than as a result of a subdivision or combination of shares of Common Stock covered by Section 8(a) above) (in any such case, a
“Fundamental Transaction”), then the Holder shall have the right thereafter to receive, upon exercise of this Warrant, on a per share basis, the same amount and kind 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 the number of Warrant Shares then issuable upon exercise of this Warrant (the “Alternate
Consideration”). The aggregate Exercise Price for this Warrant will not be affected by any such Fundamental Transaction, but the Company shall apportion such aggregate Exercise Price among the Alternate Consideration 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 Holder shall be
given the same choice as to the Alternate Consideration it receives upon any exercise of this Warrant following such Fundamental Transaction. At the Holder’s request, any successor to the Company or surviving entity in such Fundamental
Transaction shall issue to the Holder a new warrant consistent with the foregoing provisions and evidencing the Holder’s right to purchase the Alternate Consideration for the aggregate Exercise Price upon exercise thereof. The terms of any
agreement 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 paragraph (c) and insuring that the Warrant (or any such replacement
security) will be similarly adjusted upon any subsequent transaction analogous to a Fundamental Transaction. 

  
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 (d) Number of Warrant Shares. Simultaneously with any adjustment to the Exercise
Price pursuant to Section 8(a), the number of Warrant Shares that may be purchased upon exercise of this Warrant shall be adjusted proportionately, so that after such adjustment the aggregate Exercise Price payable hereunder for the increased
or decreased number of Warrant Shares, as applicable, shall be the same as the aggregate Exercise Price in effect immediately prior to such adjustment. 
 (e) Calculations. All calculations under this Section 8 shall be made to the nearest cent or the nearest 1/100th of a share, as applicable. The number of shares of Common Stock outstanding at
any given time shall not include shares owned or held by or for the account of the Company, and the disposition of any such shares shall be considered an issue or sale of Common Stock. 

(f) Notice of Adjustments. Upon the occurrence of each adjustment pursuant to this Section 8, the Company at its expense will
promptly compute such adjustment in accordance with the terms of this Warrant and prepare a certificate setting forth such adjustment, including a statement of the adjusted Exercise Price and adjusted number or type of Warrant Shares or other
securities issuable upon exercise of this Warrant (as applicable), describing the transactions giving rise to such adjustments and showing in detail the facts upon which such adjustment is based. Upon written request, the Company will promptly
deliver a copy of each such certificate to the Holder and to the Company’s transfer agent. 
 (g) Notice of Corporate
Events. If the Company (i) declares a dividend or any other distribution of cash, securities or other property in respect of its Common Stock, including without limitation any granting of rights or warrants to subscribe for or purchase any
capital stock of the Company or any direct or indirect subsidiary of the Company, (ii) authorizes or approves, enters into any agreement contemplating or solicits stockholder approval for any Fundamental Transaction or (iii) authorizes the
voluntary dissolution, liquidation or winding up of the affairs of the Company, then the Company shall deliver to the Holder a notice describing the material terms and conditions of such transaction, at least ten (10) calendar days prior to the
applicable record or effective date on which a Person would need to hold Common Stock in order to participate in or vote with respect to such transaction, and the Company will take all steps reasonably necessary in order to insure that the Holder is
given the practical opportunity to exercise this Warrant prior to such time so as to participate in or vote with respect to such transaction; provided, however, that the failure to deliver such notice or any defect therein shall not
affect the validity of the corporate action required to be described in such notice. 
 9. Payment of Exercise Price. The
Holder shall pay the Exercise Price (i) in cash in immediately available funds or (ii) if a registration statement registering the issuance of the Warrant Shares that are subject of the Exercise Notice (the “Unavailable Warrant
Shares”) is not available for the issuance of such Unavailable Warrant Shares, the Holder may, at its election, satisfy its obligation to pay the Exercise Price through a “Cashless Exercise,” in which event the Company
shall issue to the Holder the number of Warrant Shares determined as follows: 
 X = Y [(A-B)/A] 

where: 

  
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 X = the number of Warrant Shares to be issued to the Holder. 

Y = the number of Warrant Shares with respect to which this Warrant is being exercised. 

A = the average of the Closing Price of the Company’s Common Stock for the five Trading Days immediately prior to (but not
including) the Exercise Date. 
 B = the Exercise Price. 
 “Closing Price” shall mean, for any security as of any date, the last closing trade price for such security on the Trading Market, as reported by Bloomberg Financial Markets
(“Bloomberg”), or if the Trading Market begins to operate on an extended basis and does not designate the closing trade price, then the last trade price of such security prior to 4:00:00 PM, New York time, as reported by Bloomberg.
If the Closing Price cannot be calculated for a security on a particular date on any of the foregoing bases, the Closing Price of such security shall be the fair market value as mutually determined by the Company and the Holder. All such
determinations to be appropriately adjusted for any stock dividend, stock split, stock combination or other similar transaction during the applicable calculation period. 
 “Trading Day” means (i) a day on which the Common Stock is traded on a Trading Market (other than the OTC Bulletin Board), or (ii) if the Common Stock is not listed on a Trading
Market (other than the OTC Bulletin Board), a day on which the Common Stock is traded in the over-the-counter market, as reported by the OTC Bulletin Board, or (iii) if the Common Stock is not listed or quoted on any Trading Market, a day on
which the Common Stock is quoted in the over-the-counter market as reported by the Pink Sheets LLC (or any similar organization or agency succeeding to its functions of reporting prices); provided, that if the Common Stock is not listed or quoted as
set forth in (i), (ii) or (iii) hereof, then Trading Day shall mean any day other than 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. 
 “Trading Market” on any date means the NASDAQ
Capital Market or whichever of the New York Stock Exchange, NYSE Amex, the NASDAQ Global Select Market, the NASDAQ Global Market or OTC Bulletin Board on which the Common Stock is listed or quoted for trading on the date in question. 

For purposes of Rule 144 promulgated under the Securities Act of 1933, as amended (the “Securities Act”), it is intended, understood and
acknowledged that the Warrant Shares issued in a cashless exercise transaction 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. 
 10. Fractional Shares. The Company shall not be required to issue or cause to be issued fractional
Warrant Shares on the exercise of this Warrant. If any fraction of a Warrant 

  
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Share would, except for the provisions of this Section, be issuable upon exercise of this Warrant, the number of Warrant Shares to be issued will be rounded up to the nearest whole share.

 11. Notices. Any and all notices or other communications or deliveries hereunder (including without limitation any
Exercise Notice) shall be in writing and shall be deemed given and effective on the earliest of (i) the date of transmission, if such notice or communication is delivered via facsimile prior to 6:30 p.m. (New York City time) on a Trading Day,
(ii) the next Trading Day after the date of transmission, if such notice or communication is delivered via facsimile on a day that is not a Trading Day or later than 6:30 p.m. (New York City time) on any Trading Day, (iii) the Trading 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. The address for such notices or communications shall be as set
forth in the Prospectus with respect to the Company and, with respect to the Holder, the Holder’s last address as shown on the Warrant Register. 
 12. Warrant Agent. The Company shall serve as warrant agent under this Warrant. Upon thirty (30) days’ notice to the Holder, the Company may appoint a new warrant agent. Any corporation
into which the Company or any new warrant agent may be merged or any corporation resulting from any consolidation to which the Company or any new warrant agent shall be a party or any corporation to which the Company or any new warrant agent
transfers substantially all of its corporate trust or stockholder services business shall be a successor warrant agent under this Warrant without any further act. Any such successor warrant agent shall promptly cause notice of its succession as
warrant agent to be mailed (by first class mail, postage prepaid) to the Holder at the Holder’s last address as shown on the Warrant Register. 
 13. Acknowledgments. 
 (a) The Holder represents that it has been afforded:
(i) the opportunity to ask such questions as it has deemed necessary of, and to receive answers from, representatives of the Company concerning the terms and conditions of this Warrant or the exercise of the Warrant and the finance, operations
and business of the Company; and (ii) the opportunity to request such additional information which the Company possesses or can acquire without unreasonable effort or expense. Nothing contained in this Section 13(a) shall alter, amend or
change the Holder’s reliance on the representations, covenants or warranties contained herein. 
 (b) The Holder represents
that it has the ability to bear the economic risks of its investment for an indefinite period of time and could afford a complete loss of its investment. 
 14. Limitation on Exercise. 
 Notwithstanding anything to the contrary contained herein,
the number of shares of Common Stock that may be acquired by the Holder upon any exercise of this Warrant (or otherwise in respect hereof) shall be limited to the extent necessary to insure that, following such exercise (or other issuance), the
total number of shares of Common Stock then beneficially owned by such Holder and its Affiliates and any other Persons whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the
Securities Exchange Act of 1934, as amended (the “Exchange Act”), does not exceed [4.99%] [9.99%] (the 

  
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“Maximum Percentage”) of the total number of issued and outstanding shares of Common Stock (including for such purpose the shares of Common Stock issuable upon such exercise).
“Affiliate” means any Person that, directly or indirectly through one or more intermediaries, controls or is controlled by or is under common control with a Person, as such terms are used in and construed under Rule 144 under the
Securities Act. For purposes of this Warrant, beneficial ownership shall be determined in accordance with Section 13(d) of the Exchange Act and the rules and regulations promulgated thereunder. By written notice to the Company, the Holder may
waive the provisions of this Section 14(a) or increase or decrease the Maximum Percentage to any other percentage specified in such notice, but (i) any such waiver or increase will not be effective until the 61st day after such notice is delivered to the Company and (ii) any
such waiver or increase or decrease will apply only to the Holder and not to any other holder of Warrants. 
 (a)
Notwithstanding anything to the contrary contained herein, the number of shares of Common Stock that may be acquired by the Holder upon any exercise of this Warrant (or otherwise in respect hereof) shall be limited to the extent necessary to insure
that, following such exercise (or other issuance), the total number of shares of Common Stock then beneficially owned by such Holder and its Affiliates and any other Persons whose beneficial ownership of Common Stock would be aggregated with the
Holder’s for purposes of the rules of the Nasdaq Stock Market does not exceed 19.9% of the total number of issued and outstanding shares of Common Stock (including for such purpose the shares of Common Stock issuable upon such exercise).

 (b) Each delivery of an Exercise Notice hereunder will constitute a representation by the Holder that it has evaluated the
limitation set forth in this paragraph and determined that issuance of the full number of Warrant Shares requested in such Exercise Notice is permitted under this paragraph. Upon the written or oral request of a Holder, the Company shall within two
Trading Days confirm orally and in writing to such 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 such Holder or its Affiliates since the date as of which such number of outstanding shares of Common Stock was reported. The Company’s obligation to issue shares of Common Stock in excess of
the limitation referred to in this Section shall be suspended (and shall not terminate or expire notwithstanding any contrary provisions hereof) until such time, if any, as such shares of Common Stock may be issued in compliance with such
limitation, but in no event later than the Expiration Date. 
 15. Miscellaneous. 

(a) This Warrant may be assigned by the Holder. This Warrant may not be assigned by the Company except to a successor in the event of a
Fundamental Transaction. This Warrant shall be binding on and inure to the benefit of the parties hereto and their respective successors and assigns. Subject to the preceding sentence, nothing in this Warrant shall be construed to give to any Person
other than the Company and the Holder any legal or equitable right, remedy or cause of action under this Warrant. This Warrant may be amended only in writing signed by the Company and the Holder and their successors and assigns. 

  
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 (b) The Company will not, by amendment of its governing documents or through any
reorganization, transfer of assets, consolidation, merger, 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, but will at all times in
good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the Holder against impairment. Without limiting the generality of the foregoing, the
Company (i) will not increase the par value of any Warrant Shares above the amount payable therefor on such exercise, (ii) will take all such action as may be reasonably necessary or appropriate in order that the Company may validly and
legally issue fully paid and nonassessable Warrant Shares on the exercise of this Warrant, and (iii) will not close its stockholder books or records in any manner which interferes with the timely exercise of this Warrant. 

(c) All questions concerning the construction, validity, enforcement and interpretation of this Warrant shall be governed by and
construed and enforced in accordance with the laws of the State of New York. Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts sitting in the city of New York, borough of Manhattan, for the
adjudication of any dispute hereunder or in connection herewith or with any transaction contemplated hereby or discussed herein (including with respect to the enforcement of any of the transaction documents), and hereby irrevocably waives, and
agrees not to assert in any suit, action or proceeding, any claim that it is not personally subject to the jurisdiction of any such court, or that such suit, action or proceeding is improper. Each party hereby irrevocably waives personal service of
process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof via registered or certified mail or overnight delivery (with evidence of delivery) to such party at the address in effect for notices to it
under Section 11 hereof and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in any way any right to serve process in any manner permitted by
law. The Company hereby waives all rights to a trial by jury. 
 (d) The headings herein are for convenience only, do not
constitute a part of this Warrant and shall not be deemed to limit or affect any of the provisions hereof. 
 (e) In case any
one or more of the provisions of this Warrant shall be invalid or unenforceable in any respect, the validity and enforceability of the remaining terms and provisions of this Warrant shall not in any way be affected or impaired thereby and the
parties will attempt in good faith to agree upon a valid and enforceable provision which shall be a commercially reasonable substitute therefor, and upon so agreeing, shall incorporate such substitute provision in this Warrant. 

REMAINDER OF PAGE INTENTIONALLY LEFT BLANK, 
 SIGNATURE PAGE FOLLOWS 

  
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 IN WITNESS WHEREOF, the Company has caused this Warrant to be duly executed by its
authorized officer as of the date first indicated above. 
  

			
	THRESHOLD PHARMACEUTICALS, INC.
		
	By:	 	  

	Name:	 	Harold E. Selick, Ph.D.
	Title:	 	Chief Executive Officer

  
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 FORM OF EXERCISE NOTICE 

(To be executed by the Holder to exercise the right to purchase shares of 

Common Stock under the foregoing Warrant) 
 To Threshold Pharmaceuticals, Inc.: 
 The undersigned is the Holder of Warrant No.
             (the “Warrant”) issued by Threshold Pharmaceuticals, Inc., a Delaware corporation (the “Company”). As a condition to this exercise, the
undersigned Holder hereby represents and warrants to the Company that the representations and warranties set forth in Section 13 of the Warrant are true and correct as of the date hereof as if they had been made on such date with respect to the
Warrant Shares. The undersigned Holder further acknowledges that the sale, transfer, assignment or hypothecation of the Warrant Shares to be issued upon exercise of this Warrant is subject to the terms and conditions contained in Section 13 and
Section 14 of this Warrant. Capitalized terms used herein and not otherwise defined have the respective meanings set forth in the Warrant. 
  

	1.	The Warrant is currently exercisable to purchase a total of              Warrant Shares.

  

	2.	The undersigned Holder hereby exercises its right to purchase              Warrant Shares pursuant to
the Warrant. 

  

	3.	The Holder intends that payment of the Exercise Price shall be made as (check one): 

 

					
		 	
             
	 	“Cash Exercise” under Section 9
		 	
             
	 	“Cashless Exercise” if permitted under Section 9

  

	4.	If the holder has elected a Cash Exercise, the holder shall pay the sum of $             to the
Company in accordance with the terms of the Warrant. 

  

	5.	Pursuant to this exercise, the Company shall deliver to the holder              Warrant Shares in
accordance with the terms of the Warrant. 

  

	6.	Following this exercise, the Warrant shall be exercisable to purchase a total of              Warrant
Shares. 

  

					
	Dated:                   ,
        	 	Name of Holder:
			
		 	(Print)	 	  

			
		 	By:	 	  

		 	Name:	 	  

		 	Title:	 	  

		
		 	(Signature must conform in all respects to name of holder as specified on the face of the

			
	Warrant)
	
	  

	Taxpayer Identification Number

  

			
	 ACKNOWLEDGED AND

AGREED TO this      day of 
                 , 20    

	
	THRESHOLD PHARMACEUTICALS, INC.
		
	By:	 	
	Name:	 	  

	Title:	 	  

 FORM OF ASSIGNMENT 
 [To be completed and signed only upon transfer of Warrant] 
 FOR VALUE RECEIVED,
the undersigned hereby sells, assigns and transfers unto
                                         
            the right represented by the within Warrant to purchase
                     shares of Common Stock of Threshold Pharmaceuticals, Inc. to which the within Warrant relates and appoints
                             attorney to transfer said right on the books of Threshold
Pharmaceuticals, Inc. with full power of substitution in the premises. As a condition to this assignment, the Holder acknowledges that its assignee must deliver a written instrument to the Company that the representations and warranties of
Section 13 of the Warrant are true and correct as of the date hereof as if they had been made by such assignee on such date with respect to the Warrants. 
 Dated:                     ,          

 

	
	  

	(Signature must conform in all respects to name of holder as specified on the face of the Warrant)
	
	  

	Address of Transferee
	
	  

	
	  

	
	  

	Taxpayer Identification Number

  

	
	 In the presence of:Third Amendment to Rights Agreement

 Exhibit 4.2 
 THIRD AMENDMENT TO RIGHTS AGREEMENT 
 This Third Amendment to the Preferred
Shares Rights Agreement (this “Amendment”), dated as of March 11, 2011, between Threshold Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and Mellon Investor Services LLC, a New Jersey
limited liability company, as Rights Agent (the “Rights Agent”), amends that certain Preferred Shares Rights Agreement, dated as of August 8, 2006, as amended (the “Rights Agreement”), by and between
the Company and the Rights Agent. 
 WHEREAS, the Company and the Rights Agent have previously executed and entered into the
Rights Agreement dated August 8, 2006, the Amendment to Rights Agreement dated July 10, 2008 and the Second Amendment to Rights Agreement dated September 29, 2009. 

WHEREAS, pursuant to Section 27 of the Rights Agreement, the Company may from time to time supplement or amend the Rights Agreement
in accordance with the provisions of Section 27 thereof, and the Company desires and directs the Rights Agent to so amend the Rights Agreement. All acts and things necessary to make this Amendment a valid agreement according to its terms have
been done and performed, and the execution and delivery of this Amendment by the Company and the Rights Agent have been in all respects authorized by the Company and the Rights Agent. 

WHEREAS, the Company proposes to offer to sell shares of the Company’s Common Stock and warrants to purchase shares of the
Company’s Common Stock pursuant to an Underwriting Agreement with Cowen and Company, LLC, dated as of March 11, 2011 (the 2011 Registered Direct Offering). 
 In consideration of the foregoing premises and mutual agreements set forth in the Rights Agreement and this Amendment, the parties hereto agree as follows: 

1. Section 1(a) of the Rights Agreement is hereby amended by adding as the final sentence thereof the following: 

“Notwithstanding the foregoing, any purchaser of Common Stock and warrants to purchase Common Stock pursuant to the 2011 Registered
Direct Offering or any Affiliate thereof (the “2011 Securities Investors”), shall not become an “Acquiring Person” by virtue of purchasing shares of Common Stock or warrants to purchase Common Stock pursuant to the 2011
Registered Direct Offering or upon the exercise of warrants purchased in the 2011 Registered Direct Offering.” 
 2. This
Amendment shall be deemed effective as of, and immediately prior to, the first date upon which there is an offering of shares pursuant to the 2011 Registered Direct Offering (the “Effective Time”). Except as expressly amended
hereby, the Rights Agreement remains in full force and effect in accordance with its terms. 
 3. This Amendment to the Rights
Agreement shall be governed by and construed in accordance with the laws of the State of Delaware; provided, however, that the rights, duties, liabilities and obligations of the Rights Agent shall be shall be governed by and construed in accordance
with the laws of the State of New York applicable to contracts made and to be performed entirely within such state. 

 4. The Company shall give the Rights Agent prompt written notice of the Effective Date.

 5. This Amendment may be executed in any number of counterparts and each of such counterparts shall for all purposes be
deemed an original, and all such counterparts shall together constitute but one and the same instrument. 
 6. Except as
expressly set forth herein, this Amendment shall not by implication or otherwise alter, modify, amend or in any way affect any of the terms, conditions, obligations, covenants or agreements contained in the Rights Agreement, all of which are
ratified and affirmed in all respects and shall continue in full force and effect. Without limiting the foregoing, the Rights Agent shall not be subject to, nor required to interpret or comply with, or determine if any Person has complied with, the
Securities Purchase Agreement, even though reference thereto may be made in this Amendment and the Rights Agreement. 
 7.
Capitalized terms used herein but not defined shall have the meanings given to them in the Rights Agreement. 
 [Signatures
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 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to the Rights Agreement to
be duly executed as of the day and year first above written. 
  

					
	THRESHOLD PHARMACEUTICALS, INC.
		
	By:	 	 /s/ Harold E. Selick

		 	Name:	 	 Harold E. Selick

		 	Title:	 	 Chief Executive Officer

	
	 MELLON INVESTOR SERVICES LLC
 as Rights Agent

		
	By:	 	 /s/ Joshua P. McGinn

		 	Name:	 	 Joshua P. McGinn

		 	Title:	 	 Vice President

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