
	UNITED STATES
	SECURITIES AND EXCHANGE COMMISSION
	Washington, D.C. 20549

SCHEDULE 13G/A

(Amendment No. 5)

Under the Securities Exchange Act of 1934

Threshold Pharmaceuticals, Inc.

(Name of Issuer)

COMMON STOCK

(Title of Class of Securities)

885807 20 6

(CUSIP Number)

October 5, 2009

(Date of Event Which Requires Filing of this Statement)

Check appropriate box to designate the rule pursuant to which this Schedule is filed:

[ o ]	Rule 13d-1(b)
[ x ]	Rule 13d-1(c)
[ o ]	Rule 13d-1(d)

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

(Continued on following pages)

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Three Arch Partners III, L.P. (“TAP III”)

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization Delaware

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 3,079,649*

			6		Shared Voting Power See response to row 5

			7		Sole Dispositive Power 3,079,649*

			8		Shared Dispositive Power See response to row 7

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 3,079,649*

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 9.07%**

	12	Type of Reporting Person PN

*	Includes warrants to purchase 769,627 shares of common stock that is exercisable within 60 days of October 5, 2009.

**	Approximately 9.07% of the shares of Common Stock outstanding as of October 5, 2009, assuming 33,944,682 shares outstanding, representing (i) 15,222,605 shares outstanding as of July 31, 2009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (ii) 18,324,599 shares of common stock issued pursuant to the Purchase Agreement (as defined below), and (ii) the assumed exercise of 769,627 shares subject to warrants exercisable within 60 days of October 5, 2009.

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Three Arch Associates III, L.P. (“TAA III”)

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization Delaware

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 165,563*

			6		Shared Voting Power See response to row 5

			7		Sole Dispositive Power 165,563*

			8		Shared Dispositive Power See response to row 7

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 165,563*

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 0.49%**

	12	Type of Reporting Person PN

*	Includes warrants to purchase 41,376 shares of common stock that is exercisable within 60 days of October 5, 2009

**	Approximately 0.49% of the shares of Common Stock outstanding as of October 5, 2009, assuming 33,568,573 shares outstanding, representing (i) 15,222,605 shares outstanding as of July 31, 2009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (ii) 18,324,599 shares of common stock issued pursuant to the Purchase Agreement (as defined below), and (ii) the assumed exercise of 41,376 shares subject to warrants exercisable within 60 days of October 5, 2009.

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Three Arch Management III, L.L.C. (“TAM III”)

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization Delaware

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 3,245,212*

			6		Shared Voting Power See response to row 5

			7		Sole Dispositive Power 3,245,212*

			8		Shared Dispositive Power See response to row 7

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 3,245,212*

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 9.55%**

	12	Type of Reporting Person OO

*	Includes warrants to purchase 811,003 shares of common stock that is exercisable within 60 days of October 5, 2009

**	Approximately 9.55% of the shares of Common Stock outstanding as of October 5, 2009, assuming 33,966,051 shares outstanding, representing (i) 15,222,605 shares outstanding as of July 31, 2009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (ii) 18,324,599 shares of common stock issued pursuant to the Purchase Agreement (as defined below), and (ii) the assumed exercise of 811,003 shares subject to warrants exercisable within 60 days of October 5, 2009.

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Mark A. Wan

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization USA

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 3,245,212*

			6		Shared Voting Power See response to row 5

			7		Sole Dispositive Power 3,245,212*

			8		Shared Dispositive Power See response to row 7

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 3,245,212*

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 9.55%**

	12	Type of Reporting Person IN

Includes warrants to purchase 811,003 shares of common stock that are exercisable within 60 days of October 5, 2009.

Approximately 9.55% of the shares of Common Stock outstanding as of October 5, 2009, assuming 33,966,051 shares outstanding, representing (i) 15,222,605 shares outstanding as of July 31, 2009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (ii) 18,324,599 shares of common stock issued pursuant to the Purchase Agreement (as defined below), and (ii) the assumed exercise of 811,003 shares subject to warrants exercisable within 60 days of October 5, 2009.

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Wilfred E. Jaeger

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization Canada

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 3,266,877*

			6		Shared Voting Power 3,245,212

			7		Sole Dispositive Power 3,266,877*

			8		Shared Dispositive Power 3,245,212

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 3,266,877

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 9.61%**

	12	Type of Reporting Person IN

*	Includes 21,665 shares of common stock subject to options exercisable within 60 days of October 5, 2009.

**	Approximately 9.61% of the shares of Common Stock outstanding as of October 5, 2009, assuming 33,987,716 shares outstanding, representing (i) 15,222,605 shares outstanding as of July 31, 2009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (ii) 18,324,599 shares of common stock issued pursuant to the Purchase Agreement (as defined below), (ii) the assumed exercise of 811,003 shares subject to warrants exercisable within 60 days of October 5, 2009 and (iv) the assumed exercise of 21,665 shares of common stock pursuant to an option grant to Wilfred E. Jaeger.

CUSIP No. 885807 20 6

	1	Name of Reporting Person S.S OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Barclay Nicholson

	2	Check the Appropriate Box if a Member of a Group
		(a)		x
		(b)		o

	3	SEC Use Only

	4	Citizenship or Place of Organization USA

Number of Shares Beneficially Owned by Each Reporting Person With			5		Sole Voting Power 3,245,212*

			6		Shared Voting Power See response to row 5

			7		Sole Dispositive Power 3,245,212*

			8		Shared Dispositive Power See response to row 7

	9	Aggregate Amount Beneficially Owned by Each Reporting Person 3,245,212*

	10	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	11	Percent of Class Represented by Amount in Row 9 9.55%**

	12	Type of Reporting Person IN

Includes warrants to purchase 811,003 shares of common stock that are exercisable within 60 days of October 5, 2009.

CUSIP No. 885807 20 6

Item 1.
	(a)		Name of Issuer: Threshold Pharmaceuticals, Inc. (the “Issuer”)
	(b)		Address of Issuer’s Principal Executive Offices: 1300 Seaport Boulevard, Redwood City, CA 94063

Item 2.
	(a)		Name of Person Filing: Three Arch Partners III, L.P. (“TAP III”), Three Arch Associates III, L.P. (“TAA III”), Three Arch Management III, L.L.C. (“TAM III”), Mark A. Wan (“Wan”), Wilfred E. Jaeger (“Jaeger”), and Barclay Nicholson (“Nicholson”). The foregoing entities and individuals are collectively referred to as the “Reporting Persons.” Wan, Jaeger, and Nicholson are the sole managing members of TAM III, the sole general partner of TAP III and TAA III and may be deemed to have sole power to vote the shares reported. TAA III invests alongside TAP III in all investments made by TAP III.
	(b)		Address of Principal Business Office: 3200 Alpine Road, Portola Valley, CA 94028
	(c)		Citizenship: See Row 4 of each cover page
	(d)		Title of Class of Securities: Common Stock, $0.001 par value per share
	(e)		CUSIP Number: 885807 20 6

Item 3.	If this statement is filed pursuant to Rules 240.13d-1(b), or 240.13d-2(b) or (c), check whether the person filing is a:
Not applicable.

Item 4.		Ownership
The following information with respect to the ownership of the Common Stock of the Issuer by the person filing this statement is provided as of December 31, 2008:
		(a)		Amount beneficially owned: See Row 9 of each cover page
		(b)		Percent of class: See Row 11 of each cover page. The approximate percentages of common stock reported as beneficially owned by the Reporting Persons is based (a) on 15,222,605 shares of common stock outstanding as of July 31, 009 as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2009, (b) the assumed exercise of shares subject to options or warrants exercisable within 60 days of October 5, 2009 and (c) the shares of common stock issued pursuant to the close of the securities purchase agreement (the “Purchase Agreement”) by and among the Issuer, TAP III and TAA III on September 29, 2009, as disclosed on the Form 8-K filed by the Issuer on October 6, 2009.

CUSIP No. 885807 20 6

	(c)	Number of shares as to which such person has:
		(i)	Sole power to vote or to direct the vote: See Row 5 of each cover page
		(ii)	Shared power to vote or to direct the vote: See Row 6 of each cover page
		(iii)	Sole power to dispose or to direct the disposition of: See Row 7 of each cover page
		(iv)	Shared power to dispose or to direct the disposition of: See Row 8 of each cover page

Item 5.	Ownership of Five Percent or Less of a Class
Not applicable.

Item 6.	Ownership of More than Five Percent on Behalf of Another Person
Under certain circumstances set forth in the limited partnership agreements of TAP III and TAA III and the limited liability company agreement of TAM III, the general and limited partners of each such entity may be deemed to have the right to receive dividends from, or the proceeds from, the sale of shares of the issuer owned by each such entity of which they are a partner.

Item 7.	Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on By the Parent Holding Company
Not applicable.

Item 8.	Identification and Classification of Members of the Group
Not applicable.

Item 9.	Notice of Dissolution of the Group
Not applicable.

Item 10.	Certification
By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

CUSIP No. 885807 20 6

SIGNATURE

After reasonable inquiry and to the best of our knowledge and belief, the undersigned certify that the information set forth in this statement is true, complete and correct.

	Date: October 8, 2009

	THREE ARCH PARTNERS III, L.P.
	By: Three Arch Management III, L.L.C.

	By:	/s/ Barclay Nicholson
		Barclay Nicholson
		Managing Member

	THREE ARCH ASSOCIATES III, L.P.
	By: Three Arch Management III, L.L.C.

	By:	/s/ Barclay Nicholson
		Barclay Nicholson
		Managing Member

	THREE ARCH MANAGEMENT III, L.L.C.

	By:	/s/ Barclay Nicholson
		Barclay Nicholson
		Managing Member

	MARK A. WAN

	By:	/s/ Barclay Nicholson
		Barclay Nicholson
		Authorized Signature

	WILFRED E. JAEGER

	By:	/s/ Barclay Nicholson
		Barclay Nicholson
		Authorized Signature

	BARCLAY NICHOLSON

	By:	/s/ Barclay Nicholson
		Barclay Nicholson

This Schedule 13G was executed pursuant to a Statement Appointing Designated Filer and Authorized Signatories. Note that copies of the applicable Statement Appointing Designated Filer and Authorized Signatories are already on file with the appropriate agencies.