Amended Statement of Ownership (sc 13g/a)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G/A

Under the Securities Exchange Act of 1934
(Amendment No. 1)*

Protagonist Therapeutics, Inc.

(Name of Issuer)

Common Stock, par value $0.00001 per share

(Title of Class of Securities)

74366E 102

(CUSIP Number)

December 31, 2019

(Date of Event Which Requires Filing of this Statement)

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

¨	Rule 13d-1(b)
x	Rule 13d-1(c)
¨	Rule 13d-1(d)

*The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page.

The information required in 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).

CUSIP No. 74366E 102


1.	Name of Reporting Persons Venrock Healthcare Capital Partners II, L.P.

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) PN

(1)

Venrock Healthcare Capital Partners II, L.P., VHCP Co-Investment Holdings II, LLC, Venrock Healthcare Capital Partners III, L.P., VHCP Co-Investment Holdings III, LLC, VHCP Management II, LLC, VHCP Management III, LLC, Nimish Shah and Bong Koh are members of a group for the purposes of this Schedule 13G/A.

(2)

Consists of 22,922 shares owned by Venrock Healthcare Capital Partners II, L.P., 9,289 shares owned by VHCP Co-Investment Holdings II, LLC, 73,577 shares owned by Venrock Healthcare Capital Partners III, L.P. and 7,352 shares owned by VHCP Co-Investment Holdings III, LLC.

(3)

This percentage is calculated based upon 27,206,447 shares of the Issuer’s common stock outstanding as of September 30, 2019, as reported in the Issuer’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on November 6, 2019.

CUSIP No. 74366E 102


1.	Name of Reporting Persons VHCP Co-Investment Holdings II, LLC

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) OO

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons Venrock Healthcare Capital Partners III, L.P.

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) PN

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons VHCP Co-Investment Holdings III, LLC

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) OO

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons VHCP Management II, LLC

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) OO

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons VHCP Management III, LLC

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(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 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) OO

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons Shah, Nimish

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(b)	o

3.	SEC Use Only

4.	Citizenship or Place of Organization United States


Number of Shares Beneficially Owned by Each Reporting Person With:	5.	Sole Voting Power 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) IN

(1)

(2)

(3)

CUSIP No. 74366E 102


1.	Name of Reporting Persons Koh, Bong

2.	Check the Appropriate Box if a Member of a Group (See Instructions)
	(a)	x(1)
	(b)	o

3.	SEC Use Only

4.	Citizenship or Place of Organization United States


Number of Shares Beneficially Owned by Each Reporting Person With:	5.	Sole Voting Power 0

	6.	Shared Voting Power 113,140(2)

	7.	Sole Dispositive Power 0

	8.	Shared Dispositive Power 113,140(2)


	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 113,140(2)

	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions) o

	11.	Percent of Class Represented by Amount in Row (9) 0.4%(3)

	12.	Type of Reporting Person (See Instructions) IN

(1)

(2)

(3)

CUSIP No. 74366E 102

Introductory Note: This Schedule 13G/A is filed on behalf of Venrock Healthcare Capital Partners II, L.P., a limited partnership organized under the laws of the State of Delaware (“VHCP II LP”), VHCP Co-Investment Holdings II, LLC, a limited liability company organized under the laws of the State of Delaware (“VHCP Co-Investment II”), Venrock Healthcare Capital Partners III, L.P., a limited partnership organized under the laws of the State of Delaware (“VHCP III LP”), VHCP Co-Investment Holdings III, LLC, a limited liability company organized under the laws of the State of Delaware (“VHCP Co-Investment III”), VHCP Management II, LLC, a limited liability company organized under the laws of the State of Delaware (“VHCP Management II”), VHCP Management III, LLC, a limited liability company organized under the laws of the State of Delaware (“VHCP Management III” and collectively with VHCP II LP, VHCP Co-Investment II, VHCP III LP, VHCP Co-Investment III and VHCP Management II, the “Venrock Entities”), Nimish Shah (“Shah”) and Bong Koh (“Koh”) in respect of Common Stock of Protagonist Therapeutics, Inc.

Item 1.
	(a)	Name of Issuer Protagonist Therapeutics, Inc.
	(b)	Address of Issuer’s Principal Executive Offices 7707 Gateway Boulevard, Suite 140 Newark, California 94560

Item 2.
	(a)	Name of Person Filing Venrock Healthcare Capital Partners II, L.P. VHCP Co-Investment Holdings II, LLC Venrock Healthcare Capital Partners III, L.P. VHCP Co-Investment Holdings III, LLC VHCP Management II, LLC VHCP Management III, LLC Nimish Shah Bong Koh
	(b)	Address of Principal Business Office or, if none, Residence
		New York Office: 7 Bryant Park 23rd Floor New York, NY 10018	Palo Alto Office: 3340 Hillview Avenue Palo Alto, CA 94304
	(c)	Citizenship All of the Venrock Entities were organized in Delaware. The individuals are both United States citizens.
	(d)	Title of Class of Securities Common Stock, par value $0.00001 per share

(e)

CUSIP Number
74366E 102

CUSIP No. 74366E 102

Item 3.	If this statement is filed pursuant to §§240.13d-1(b), or 240.13d-2(b) or (c), check whether the person filing is a:

Not applicable

Item 4.		Ownership
		(a)	Amount Beneficially Owned as of December 31, 2019:

Venrock Healthcare Capital Partners II, L.P.	113,140	(1)
VHCP Co-Investment Holdings II, LLC	113,140	(1)
Venrock Healthcare Capital Partners III, L.P.	113,140	(1)
VHCP Co-Investment Holdings III, LLC	113,140	(1)
VHCP Management II, LLC	113,140	(1)
VHCP Management III, LLC	113,140	(1)
Nimish Shah	113,140	(1)
Bong Koh	113,140	(1)

(b)

Percent of Class as of December 31, 2019:

Venrock Healthcare Capital Partners II, L.P.	0.4	%
VHCP Co-Investment Holdings II, LLC	0.4	%
Venrock Healthcare Capital Partners III, L.P.	0.4	%
VHCP Co-Investment Holdings III, LLC	0.4	%
VHCP Management II, LLC	0.4	%
VHCP Management III, LLC	0.4	%
Nimish Shah	0.4	%
Bong Koh	0.4	%

(c)

Number of shares as to which the person has, as of December 31, 2019:

(i)

Sole power to vote or to direct the vote

Venrock Healthcare Capital Partners II, L.P.		0
VHCP Co-Investment Holdings II, LLC		0
Venrock Healthcare Capital Partners III, L.P.		0
VHCP Co-Investment Holdings III, LLC		0
VHCP Management II, LLC		0
VHCP Management III, LLC		0
Nimish Shah		0
Bong Koh		0

CUSIP No. 74366E 102
		(ii)	Shared power to vote or to direct the vote

Venrock Healthcare Capital Partners II, L.P.	113,140	(1)
VHCP Co-Investment Holdings II, LLC	113,140	(1)
Venrock Healthcare Capital Partners III, L.P.	113,140	(1)
VHCP Co-Investment Holdings III, LLC	113,140	(1)
VHCP Management II, LLC	113,140	(1)
VHCP Management III, LLC	113,140	(1)
Nimish Shah	113,140	(1)
Bong Koh	113,140	(1)

(iii)

Sole power to dispose or to direct the disposition of

Venrock Healthcare Capital Partners II, L.P.		0
VHCP Co-Investment Holdings II, LLC		0
Venrock Healthcare Capital Partners III, L.P.		0
VHCP Co-Investment Holdings III, LLC		0
VHCP Management II, LLC		0
VHCP Management III, LLC		0
Nimish Shah		0
Bong Koh		0

(iv)

Shared power to dispose or to direct the disposition of

Venrock Healthcare Capital Partners II, L.P.	113,140	(1)
VHCP Co-Investment Holdings II, LLC	113,140	(1)
Venrock Healthcare Capital Partners III, L.P.	113,140	(1)
VHCP Co-Investment Holdings III, LLC	113,140	(1)
VHCP Management II, LLC	113,140	(1)
VHCP Management III, LLC	113,140	(1)
Nimish Shah	113,140	(1)
Bong Koh	113,140	(1)

(1) These shares are owned directly as follows: 22,922 shares are owned by Venrock Healthcare Capital Partners II, L.P., 9,289 shares are owned by VHCP Co-Investment Holdings II, LLC, 73,577 shares are owned by Venrock Healthcare Capital Partners III, L.P. and 7,352 shares are owned by VHCP Co-Investment Holdings III, LLC. VHCP Management II, LLC is the general partner of Venrock Healthcare Capital Partners II, L.P. and the manager of VHCP Co-Investment Holdings II, LLC. VHCP Management III, LLC is the general partner of Venrock Healthcare Capital Partners III, L.P. and the manager of VHCP Co-Investment Holdings III, LLC. Messrs. Shah and Koh are the voting members of VHCP Management II, LLC and VHCP Management III, LLC.

Item 5.	Ownership of Five Percent or Less of a Class
If this statement is being filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five percent of the class of securities, check the following x.

Item 6.	Ownership of More than Five Percent on Behalf of Another Person
Not Applicable

CUSIP No. 74366E 102

Item 7.	Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on By the Parent Holding Company or Control Person.

Not Applicable

Item 8.	Identification and Classification of Members of the Group

Not Applicable

Item 9.	Notice of Dissolution of a 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, other than activities solely in connection with a nomination under § 240.14a-11.

CUSIP No. 74366E 102

SIGNATURE

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

Dated: February 14, 2020


Venrock Healthcare Capital Partners II, L.P.			Venrock Healthcare Capital Partners III, L.P.

By:	VHCP Management II, LLC		By:	VHCP Management III, LLC
Its:	General Partner		Its:	General Partner

By:	/s/ David L. Stepp		By:	/s/ David L. Stepp
	Name:	David L. Stepp		Name:	David L. Stepp
	Its:	Authorized Signatory		Its:	Authorized Signatory

VHCP Co-Investment Holdings II, LLC			VHCP Co-Investment Holdings III, LLC

By:	VHCP Management II, LLC		By:	VHCP Management III, LLC
Its:	Manager		Its:	Manager

By:	/s/ David L. Stepp		By:	/s/ David L. Stepp
	Name:	David L. Stepp		Name:	David L. Stepp
	Its:	Authorized Signatory		Its:	Authorized Signatory

VHCP Management II, LLC			VHCP Management III, LLC

By:	/s/ David L. Stepp		By:	/s/ David L. Stepp
	Name:	David L. Stepp		Name:	David L. Stepp
	Its:	Authorized Signatory		Its:	Authorized Signatory


Nimish Shah		Bong Koh

By:	/s/ David L. Stepp	By:	/s/ David L. Stepp
	David L. Stepp, as attorney-in-fact		David L. Stepp, as attorney-in-fact

CUSIP No. 74366E 102

EXHIBITS

A: Joint Filing Agreement (incorporated by reference to Exhibit A to the Schedule 13G filed with the Securities and Exchange Commission on June 17, 2019)

B: Power of Attorney for Nimish Shah (incorporated by reference to Exhibit B to the Schedule 13G filed with the Securities and Exchange Commission on June 17, 2019)

C: Power of Attorney for Bong Koh (incorporated by reference to Exhibit C to the Schedule 13G filed with the Securities and Exchange Commission on June 17, 2019)