Protagonist Therapeutics Inc (PTGX): RA Capital Management Acquires 6.8% Stake

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

SCHEDULE 13G

Under the Securities Exchange Act of
1934

(Amendment No. __)*

Protagonist Therapeutics, Inc.

---

(Name of Issuer)

Common Stock, par value $0.00001 per
share

---

(Title of Class of Securities)

74366E102

---

(CUSIP Number)

August 16, 2016

---

(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. 74366E102

13G

	1.	Names of Reporting Persons. I.R.S. Identification Nos. of above persons (entities only). RA Capital Management, LLC
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a) ¨
		(b) ¨
	3.	SEC Use Only
	4.	Citizenship or Place of Organization         Massachusetts

Number of Shares Beneficially Owned by Each Reporting Person With	5.	Sole Voting Power                           0
	6.	Shared Voting Power             1,109,229
	7.	Sole Dispositive Power                 0
	8.	Shared Dispositive Power      1,109,229

	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,109,229
	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions)      ¨
	11.	Percent of Class Represented by Amount in Row (9) 6.8%1
	12.	Type of Reporting Person (See Instructions) IA

¹
The reporting person is the beneficial owner of 1,109,229 shares of Common Stock which constitutes approximately 6.8% of the Issuer’s
outstanding Common Stock shares. The percentage calculation assumes that there are currently 16,323,551 outstanding shares of Common
Stock, after the completion of the Issuer’s initial public offering, as reported in the Issuer’s final prospectus filed
with the Securities and Exchange Commission (“SEC”) on August 12, 2016.

CUSIP No. 74366E102

13G

	1.	Names of Reporting Persons. I.R.S. Identification Nos. of above persons (entities only). Peter Kolchinsky
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a) ¨
		(b) ¨
	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              1,109,229
	7.	Sole Dispositive Power                 0
	8.	Shared Dispositive Power       1,109,229

	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,109,229
	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions)     ¨
	11.	Percent of Class Represented by Amount in Row (9) 6.8%2
	12.	Type of Reporting Person (See Instructions) IN

 

²
The reporting person is the beneficial owner of 1,109,229 shares of Common Stock which constitutes approximately
6.8% of the Issuer’s outstanding Common Stock shares. The percentage calculation assumes that there are currently 16,323,551
outstanding shares of Common Stock, after the completion of the Issuer’s initial public offering, as reported in the Issuer’s
final prospectus filed with the Securities and Exchange Commission (“SEC”) on August 12, 2016.

CUSIP No. 74366E102

13G

	1.	Names of Reporting Persons. I.R.S. Identification Nos. of above persons (entities only). RA Capital Healthcare Fund, L.P.
	2.	Check the Appropriate Box if a Member of a Group (See Instructions)
		(a) ¨
		(b) ¨
	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              909,203
	7.	Sole Dispositive Power                 0
	8.	Shared Dispositive Power      909,203

	9.	Aggregate Amount Beneficially Owned by Each Reporting Person 909,203
	10.	Check if the Aggregate Amount in Row (9) Excludes Certain Shares (See Instructions)     ¨
	11.	Percent of Class Represented by Amount in Row (9) 5.6%3
	12.	Type of Reporting Person (See Instructions) PN (Limited Partnership)

³
The reporting person is the beneficial owner of 909,203 shares of Common Stock which constitutes approximately 5.6%
of the Issuer’s outstanding Common Stock shares. The percentage calculation assumes that there are currently 16,323,551
outstanding shares of Common Stock, after the completion of the Issuer’s initial public offering, as reported in the Issuer’s
final prospectus filed with the Securities and Exchange Commission (“SEC”) on August 12, 2016.

Item 1.

(a) Name of Issuer: Protagonist
Therapeutics, Inc. (the “Issuer”).

(b) Address of the Issuer’s Principal Executive
Offices: 521 Cottonwood Drive, Suite 100, Milpitas, CA 95035.

 

Item 2.

(a) Name of Person
Filing: This joint statement on Schedule 13G is being filed by Peter Kolchinsky, RA Capital Management, LLC (“Capital”),
and RA Capital Healthcare Fund, L.P. (the “Fund”). Mr. Kolchinsky, Capital and the Fund are collectively referred to
herein as the “Reporting Persons.” Capital is the general partner of the Fund and serves
as investment adviser for a separately managed account (the “Account”). Mr. Kolchinsky is the manager of Capital. As
the investment adviser to the Fund and the Account, Capital may be deemed a beneficial owner, for purposes of Section 13(d) of
the Securities Exchange Act of 1934 (the “Act”), of any securities of the Issuer owned by the Fund or the Account.
As the manager of Capital, Mr. Kolchinsky may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities
of the Issuer beneficially owned by Capital. Capital is a registered investment adviser within the meaning of Rule 13d-1(b)(1)(ii)(E)
and Rule 16a-1(a)(v), and Mr. Kolchinsky is a parent or control person of Capital within the meaning of Rule 13d-1(b)(1)(ii)(G)
and Rule 16a-1(a)(1)(vii). Capital and Mr. Kolchinsky disclaim beneficial ownership of the securities reported in this Schedule
13G Statement (the “Statement”) other than for the purpose of determining their obligations under Section 13(d) of
the Act, and neither the filing of the Statement nor the filing of this Amendment shall not be deemed an admission that either
Capital or Mr. Kolchinsky is or was the beneficial owner of such securities for any other purpose.

(b) Address of
Principal Business Office: The principal business office of the Reporting Persons is c/o RA Capital Management, LLC, 20 Park
Plaza, Suite 1200, Boston, MA 02116.

(c) Citizenship:
Capital is a Massachusetts limited liability company. The Fund is a Delaware limited partnership. Mr. Kolchinsky is a United States
citizen.

(d) Title and Class
of Securities: Common stock (“Common Stock”) of the Issuer.

(e) CUSIP Number:
74366E102

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: See the response(s) to Item 9 on the attached cover page(s).
(b)	Percent of Class: See the response(s) to Item 11 on the attached cover page(s).

(c)	Number of shares as to which such person has:
	(i)	sole power to vote or to direct the vote: See the response(s) to Item 5 on the attached cover page(s).
	(ii)	shared power to vote or to direct the vote See the response(s) to Item 6 on the attached cover page(s).
	(iii)	sole power to dispose or to direct the disposition of See the response(s) to Item 7 on the attached cover page(s).
	(iv)	shared power to dispose or to direct the disposition of See the response(s) to Item 8 on the attached cover page(s).

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:

Not applicable.

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
Group:

Not applicable.

Item 10. Certification:

By signing below I hereby 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.

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.

Date: August
25, 2016

 

RA CAPITAL MANAGEMENT, LLC

By: /s/ Rajeev Shah

————————————————-

Rajeev Shah

Authorized Signatory

PETER KOLCHINSKY

/s/ Peter Kolchinsky

————————————————-

 

 

RA CAPITAL HEALTHCARE FUND, L.P.

By: RA Capital Management, LLC

Its: General Partner

By: /s/ Rajeev Shah

————————————————-

Rajeev Shah

Authorized Signatory