Sec Form 4 Filing - MORGENTHALER VENTURE PARTNERS IX LP @ Ra Pharmaceuticals, Inc. - 2016-10-31

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person MORGENTHALER VENTURE PARTNERS IX LP 2. Issuer Name and Ticker or Trading Symbol Ra Pharmaceuticals, Inc. [ RARX] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director X __ 10% Owner _____ Officer (give title below) _____ Other (specify below) (Last) (First) (Middle) 3200 ALPINE ROAD 3. Date of Earliest Transaction (MM/DD/YY) 10/31/2016 (Street) PORTOLA VALLEY, CA94028 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) _____ Form filed by One Reporting Person __ X __ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 10/31/2016 X 63,019 A $ 0.07 ( 2 ) 80,161 D ( 1 ) Common Stock 10/31/2016 S( 2 ) 340 D $ 13 ( 2 ) 79,821 D ( 1 ) Common Stock 10/31/2016 C 1,392,130 A 1,471,951 D ( 1 ) Common Stock 10/31/2016 C 523,438 A 1,995,389 D ( 1 ) Common Stock 10/31/2016 C 486,919 A 2,482,308 D ( 1 ) Common Stock 10/31/2016 P 263,538 A $ 13 2,745,846 D ( 1 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares Warrants to Purchase Common Stock $ 0.07 ( 2 ) 10/31/2016 X 63,019 ( 2 ) 04/01/2022 Common Stock 63,019 $ 0 0 D ( 1 ) Series A Preferred Stock ( 3 ) 10/31/2016 C 9,744,916 ( 3 ) ( 3 ) Common Stock 1,392,130 ( 3 ) 0 D ( 1 ) Series B-1 Preferred Stock ( 4 ) 10/31/2016 C 3,664,071 ( 4 ) ( 4 ) Common Stock 523,438 ( 4 ) 0 D ( 1 ) Series B-2 Preferred Stock ( 5 ) 10/31/2016 C 3,408,439 ( 5 ) ( 5 ) Common Stock 486,919 ( 5 ) 0 D ( 1 )

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other MORGENTHALER VENTURE PARTNERS IX LP 3200 ALPINE ROAD PORTOLA VALLEY, CA94028 X Morgenthaler Management Partners IX, LLC 3200 ALPINE ROAD PORTOLA VALLEY, CA94028 X Signatures MORGENTHALER VENTURE PARTNERS IX, L.P.By: Morgenthaler Management Partners IX, LLC, its General Partner, By: /s/ Jason Lettmann Name: Jason Lettmann, Its: Member 10/31/2016 Signature of Reporting Person Date MORGENTHALER MANAGEMENT PARTNERS IX, LLC, By: /s/ Jason Lettmann, Its: Member 10/31/2016 Signature of Reporting Person Date

Explanation of Responses:

( 1 )The securities are held by Morgenthaler Venture Partners IX, L.P. ("MVP IX"). The general partner of MVP IX is Morgenthaler Management Partners IX, LLC ("MMP IX"). MMP IX may be deemed to indirectly beneficially own the securities directly held by MVP IX. MMP IX disclaims beneficial ownership of the securities held by MVP IX except to the extent of its pecuniary interest therein. ( 2 )The Warrants were automatically exercised immediately prior to the closing of the Issuer's initial public offering for such number of shares issuable pursuant to a cashless net exercise provision, resulting in the Issuer withholding 340 of the warrant shares to pay the aggregate exercise price, using the offering price in the Issuer's initial public offering of $13.00, and issuing to the reporting person the remaining 62,679 shares. ( 3 )Each share of the Series A Preferred Stock converted into Common Stock on a 1-for-7 basis automatically and without additional consideration upon the closing of the Issuer's initial public offering, and had no expiration date. ( 4 )Each share of the Series B-1 Preferred Stock converted into Common Stock on a 1-for-7 basis automatically and without additional consideration upon the closing of the Issuer's initial public offering, and had no expiration date. ( 5 )Each share of the Series B-2 Preferred Stock converted into Common Stock on a 1-for-7 basis automatically and without additional consideration upon the closing of the Issuer's initial public offering, and had no expiration date.

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