SEC Form 4

FORM 4		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 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* RA CAPITAL MANAGEMENT, LLC (Last) (First) (Middle) C/O RA CAPITAL MANAGEMENT, LLC 20 PARK PLAZA, SUITE 1200 (Street) BOSTON MA 02116 (City) (State) (Zip)	2. Issuer Name and Ticker or Trading Symbol ACHILLION PHARMACEUTICALS INC [ ACHN ]	5. Relationship of Reporting Person(s) to Issuer (Check all applicable) Director X 10% Owner Officer (give title below) X Other (specify below) See Footnotes (1)-(9)
	3. Date of Earliest Transaction (Month/Day/Year) 10/11/2013
	4. If Amendment, Date of Original Filed (Month/Day/Year)	6. Individual or Joint/Group Filing (Check Applicable Line) Form filed by One Reporting Person X Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	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, $0.001 par value	10/11/2013		P		750,000(1)	A	$2.5	15,207,061	I	See Footnotes(8)(9)
Common Stock, $0.001 par value	10/11/2013		P		99,900(2)	A	$2.5221	15,306,961	I	See Footnotes(8)(9)
Common Stock, $0.001 par value	10/11/2013		P		250,000(3)	A	$2.55	15,556,961	I	See Footnotes(8)(9)
Common Stock, $0.001 par value	10/11/2013		P		147,500(4)	A	$2.5533	15,704,461	I	See Footnotes(8)(9)
Common Stock, $0.001 par value	10/11/2013		P		92,002(5)	A	$2.5579	15,769,463	I	See Footnotes(8)(9)
Common Stock, $0.001 par value	10/11/2013		P		1,109,308(6)	A	$2.6166	16,905,771(7)	I	See Footnotes(8)(9)

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 (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	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 (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (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: 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

1. Name and Address of Reporting Person* RA CAPITAL MANAGEMENT, LLC (Last) (First) (Middle) C/O RA CAPITAL MANAGEMENT, LLC 20 PARK PLAZA, SUITE 1200 (Street) BOSTON MA 02116 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) X Other (specify below) See Footnotes (1)-(9)

1. Name and Address of Reporting Person* Kolchinsky Peter (Last) (First) (Middle) C/O RA CAPITAL MANAGEMENT, LLC 20 PARK PLAZA, SUITE 1200 (Street) BOSTON MA 02116 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) X Other (specify below) See Footnotes (1)-(9)

1. Name and Address of Reporting Person* RA Capital Healthcare Fund LP (Last) (First) (Middle) C/O RA CAPITAL MANAGEMENT, LLC 20 PARK PLAZA, SUITE 1200 (Street) BOSTON MA 02116 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) X Other (specify below) See Footnotes (1)-(9)

Explanation of Responses:

1. The securities purchased include 588,752 shares for RA Capital Healthcare Fund, L.P. (the "Fund") and 161,248 shares for an account owned by Blackwell Partners, LLC (the "Blackwell Account").

2. The securities purchased include 99,900 shares for the Fund and 21,478 shares for the Blackwell Account.

3. The securities purchased include 196,251 shares for the Fund and 53,749 shares for the Blackwell Account.

4. The securities purchased include 115,789 shares for the Fund and 31,711 shares for the Blackwell Account.

5. The securities purchased include 72,223 shares for the Fund and 19,779 shares for the Blackwell Account.

6. The securities purchased include 870,808 shares for the Fund and 238,500 shares for the Blackwell Account.

7. Following the transactions set forth on Table I above, 13,039,300 shares are held by the Fund, and 3,866,471 shares are held in the Blackwell Account.

8. RA Capital Management, LLC (the "Adviser") is the general partner of the Fund and the investment adviser of the Blackwell Account. Peter Kolchinsky is the sole manager of the Adviser. In their respective capacities, each of Mr. Kolchinsky and the Adviser may be deemed to beneficially own the reported securities.

9. Pursuant to Rule 16a-1 under the Securities Exchange Act of 1934, as amended (the "Act"), each of the Reporting Persons disclaims beneficial ownership of the securities reported herein except to the extent of their respective pecuniary interests therein. The filing of this Form 4 shall not be construed as an admission that Mr. Kolchinsky or the Adviser is or was for the purposes of Section 16(a) of the Act, or otherwise, the beneficial owner of any of securities reported herein.

	/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC	10/15/2013
	/s/ Peter Kolchinsky, individually	10/15/2013
	/s/ Peter Kolchinsky, Manager of RA Capital Management, LLC, the General Partner of RA Capital Healthcare Fund, L.P.	10/15/2013
	** Signature of Reporting Person	Date
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 4 (b)(v).
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