SEC FORM 4/A

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

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)		Other (specify below)

3. Date of Earliest Transaction (Month/Day/Year)
09/10/2014

4. If Amendment, Date of Original Filed (Month/Day/Year)
09/12/2014

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)
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	Code	V	Amount	(A) or (D)	Price		6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
Common Stock, $0.001 par value	09/10/2014		S		8,600⁽¹⁾	D	$12.7259	14,695,762	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/10/2014		S		49,057⁽¹⁾	D	$12.6908	14,646,705	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/10/2014		S		273,017⁽²⁾	D	$12.7013	14,373,688	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/10/2014		S		69,833⁽³⁾	D	$12.6288	14,303,855	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/10/2014		S		121,943⁽⁴⁾	D	$12.6098	14,181,912	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		184,643⁽⁵⁾	D	$12.4132	13,997,269	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		83,560⁽⁶⁾	D	$12.6238	13,913,709	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		531,352⁽⁷⁾	D	$12.3053	13,382,357	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		115,000⁽⁸⁾	D	$12.3348	13,267,357	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		17,357⁽⁹⁾	D	$12.3248	13,250,000	I	See Footnotes⁽¹²⁾⁽¹³⁾
Common Stock, $0.001 par value	09/11/2014		S		250,000⁽¹⁰⁾	D	$12.35	13,000,000⁽¹¹⁾	I	See Footnotes⁽¹²⁾⁽¹³⁾

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)
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)	Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares	8. Price of Derivative Security (Instr. 5)		10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)

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

02116

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

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

02116

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

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

02116

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

Director	X	10% Owner
Officer (give title below)		Other (specify below)

Explanation of Responses:

1. All such shares were sold by RA Capital Healthcare Fund, L.P. (the "Fund").

2. The securities sold include 223,874 shares for the Fund and 49,143 shares for an account owned by Blackwell Partners, LLC (the "Blackwell Account").

3. The securities sold include 57,263 shares for the Fund and 12,570 shares for an account owned by the Blackwell Account.

4. The securities sold include 99,993 shares for the Fund and 21,950 shares for an account owned by the Blackwell Account.

5. The securities sold include 151,407 shares for the Fund and 33,236 shares for an account owned by the Blackwell Account.

6. The securities sold include 68,519 shares for the Fund and 15,041 shares for an account owned by the Blackwell Account.

7. The securities sold include 435,709 shares for the Fund and 95,643 shares for an account owned by the Blackwell Account.

8. The securities sold include 94,299 shares for the Fund and 20,701 shares for an account owned by the Blackwell Account.

9. The securities sold include 14,231 shares for the Fund and 3,126 shares for an account owned by the Blackwell Account.

10. The securities sold include 205,003 shares for the Fund and 44,997 shares for an account owned by the Blackwell Account.

11. Following the transactions set forth on Table I above, 9,982,562 shares are held by the Fund, and 3,017,438 shares are held in the Blackwell Account.

12. 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.

13. 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.

	Peter Kolchinsky, Manager of RA Capital Management, LLC	09/12/2014
	Peter Kolchinsky, individually	09/12/2014
	Peter Kolchinsky, Manager of RA Capital Management, LLC, the General Partner of RA Capital Healthcare Fund, L.P.	09/12/2014
	** 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).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB Number.