Sec Form 4 Filing - BAKER BROS. ADVISORS LP @ AQUINOX PHARMACEUTICALS, INC - 2017-01-09

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 BAKER BROS. ADVISORS LP 2. Issuer Name and Ticker or Trading Symbol AQUINOX PHARMACEUTICALS, INC [ AQXP] 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) 667 MADISON AVENUE, 21ST FLOOR 3. Date of Earliest Transaction (MM/DD/YY) 01/09/2017 (Street) NEW YORK, NY10065 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 2,260 D ( 1 ) Common Stock 2,260 D ( 2 ) Common Stock 01/09/2017 P 603 A $ 16.7395 ( 3 ) 1,132,228 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 5,697 A $ 16.7395 ( 3 ) 9,410,164 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 1,195 A $ 15.321 ( 6 ) 1,133,423 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 11,305 A $ 15.321 ( 6 ) 9,421,469 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 258 A $ 16.8533 ( 7 ) 1,133,681 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 2,442 A $ 16.8533 ( 7 ) 9,423,911 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 917 A $ 15.3475 ( 8 ) 1,134,598 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 8,671 A $ 15.3475 ( 8 ) 9,432,582 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 967 A $ 16.197 ( 9 ) 1,135,565 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 9,143 A $ 16.197 ( 9 ) 9,441,725 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 1,602 A $ 15.13 ( 10 ) 1,137,167 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 15,148 A $ 15.13 ( 10 ) 9,456,873 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 529 A $ 15.6226 ( 11 ) 1,137,696 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 5,006 A $ 15.6226 ( 11 ) 9,461,879 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 3,739 A $ 16.3053 ( 12 ) 1,141,435 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 35,360 A $ 16.3053 ( 12 ) 9,497,239 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 24,871 A $ 17.5996 ( 13 ) 1,166,306 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 235,169 A $ 17.5996 ( 13 ) 9,732,408 I See Footnotes ( 5 ) ( 14 ) Common Stock 01/09/2017 P 3,389 A $ 17.76 1,169,695 I See Footnotes ( 4 ) ( 14 ) Common Stock 01/09/2017 P 32,051 A $ 17.76 9,764,459 I See Footnotes ( 5 ) ( 14 )

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

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other BAKER BROS. ADVISORS LP 667 MADISON AVENUE, 21ST FLOOR NEW YORK, NY10065 X Baker Bros. Advisors (GP) LLC 667 MADISION AVENUE, 21ST FLOOR NEW YORK, NYNew York X BAKER FELIX 667 MADISON AVENUE, 21ST FLOOR NEW YORK, NY10065 X BAKER JULIAN 667 MADISON AVENUE, 21ST FLOOR NEW YORK, NY10065 X Signatures Baker Bros. Advisors LP: Name: Scott L. Lessing Title: President /s/ Scott L. Lessing 01/09/2017 Signature of Reporting Person Date By: Baker Bros. Advisors (GP) LLC: Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 01/09/2017 Signature of Reporting Person Date /s/ Felix J. Baker 01/09/2017 Signature of Reporting Person Date /s/ Julian C. Baker 01/09/2017 Signature of Reporting Person Date

Explanation of Responses:

( 1 )Common shares held directly by Felix J. Baker and for which Felix J. Baker has sole beneficial ownership. These shares were received in an in kind pro ratadistribution from an affiliated investment fund in January 2015 without consideration. ( 2 )Common shares held directly by Julian C. Baker and for which Julian C. Baker has sole beneficial ownership. These shares were received in an in kind pro ratadistribution from an affiliated investment fund in January 2015 without consideration. ( 3 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $16.69 to $16.75, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 4 )After giving effect to the transactions reported herein, and as a result of their ownership interest in Baker Biotech Capital (GP), LLC, Julian C. Baker and Felix J. Baker may be deemed to have an indirect pecuniary interest in the Issuer's shares of Common Stock reported in column 5 of Table I directly held by 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667. ( 5 )After giving effect to the transactions reported herein, and as a result of their ownership interest in Baker Brothers Life Sciences Capital (GP), LLC, Julian C. Baker and Felix J. Baker may be deemed to have an indirect pecuniary interest in the Issuer's shares of Common Stock reported in column 5 of Table I directly held by Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences. ( 6 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.26 to $15.46, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 7 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $16.72 to $16.99, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 8 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.19 to $15.48, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 9 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.75 to $16.75, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 10 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.01 to $15.74, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 11 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.38 to $15.79, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 12 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $15.81 to $16.80, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 13 )The price reported in Column 4 is a weighted average price. These shares were traded by the Funds in multiple transactions at prices ranging from $16.81 to $17.80, inclusive. The reporting persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares traded at each separate price within the range set forth in this footnote. ( 14 )Baker Bros. Advisors LP (the "Adviser") serves as the Investment Adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held by the Funds. Baker Bros. Advisors (GP) LLC (the "Adviser GP") is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are principals of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held by the Funds. Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

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).

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