Page 8 of 9 – SEC Filing Certain securities of the Issuer are held directly by Baker
Brothers Life Sciences, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital,
L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker
and Felix J. Baker are the controlling members of Baker Brothers Life Sciences Capital (GP), LLC.
(e) Not applicable.
Item 6. Contracts, Arrangements, Understandings or Relationships
with Respect to the Securities of the Issuer.
Item 6 of this Schedule 13D is hereby supplemented and amended,
as the case may be, as follows:
On September 19, 2016 the Issuer entered
into a registration rights agreement (the “Registration Rights Agreement”) with the Funds. Under the Registration Rights
Agreement, the Issuer agreed that, if at any time and from time to time after December 19, 2016, the Funds demand that the Issuer
register shares of common stock directly held by them for resale under the Securities Act of 1933, as amended, the Issuer would
be obligated to effect such registration. The Issuer’s registration obligations under the Registration Rights Agreement cover
all shares of common stock now held or later acquired by the Funds, including shares of common stock issued or issuable upon the
exercise or conversion of any other securities , will continue in effect for up to ten years as long as shares of common stock
held by the Funds remain Registrable Securities (as defined in the Registration Rights Agreement), and include the Issuer’s
obligation to facilitate certain underwritten public offerings of common stock by the Funds in the future, including one underwritten
public offering per calendar year and a total of no more than three total underwritten public offerings. The Funds will bear all
expenses incurred in effecting any registration pursuant to the Registration Rights Agreement.
The foregoing description of the Registration
Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the Registration
Rights Agreement, which is incorporated by reference as Exhibit 99.1, and is incorporated herein by reference.
Item 7. Material to be Filed as Exhibits.
Exhibit Description 99.1 Registration Rights Agreement, dated September 19, 2016, by and among Aquinox Pharmaceuticals, Inc., 667, L.P. and Baker Brothers Life Sciences, L.P. (incorporated by reference to Exhibit 10.1 to the Issuer’s Current Report on Form 8-K, filed with the SEC on September 20, 2016).
Certain securities of the Issuer are held directly by Baker
Brothers Life Sciences, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital,
L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker
and Felix J. Baker are the controlling members of Baker Brothers Life Sciences Capital (GP), LLC.
(e) Not applicable.
Item 6. Contracts, Arrangements, Understandings or Relationships
with Respect to the Securities of the Issuer.
Item 6 of this Schedule 13D is hereby supplemented and amended,
as the case may be, as follows:
On September 19, 2016 the Issuer entered
into a registration rights agreement (the “Registration Rights Agreement”) with the Funds. Under the Registration Rights
Agreement, the Issuer agreed that, if at any time and from time to time after December 19, 2016, the Funds demand that the Issuer
register shares of common stock directly held by them for resale under the Securities Act of 1933, as amended, the Issuer would
be obligated to effect such registration. The Issuer’s registration obligations under the Registration Rights Agreement cover
all shares of common stock now held or later acquired by the Funds, including shares of common stock issued or issuable upon the
exercise or conversion of any other securities , will continue in effect for up to ten years as long as shares of common stock
held by the Funds remain Registrable Securities (as defined in the Registration Rights Agreement), and include the Issuer’s
obligation to facilitate certain underwritten public offerings of common stock by the Funds in the future, including one underwritten
public offering per calendar year and a total of no more than three total underwritten public offerings. The Funds will bear all
expenses incurred in effecting any registration pursuant to the Registration Rights Agreement.
The foregoing description of the Registration
Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the Registration
Rights Agreement, which is incorporated by reference as Exhibit 99.1, and is incorporated herein by reference.
Item 7. Material to be Filed as Exhibits.
| Exhibit | Description | |
| 99.1 | Registration Rights Agreement, dated September 19, 2016, by and among Aquinox Pharmaceuticals, Inc., 667, L.P. and Baker Brothers Life Sciences, L.P. (incorporated by reference to Exhibit 10.1 to the Issuer’s Current Report on Form 8-K, filed with the SEC on September 20, 2016). |
