13D Filing: James E. Flynn and Nivalis Therapeutics Inc. (NVLS)

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

[Rule 13d-101]

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO §
24.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13D-2(a)

(Amendment No. 2)*

Nivalis
Therapeutics, Inc.

(Name
of Issuer)

Common
Stock, par value $0.001 per share

(Title
of Class of Securities)

65481J109

(CUSIP
Number)

David Clark Deerfield Mgmt, L.P. 780 Third Avenue, 37th Floor New York, New York 10017 (212) 551-1600 With a copy to: Mark Wood Jonathan D. Weiner Katten Muchin Rosenman LLP 575 Madison Avenue New York, New York 10022 (212) 940-8800

(Name,
Address and Telephone Number of Person Authorized to Receive Notices and Communications)

April
17, 2017

(Date
of Event which Requires Filing of this Statement)

If the filing person
has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing
this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box ☐.

Note: Schedules
filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7
for other parties to whom copies are to be sent.

(Continued on following
pages)

(Page 1 of 15 Pages)

* The remainder of this cover page shall be filled out for a
reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment
containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page
shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”)
or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however,
see the Notes).