BAKER BROS. ADVISORS LP - 11 Dec 2025 Form 4 Insider Report for Denali Therapeutics Inc. (DNLI)

Role
Director
Signature
By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing
Issuer symbol
DNLI
Transactions as of
11 Dec 2025
Net transactions value
+$39,977,138
Form type
4
Filing time
15 Dec 2025, 16:33:24 UTC
Previous filing
24 Nov 2025
Next filing
19 Dec 2025

Reporting Owners (6)

Name Relationship Address Signature Signature date CIK
BAKER BROS. ADVISORS LP Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 15 Dec 2025 0001263508
667, L.P. Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to 667, L.P., pursuant to authority granted by Baker Biotech Capital, L.P., GP to 667, L.P. Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 15 Dec 2025 0001551139
Baker Bros. Advisors (GP) LLC Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK By: Baker Bros. Advisors (GP) LLC, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing 15 Dec 2025 0001580575
Baker Brothers Life Sciences LP Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to BAKER BROTHERS LIFE SCIENCES, L.P., pursuant to authority granted by Baker Brothers Life Sciences Capital, L.P., GP to Baker Brothers Life Sciences, L.P., /s/ Name: Scott L. Lessing, Title: President 15 Dec 2025 0001363364
BAKER FELIX Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK /s/ Felix J. Baker 15 Dec 2025 0001087940
BAKER JULIAN Director 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK /s/ Julian C. Baker 15 Dec 2025 0001087939

Derivative Securities (e.g., puts, calls, warrants, options, convertible securities)

Type Sym Class Transaction Value $ Shares Change % * Price $ Shares After Date Underlying Class Amount Exercise Price Ownership Footnotes
transaction DNLI $0.01 Prefunded Warrants Purchase $3,332,247 +190,523 +8.9% $17.49 2,335,469 11 Dec 2025 Common Stock 190,523 $0.0100 See Footnotes F1, F2, F3, F4, F5
transaction DNLI $0.01 Prefunded Warrants Purchase $36,644,891 +2,095,191 +8.8% $17.49 25,996,310 11 Dec 2025 Common Stock 2,095,191 $0.0100 See Footnotes F1, F2, F4, F5, F6
* An asterisk sign (*) next to the price indicates that the price is likely invalid.

Explanation of Responses:

Id Content
F1 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences" and together with 667, the "Funds") purchased, respectively, 190,523 and 2,095,191 warrants to purchase common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") at an exercise price of $0.01 per share with no expiration date ("$0.01 Prefunded Warrants") for $17.49 per share in a public offering that closed on December 11, 2025.
F2 The $0.01 Prefunded Warrants are exercisable at any time, at the holder's election, on a 1-for-1 basis into Common Stock to the extent that immediately prior to or after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more thn 4.99% of the outstanding shares of Common Stock (the "Maximum Percentage"). By written notice to the Issuer, the Funds may increase or decrease the Maximum Percentage applicable to that fund to any other percentage not in excess of 19.99%; provided that any such increase will not be effective until the 61st day after such notice is delivered to the Issuer.
F3 After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly 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 their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667.
F4 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 directly by the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members 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 directly 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 directly by the Funds.
F5 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.
F6 After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly 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 their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

Remarks:

Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC is a director of Denali Therapeutics Inc. (the "Issuer"). By virtue of their representation on the board of directors of the Issuer, for purposes of Section 16 of the Securities Exchange Act of 1934, as amended, the reporting persons other than Julian C. Baker are deemed directors by deputization of the Issuer.