BAKER BROS. ADVISORS LP - 03 Jun 2025 Form 4 Insider Report for Denali Therapeutics Inc. (DNLI)

Reporting relationship: Director
Issuer ticker: DNLI
Reported as of: 03 Jun 2025
Net transaction value: $0
SEC form: 4
Accepted by SEC: 05 Jun 2025, 17:02:52 UTC
Prior SEC filing: 02 Jun 2025
Next SEC filing: 12 Jun 2025
Source filing: View source filing
Reporting owner signature: By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing

Key filing fact

BAKER BROS. ADVISORS LP filed Form 4 for Denali Therapeutics Inc. (DNLI) on 05 Jun 2025.

Key facts

This page summarizes BAKER BROS. ADVISORS LP's Form 4 filing for Denali Therapeutics Inc. (DNLI).
4 reported transactions and 2 derivative rows are listed below.
Accepted by SEC: 05 Jun 2025, 17:02.

Change

Previous filing in this sequence was filed on 02 Jun 2025.
Current net transaction value: $0.

Research use

This tells you what this filing adds before you inspect full transaction and derivative tables.
You can trace every row back to the original SEC filing document.

Evidence

Filed on Form 4

Ownership activity is grounded in SEC Form 4 disclosures.

View source filing

Reporting Owners (6)

CIK 0001263508 Primary reporting owner

BAKER BROS. ADVISORS LP

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing
Signature date: 05 Jun 2025

CIK 0001551139

667, L.P.

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: 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
Signature date: 05 Jun 2025

CIK 0001580575

Baker Bros. Advisors (GP) LLC

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: By: Baker Bros. Advisors (GP) LLC, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing
Signature date: 05 Jun 2025

CIK 0001363364

Baker Brothers Life Sciences LP

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: 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
Signature date: 05 Jun 2025

CIK 0001087940

BAKER FELIX

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: /s/ Felix J. Baker
Signature date: 05 Jun 2025

CIK 0001087939

BAKER JULIAN

Relationship: Director
Address: 860 WASHINGTON STREET, 3RD FLOOR, NEW YORK
Signature: /s/ Julian C. Baker
Signature date: 05 Jun 2025

Reported non-derivative transactions

Shares, units, or other non-derivative securities reported in this filing.

DNLI transaction

Common Stock

Award

Transaction value: $0
Shares: +10,565
Change %: +3.2%
Price: $0.000000
Shares after: 336,867
Date: 03 Jun 2025
Ownership: See Footnotes
Footnotes: F1, F2, F3, F4, F5, F6, F7

DNLI transaction

Common Stock

Award

Transaction value: $0
Shares: +10,565
Change %: +0.31%
Price: $0.000000
Shares after: 3,415,958
Date: 03 Jun 2025
Ownership: See Footnotes
Footnotes: F1, F3, F4, F5, F6, F7, F8

Reported derivative securities

Options, warrants, convertible securities, or similar derivative positions disclosed in the filing.

DNLI transaction Derivative

Non-Qualified Stock Option (right to buy)uy)

Award

Transaction value: $0
Shares: +31,695
Change %
Price: $0.000000
Shares after: 31,695
Date: 03 Jun 2025
Ownership: See Footnotes
Underlying class: Common Stock
Underlying amount: 31,695
Exercise price: $13.93
Footnotes: F2, F3, F4, F5, F6, F7, F9

DNLI transaction Derivative

Non- Qualified Stock Option (right to buy)

Award

Transaction value: $0
Shares: +31,695
Change %
Price: $0.000000
Shares after: 31,695
Date: 03 Jun 2025
Ownership: See Footnotes
Underlying class: Common Stock
Underlying amount: 31,695
Exercise price: $13.93
Footnotes: F3, F4, F5, F6, F7, F8, F9

^* marks a reported price that did not pass the local price check.

Additional SEC filing notes

Filing notes and footnotes

Explanation of responses 9 footnotes

Footnote F1

Includes 10,565 restricted stock units (each, an "RSU") payable solely in common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") granted by the Issuer to Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC (the "Adviser GP") on June 3, 2025, pursuant to the Issuer's 2017 Equity Incentive Plan and Outside Director Compensation Policy (collectively "Incentive Plan"). The RSUs vest in four equal annual installments on June 3, 2026, June 3, 2027, June 3, 2028, and the earlier of June 3, 2029 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2028, in each case subject to Julian C. Baker's continuous service on the board of directors of the Issuer (the "Board") through such vesting dates. Julian C. Baker serves on the Board as a representative of 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences", and together with 667, the "Funds") and their affiliates and control persons.

Footnote F2

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 Common Stock reported in column 5 of Table I and the Stock Options (as defined below) reported in column 9 of Table II held directly by or held for the benefit of 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.

Footnote F3

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Footnote 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 or for the benefit of 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 or for the benefit of 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 or for the benefit of the Funds.

Footnote F5

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of 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.

Footnote F6

Pursuant the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

Footnote F7

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 10,565 RSUs on Table I and 31,695 Stock Options on Table II. These grants, totaling 10,565 RSUs and 31,695 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

Footnote F8

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 Common Stock reported in column 5 of Table I and the Stock Options reported in column 9 of Table II held directly by or held for the benefit of 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.

Footnote F9

31,695 Stock Options exercisable solely into Common Stock were granted under the Incentive Plan to Julian C. Baker in his capacity as a director of the Issuer. The Stock Options have a strike price of $13.93 and expire on June 3, 2035. One fourth of the Stock Options vest on June 3, 2026 with the remaining Stock Options vesting in 36 equal monthly installments beginning on July 3, 2026, subject to Julian C. Baker's continuous service on the Board through such vesting dates.

SEC 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.