Protagonist Therapeutics, Inc 10-Q

ITEM 5. OTHER INFORMATION (c) Trading Plans ​ On June 30, 2026 , Asif Ali , our Chief Financial Officer , adopted a trading plan intended to satisfy Rule 10b5-1(c) to sell up to (i) 73,214 shares of the Company’s common stock, (ii) 50% of the net shares issued to Mr. Ali after withholding taxes upon the vesting of restricted stock unit awards representing 21,346 shares of the Company’s common stock, and (iii) 50% of the net shares issued to Mr. Ali after withholding taxes upon the vesting of performance stock unit awards representing 12,800 shares of the Company’s common stock (assuming that such shares underlying performance stock units vest at target amounts) through September 30, 2027 , or such earlier date when all transactions under the trading plan are completed, subject to certain conditions. ​ Except as discussed above, during the fiscal quarter ended June 30, 2026, no director or Section 16 officer adopted or terminated any Rule 10b5-1 trading arrangement or a non-Rule 10b5-1 trading arrangement (in each case as defined in Item 408(a) of Regulation S-K). ​ ​ ITEM 6. EXHIBITS ​ EXHIBIT INDEX ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Exhibit ​ ​ ​ Incorporation By Reference Number ​ ​ ​ Exhibit Description ​ ​ ​ Form ​ ​ ​ SEC File No. ​ ​ ​ Exhibit ​ ​ ​ Filing Date 3.1 ​ Amended and Restated Certificate of Incorporation ​ 8-K ​ 001-37852 ​ 3.1 ​ 8/16/2016 3.2 ​ Certificate of Amendment to the Amended and Restated Certificate of Incorporation ​ 8-K ​ 001-37852 ​ 3.1 ​ 6/26/2024 3.3 ​ Amended and Restated Bylaws ​ S-1/A ​ 333-212476 ​ 3.2b ​ 8/1/2016 10.1 ​ Protagonist Therapeutics, Inc. 2026 Equity Incentive Plan ​ 8-K ​ 001-37852 ​ 10.1 ​ 6/18/2026 31.1+ ​ Certification of Chief Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities ​ ​ ​ ​ ​ ​ ​ ​ 33 Table of Contents Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 31.2+ ​ Certification of Chief Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 ​ ​ ​ ​ ​ ​ ​ ​ 32.1+* ​ Certification of Chief Executive Officer and Chief Financial Officer, as required by Rule 13a-14(b) or Rule 15d-14(b) and Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C. §1350), as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 ​ ​ ​ ​ ​ ​ ​ ​ 101.INS+ ​ Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL Document. ​ ​ ​ ​ ​ ​ ​ ​ 101.SCH+ ​ Inline XBRL Taxonomy Extension Schema Document ​ ​ ​ ​ ​ ​ ​ ​ 101.CAL+ ​ Inline XBRL Taxonomy Extension Calculation Linkbase Document ​ ​ ​ ​ ​ ​ ​ ​ 101.DEF+ ​ Inline XBRL Taxonomy Extension Definition Linkbase Document ​ ​ ​ ​ ​ ​ ​ ​ 101.LAB+ ​ Inline XBRL Taxonomy Extension Labels Linkbase Document ​ ​ ​ ​ ​ ​ ​ ​ 101.PRE+ ​ Inline XBRL Taxonomy Extension Presentation Linkbase Document ​ ​ ​ ​ ​ ​ ​ ​ 104 ​ Cover Page Interactive Data File - The cover page interactive data file does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document ​ ​ ​ ​ ​ ​ ​ ​ + Filed herewith. * This certification attached as Exhibit 32.1 that accompanies this Quarterly Report on Form 10-Q is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Protagonist Therapeutics, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of the Form 10-Q, irrespective of any general incorporation language contained in such filing. ​ 34 Table of Contents SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ​ PROTAGONIST THERAPEUTICS, INC. ​ ​ ​ ​ ​ ​ Date: August 5, 2026 By: /s/ Dinesh V. Patel, Ph.D. ​ ​ Dinesh V. Patel, Ph.D. ​ ​ President, Chief Executive Officer and Director ​ ​ (Principal Executive Officer) ​ ​ ​ Date: August 5, 2026 By: /s/ Asif Ali ​ ​ Asif Ali ​ ​ Executive Vice President, Chief Financial Officer ​ ​ (Principal Financial and Accounting Officer) ​ ​ 35