Exhibit 4.1



ZQ|CERT#|COY|CLS|RGSTRY|ACCT#|TRANSTYPE|RUN#|TRANS#   . COMMON STOCK PAR VALUE $0.01 COMMON STOCK Shares * * 000000 * * * * * * * *   * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * * * * * * * *   000000 * * * * * * * * * * * * * * * * * * * * * 000000 * * * * * * * * * * *   * * * * * * * * * * 000000 * * * * * * * * * * * * * * Certificate Number   ZQ00000000 APTINYX INC. INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE   ** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David SEE REVERSE FOR CERTAIN DEFINITIONS THIS CERTIFIES THAT Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander Alexander   David SamMple ***R* Mr. A.lexaSnderADavidMSampPle ***L* MrE. Alexan&der   DavMid SamRple **S** Mr.. AleSxandeAr DaMvid SamPple *L*** MEr.   Alex&ander David Sample **** David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander DavidMSampRle ****.Mr.   SAlexaAnderMDavidPSamLple *E*** Mr. &AlexandMer DavRid SaSmple.**** SMr.   AAlexanMder DaPvid SLampEle **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Sample **** Mr. Sample   is the owner of   **000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares***   *000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****   000000**Shar*es****0*000Z00**SEhareRs****00O0000**ShHares**U**0000N00**SDhares*R***000E000**DShares**T**000H000**SOhares*U***000S000**AShareNs****00D0000**Shares****0   THIS CERTIFICATE IS TRANSFERABLE IN CITIES DESIGNATED BY THE TRANSFER AGENT,   AVAILABLE ONLINE AT www.computershare.com 00000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****00   0000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000   000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****0000   00**Shares****0Z0000E0**ShRares***O*000000*H*ShareUs****0N00000D**SharRes****0E0000D0**ShareAs****0N00000D**SharesZ****00E0000R**SharOes****0*000*00**Shares****00000   0**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000   **Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000*   *Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**   Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**S   FULLY-PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK OF Aptinyx Inc.   (hereinafter called the “Company”), transferable on the books of the Company   in person or by duly authorized attorney, upon surrender of this Certificate   properly endorsed. This Certificate and the shares represented hereby, are   issued and shall be held subject to all of the provisions of the Certificate   of Incorporation, as amended, and the bylaws, as amended, of the Company   (copies of which are on file with the Company and with the Transfer Agent),   to all of which each holder, by acceptance hereof, assents. This Certificate   is not valid unless countersigned and registered by the Transfer Agent and   Registrar. Witness the facsimile seal of the Company and the facsimile   signatures of its duly authorized officers. DATED DD-MMM-YYYY COUNTERSIGNED   AND REGISTERED: COMPUTERSHARE TRUST COMPANY, N.A. TRANSFER AGENT AND   REGISTRAR, FACSIMILE SIGNATURE TO COME President May 23, 2018 FACSIMILE   SIGNATURE TO COME By Secretary AUTHORIZED SIGNATURE CUSIP/IDENTIFIER Holder   ID Insurance Value Number of Shares DTC Certificate Numbers   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890 Total   Transaction XXXXXX XX X XXXXXXXXXX 1,000,000.00 123456 12345678   123456789012345 PO BOX 43004, Providence, RI 02940-3004 Num/No. Denom. Total   1 2 3 4 5 6 7 1 2 3 4 5 6 1 2 3 4 5 6 MR A SAMPLE DESIGNATION (IF ANY) ADD 1   ADD 2 ADD 3 ADD 4 CUSIP XXXXXX XX X 


    




 






 



APTINYX INC.   THE COMPANY WILL FURNISH WITHOUT CHARGE TO EACH SHAREHOLDER WHO SO REQUESTS,   A SUMMARY OF THE POWERS, DESIGNATIONS, PREFERENCES AND RELATIVE,   PARTICIPATING, OPTIONAL OR OTHER SPECIAL RIGHTS OF EACH CLASS OF STOCK OF THE   COMPANY AND THE QUALIFICATIONS, LIMITATIONS OR RESTRICTIONS OF SUCH   PREFERENCES AND RIGHTS, AND THE VARIATIONS IN RIGHTS, PREFERENCES AND   LIMITATIONS DETERMINED FOR EACH SERIES, WHICH ARE FIXED BY THE CERTIFICATE OF   INCORPORATION OF THE COMPANY, AS AMENDED, AND THE RESOLUTIONS OF THE BOARD OF   DIRECTORS OF THE COMPANY, AND THE AUTHORITY OF THE BOARD OF DIRECTORS TO   DETERMINE VARIATIONS FOR FUTURE SERIES. SUCH REQUEST MAY BE MADE TO THE   OFFICE OF THE SECRETARY OF THE COMPANY OR TO THE TRANSFER AGENT. THE BOARD OF   DIRECTORS MAY REQUIRE THE OWNER OF A LOST OR DESTROYED STOCK CERTIFICATE, OR   HIS LEGAL REPRESENTATIVES, TO GIVE THE COMPANY A BOND TO INDEMNIFY IT AND ITS   TRANSFER AGENTS AND REGISTRARS AGAINST ANY CLAIM THAT MAY BE MADE AGAINST   THEM ON ACCOUNT OF THE ALLEGED LOSS OR DESTRUCTION OF ANY SUCH CERTIFICATE.   (Cust) (Minor) (State) (Cust) and not as tenants in common (Minor) (State)   PLEASE INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE For   value received, hereby sell, assign and transfer unto (PLEASE PRINT OR   TYPEWRITE NAME AND ADDRESS, INCLUDING POSTAL ZIP CODE, OF ASSIGNEE) Shares of   the common stock represented by the within Certificate, and do hereby   irrevocably constitute and appoint Attorney to transfer the said stock on the   books of the within-named Company with full power of substitution in the   premises. Dated: 20 Signature: Signature: Notice: The signature to this   assignment must correspond with the name as written upon the face of the   certificate, in every particular, without alteration or enlargement, or any   change whatever. The IRS requires that the named transfer agent (“we”) report   the cost basis of certain shares or units ac uired after January 1, 2011. If   your shares or units are covered by the legislation, and you requested to   sell or transfer the shares or units using a specific cost basis calculation   method, then we have processed as you requested. If you did not specify a   cost basis calculation method, then we have defaulted to the first in, first   out (FIFO) method. Please consult your tax advisor if you need additional   information about cost basis. If you do not keep in contact with the issuer   or do not have any activity in your account for the time period specified by   state law, your property may become subject to state unclaimed property laws   and transferred to the appropriate state. Signature(s) Guaranteed: Medallion   Guarantee Stamp THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE   GUARANTOR INSTITUTION (Banks, Stockbrokers, Savings and Loan Associations and   Credit Unions) WITH MEMBERSHIP IN AN APPROVED SIGNATURE GUARANTEE MEDALLION   PROGRAM, PURSUANT TO S.E.C. RULE 17Ad-15. The following abbreviations, when   used in the inscription on the face of this certificate, shall be construed   as though they were written out in full according to applicable laws or   regulations: TEN COM - as tenants in common UNIF GIFT MIN ACT -   ............................................Custodian   ................................................ TEN ENT - as tenants by the   entireties under Uniform Gifts to Minors Act.........................................................   JT TEN - as joint tenants with right of survivorship UNIFTRF MIN ACT -   ............................................Custodian (until age   ................................) .............................under Uniform   Transfers to Minors Act ................... Additional abbreviations may also   be used though not in the above list.