Zinc in PDB 7xud: Structure of G9A in Complex with Compound 26A

The structure of Structure of G9A in Complex with Compound 26A, PDB code: 7xud was solved by H.Niwa, F.Shirai, S.Sato, Y.Nishigaya, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.65 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.596, 77.451, 66.797, 90, 90.5, 90
R / Rfree (%)	16.1 / 17.7

The structure of Structure of G9A in Complex with Compound 26A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of G9A in Complex with Compound 26A (pdb code 7xud). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of G9A in Complex with Compound 26A, PDB code: 7xud:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:16.4 occ:1.00 SG A:CYS987 2.3 19.1 1.0 SG A:CYS1021 2.3 16.1 1.0 SG A:CYS974 2.3 19.4 1.0 SG A:CYS1017 2.4 17.7 1.0 CB A:CYS1017 3.2 19.5 1.0 CB A:CYS974 3.2 20.9 1.0 CB A:CYS1021 3.3 17.7 1.0 CB A:CYS987 3.4 19.2 1.0 N A:CYS974 3.5 18.4 1.0 CA A:CYS1017 3.6 15.0 1.0 ZN A:ZN1203 3.8 18.7 1.0 ZN A:ZN1202 3.8 17.4 1.0 CA A:CYS974 3.9 21.1 1.0 SG A:CYS1023 4.2 17.5 1.0 SG A:CYS985 4.3 23.2 1.0 N A:CYS1017 4.5 14.6 1.0 C A:HIS973 4.6 19.6 1.0 CA A:CYS1021 4.6 16.1 1.0 N A:ASN1018 4.6 15.3 1.0 SG A:CYS980 4.6 20.9 1.0 C A:CYS1017 4.7 13.3 1.0 CA A:CYS987 4.7 21.3 1.0 N A:CYS987 4.7 22.4 1.0 CA A:HIS973 4.8 20.0 1.0 C A:CYS974 4.8 25.1 1.0 O A:HOH1473 5.0 18.8 1.0 ND2 A:ASN1029 5.0 18.6 1.0

Zinc binding site 2 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:17.4 occ:1.00 SG A:CYS980 2.3 20.9 1.0 SG A:CYS1023 2.3 17.5 1.0 SG A:CYS1027 2.4 17.7 1.0 SG A:CYS1017 2.4 17.7 1.0 CB A:CYS1017 3.2 19.5 1.0 CB A:CYS1023 3.2 18.3 1.0 CB A:CYS1027 3.2 20.0 1.0 CB A:CYS980 3.4 21.9 1.0 ZN A:ZN1203 3.8 18.7 1.0 ZN A:ZN1201 3.8 16.4 1.0 SG A:CYS974 4.0 19.4 1.0 NH2 A:ARG1030 4.3 19.4 1.0 NE A:ARG1030 4.3 18.3 1.0 CB A:ASN1029 4.6 19.4 1.0 CA A:CYS1017 4.6 15.0 1.0 CA A:CYS1023 4.7 19.6 1.0 O A:TRP1024 4.7 19.8 1.0 CA A:CYS1027 4.7 20.2 1.0 CA A:CYS980 4.7 25.3 1.0 CZ A:ARG1030 4.7 17.5 1.0 CB A:CYS1021 4.9 17.7 1.0 N A:ASN1029 5.0 18.8 1.0

Zinc binding site 3 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:18.7 occ:1.00 SG A:CYS976 2.3 24.2 1.0 SG A:CYS985 2.3 23.2 1.0 SG A:CYS980 2.3 20.9 1.0 SG A:CYS974 2.4 19.4 1.0 CB A:CYS974 3.1 20.9 1.0 CB A:CYS976 3.2 27.1 1.0 CB A:CYS980 3.2 21.9 1.0 CB A:CYS985 3.3 27.1 1.0 ZN A:ZN1202 3.8 17.4 1.0 ZN A:ZN1201 3.8 16.4 1.0 CA A:CYS980 3.9 25.3 1.0 CA A:CYS985 3.9 27.7 1.0 SG A:CYS1017 4.0 17.7 1.0 N A:CYS976 4.3 25.7 1.0 CA A:CYS976 4.4 25.0 1.0 O A:HOH1354 4.6 25.6 1.0 CA A:CYS974 4.6 21.1 1.0 C A:CYS985 4.7 28.1 1.0 SG A:CYS1023 4.7 17.5 1.0 N A:CYS980 4.8 24.4 1.0 N A:LEU986 4.9 26.4 1.0 CB A:CYS1023 4.9 18.3 1.0 O A:HOH1464 4.9 27.3 1.0 C A:CYS980 4.9 28.7 1.0 O A:HOH1504 5.0 26.1 1.0

Zinc binding site 4 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:18.4 occ:1.00 SG A:CYS1175 2.3 19.4 1.0 SG A:CYS1168 2.3 16.8 1.0 SG A:CYS1170 2.3 19.5 1.0 SG A:CYS1115 2.4 21.1 1.0 CB A:CYS1115 3.3 20.9 1.0 CB A:CYS1175 3.3 21.7 1.0 CB A:CYS1168 3.4 17.9 1.0 CB A:CYS1170 3.4 21.1 1.0 CA A:CYS1175 3.8 22.5 1.0 N A:CYS1115 4.0 17.7 1.0 N A:CYS1170 4.1 18.9 1.0 N A:LYS1176 4.2 23.9 1.0 O A:HOH1451 4.2 23.4 1.0 CA A:CYS1115 4.2 20.4 1.0 CA A:CYS1170 4.3 18.6 1.0 NE2 A:HIS1113 4.4 18.9 1.0 C A:CYS1175 4.4 25.3 1.0 CD2 A:HIS1113 4.5 16.6 1.0 N A:HIS1177 4.6 20.4 1.0 CA A:CYS1168 4.6 16.4 1.0 C A:CYS1168 4.7 19.5 1.0 N A:GLY1171 4.9 21.5 1.0 O A:CYS1168 4.9 19.1 1.0 C A:CYS1170 4.9 23.7 1.0 CB A:SER1172 5.0 25.6 1.0

Zinc binding site 5 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:11.6 occ:1.00 SG B:CYS987 2.3 12.3 1.0 SG B:CYS1021 2.3 10.9 1.0 SG B:CYS1017 2.4 10.9 1.0 SG B:CYS974 2.4 11.6 1.0 CB B:CYS1017 3.2 10.6 1.0 CB B:CYS974 3.3 12.8 1.0 CB B:CYS1021 3.3 10.2 1.0 CB B:CYS987 3.4 11.2 1.0 N B:CYS974 3.5 11.6 1.0 CA B:CYS1017 3.6 10.0 1.0 ZN B:ZN1203 3.8 12.3 1.0 ZN B:ZN1202 3.8 11.5 1.0 CA B:CYS974 4.0 12.7 1.0 SG B:CYS1023 4.1 11.7 1.0 SG B:CYS985 4.2 13.0 1.0 N B:CYS1017 4.5 10.2 1.0 C B:HIS973 4.5 12.0 1.0 N B:ASN1018 4.6 10.2 1.0 CA B:CYS1021 4.6 11.3 1.0 CA B:CYS987 4.6 11.4 1.0 N B:CYS987 4.6 13.1 1.0 C B:CYS1017 4.6 10.3 1.0 SG B:CYS980 4.7 11.6 1.0 CA B:HIS973 4.7 13.6 1.0 C B:CYS974 4.8 12.6 1.0 O B:HOH1474 5.0 13.9 1.0 O B:CYS974 5.0 14.3 1.0

Zinc binding site 6 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:11.5 occ:1.00 SG B:CYS1023 2.3 11.7 1.0 SG B:CYS980 2.3 11.6 1.0 SG B:CYS1027 2.3 11.9 1.0 SG B:CYS1017 2.4 10.9 1.0 CB B:CYS1017 3.1 10.6 1.0 CB B:CYS1023 3.2 13.2 1.0 CB B:CYS1027 3.3 13.2 1.0 CB B:CYS980 3.3 13.9 1.0 ZN B:ZN1203 3.8 12.3 1.0 ZN B:ZN1201 3.8 11.6 1.0 SG B:CYS974 4.0 11.6 1.0 NH2 B:ARG1030 4.3 14.1 1.0 NE B:ARG1030 4.3 13.9 1.0 CA B:CYS1017 4.6 10.0 1.0 CB B:ASN1029 4.6 12.1 1.0 CA B:CYS1023 4.6 12.9 1.0 CA B:CYS980 4.7 14.3 1.0 CA B:CYS1027 4.7 13.8 1.0 CZ B:ARG1030 4.8 13.5 1.0 O B:TRP1024 4.8 15.4 1.0 CB B:CYS1021 4.9 10.2 1.0 SG B:CYS985 5.0 13.0 1.0

Zinc binding site 7 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:12.3 occ:1.00 SG B:CYS976 2.3 13.1 1.0 SG B:CYS985 2.3 13.0 1.0 SG B:CYS974 2.4 11.6 1.0 SG B:CYS980 2.4 11.6 1.0 CB B:CYS974 3.1 12.8 1.0 CB B:CYS985 3.2 13.4 1.0 CB B:CYS976 3.2 14.0 1.0 CB B:CYS980 3.3 13.9 1.0 ZN B:ZN1202 3.8 11.5 1.0 ZN B:ZN1201 3.8 11.6 1.0 CA B:CYS985 3.9 14.1 1.0 CA B:CYS980 3.9 14.3 1.0 SG B:CYS1017 4.0 10.9 1.0 N B:CYS976 4.3 13.8 1.0 CA B:CYS976 4.4 12.5 1.0 CA B:CYS974 4.6 12.7 1.0 O B:HOH1350 4.6 15.3 1.0 C B:CYS985 4.7 15.2 1.0 SG B:CYS1023 4.7 11.7 1.0 N B:LEU986 4.8 14.2 1.0 N B:CYS980 4.8 14.2 1.0 O B:HOH1467 4.8 21.0 1.0 CB B:CYS1023 4.9 13.2 1.0 O B:HOH1519 4.9 16.2 1.0

Zinc binding site 8 out of 8 in the Structure of G9A in Complex with Compound 26A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of G9A in Complex with Compound 26A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1204 b:20.4 occ:1.00 SG B:CYS1175 2.3 22.1 1.0 SG B:CYS1168 2.3 19.4 1.0 SG B:CYS1170 2.3 23.9 1.0 SG B:CYS1115 2.4 20.7 1.0 CB B:CYS1175 3.3 25.9 1.0 CB B:CYS1168 3.3 20.3 1.0 CB B:CYS1170 3.3 21.9 1.0 CB B:CYS1115 3.4 22.0 1.0 CA B:CYS1175 3.8 29.3 1.0 O B:HOH1484 4.0 28.7 1.0 N B:CYS1170 4.0 23.5 1.0 N B:CYS1115 4.1 21.0 1.0 N B:LYS1176 4.2 25.2 1.0 CA B:CYS1170 4.2 25.3 1.0 CA B:CYS1115 4.4 22.2 1.0 C B:CYS1175 4.4 28.1 1.0 NE2 B:HIS1113 4.4 18.2 1.0 N B:HIS1177 4.5 22.5 1.0 CD2 B:HIS1113 4.5 17.7 1.0 CA B:CYS1168 4.6 20.7 1.0 C B:CYS1168 4.7 20.7 1.0 N B:GLY1171 4.8 27.0 1.0 C B:CYS1170 4.9 33.2 1.0 O B:CYS1168 4.9 22.6 1.0 CB B:HIS1177 4.9 20.8 1.0

Y.Nishigaya, S.Takase, T.Sumiya, K.Kikuzato, T.Sato, H.Niwa, S.Sato, A.Nakata, T.Sonoda, N.Hashimoto, R.Namie, T.Honma, T.Umehara, M.Shirouzu, H.Koyama, M.Yoshida, A.Ito, F.Shirai. Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9A Inhibitors As Anticancer Agents. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36882960
DOI: 10.1021/ACS.JMEDCHEM.2C02059