Zinc in PDB 7xuc: Structure of G9A in Complex with Compound 11A

The structure of Structure of G9A in Complex with Compound 11A, PDB code: 7xuc 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)	17.55 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.572, 77.62, 66.573, 90, 90.65, 90
R / Rfree (%)	15.9 / 18.6

The structure of Structure of G9A in Complex with Compound 11A 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 11A (pdb code 7xuc). 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 11A, PDB code: 7xuc:
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 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:14.7 occ:1.00 SG A:CYS987 2.3 14.6 1.0 SG A:CYS1021 2.3 12.3 1.0 SG A:CYS1017 2.3 13.5 1.0 SG A:CYS974 2.4 15.5 1.0 CB A:CYS1017 3.1 13.4 1.0 CB A:CYS974 3.2 18.2 1.0 CB A:CYS1021 3.3 12.7 1.0 CB A:CYS987 3.5 15.8 1.0 CA A:CYS1017 3.5 14.0 1.0 N A:CYS974 3.5 15.4 1.0 ZN A:ZN1203 3.8 16.6 1.0 ZN A:ZN1202 3.8 15.9 1.0 CA A:CYS974 4.0 15.8 1.0 SG A:CYS1023 4.1 13.3 1.0 SG A:CYS985 4.3 17.0 1.0 N A:CYS1017 4.5 13.3 1.0 N A:ASN1018 4.6 10.8 1.0 CA A:CYS1021 4.6 12.1 1.0 C A:HIS973 4.6 16.0 1.0 C A:CYS1017 4.6 11.8 1.0 SG A:CYS980 4.7 16.8 1.0 CA A:CYS987 4.7 18.0 1.0 N A:CYS987 4.7 16.8 1.0 CA A:HIS973 4.7 14.9 1.0 C A:CYS974 4.8 20.1 1.0 ND2 A:ASN1029 5.0 13.0 1.0 O A:HOH1495 5.0 13.2 1.0 O A:CYS974 5.0 16.9 1.0

Zinc binding site 2 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:15.9 occ:1.00 SG A:CYS1023 2.3 13.3 1.0 SG A:CYS980 2.3 16.8 1.0 SG A:CYS1027 2.3 14.4 1.0 SG A:CYS1017 2.4 13.5 1.0 CB A:CYS1017 3.2 13.4 1.0 CB A:CYS1023 3.2 13.9 1.0 CB A:CYS1027 3.3 14.4 1.0 CB A:CYS980 3.4 18.3 1.0 ZN A:ZN1203 3.8 16.6 1.0 ZN A:ZN1201 3.8 14.7 1.0 SG A:CYS974 4.0 15.5 1.0 NH2 A:ARG1030 4.3 14.6 1.0 NE A:ARG1030 4.3 15.4 1.0 CB A:ASN1029 4.6 13.3 1.0 CA A:CYS1017 4.6 14.0 1.0 CA A:CYS1023 4.6 14.3 1.0 CZ A:ARG1030 4.7 13.4 1.0 O A:TRP1024 4.7 14.8 1.0 CA A:CYS1027 4.8 18.1 1.0 CA A:CYS980 4.8 19.0 1.0 CB A:CYS1021 5.0 12.7 1.0

Zinc binding site 3 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:16.6 occ:1.00 SG A:CYS976 2.3 18.9 1.0 SG A:CYS980 2.3 16.8 1.0 SG A:CYS985 2.3 17.0 1.0 SG A:CYS974 2.4 15.5 1.0 CB A:CYS974 3.1 18.2 1.0 CB A:CYS976 3.2 19.9 1.0 CB A:CYS985 3.2 18.7 1.0 CB A:CYS980 3.3 18.3 1.0 ZN A:ZN1202 3.8 15.9 1.0 ZN A:ZN1201 3.8 14.7 1.0 CA A:CYS985 3.9 19.3 1.0 CA A:CYS980 3.9 19.0 1.0 SG A:CYS1017 4.0 13.5 1.0 N A:CYS976 4.3 20.2 1.0 CA A:CYS976 4.4 19.4 1.0 CA A:CYS974 4.6 15.8 1.0 O A:HOH1410 4.6 18.4 1.0 SG A:CYS1023 4.7 13.3 1.0 C A:CYS985 4.7 21.0 1.0 CB A:CYS1023 4.8 13.9 1.0 N A:CYS980 4.9 22.2 1.0 N A:LEU986 4.9 20.1 1.0 C A:CYS980 5.0 22.2 1.0 O A:HOH1474 5.0 20.2 1.0 SG A:CYS987 5.0 14.6 1.0

Zinc binding site 4 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:18.7 occ:1.00 SG A:CYS1168 2.3 14.7 1.0 SG A:CYS1170 2.3 18.3 1.0 SG A:CYS1115 2.3 18.2 1.0 SG A:CYS1175 2.3 17.7 1.0 CB A:CYS1175 3.3 25.9 1.0 CB A:CYS1115 3.3 21.0 1.0 CB A:CYS1168 3.3 15.4 1.0 CB A:CYS1170 3.4 20.6 1.0 CA A:CYS1175 3.8 22.2 1.0 N A:CYS1115 4.0 16.7 1.0 N A:CYS1170 4.1 22.1 1.0 O A:HOH1471 4.1 22.1 1.0 N A:LYS1176 4.2 19.9 1.0 CA A:CYS1170 4.3 20.7 1.0 CA A:CYS1115 4.3 18.9 1.0 NE2 A:HIS1113 4.4 15.1 1.0 C A:CYS1175 4.4 23.7 1.0 CD2 A:HIS1113 4.5 12.5 1.0 CA A:CYS1168 4.6 16.5 1.0 N A:HIS1177 4.6 19.1 1.0 C A:CYS1168 4.6 19.0 1.0 N A:GLY1171 4.8 21.9 1.0 O A:CYS1168 4.8 18.1 1.0 C A:CYS1170 4.9 24.2 1.0

Zinc binding site 5 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:10.4 occ:1.00 SG B:CYS1021 2.3 7.6 1.0 SG B:CYS987 2.3 9.1 1.0 SG B:CYS1017 2.4 8.3 1.0 SG B:CYS974 2.4 8.4 1.0 CB B:CYS1017 3.2 7.5 1.0 CB B:CYS974 3.3 10.8 1.0 CB B:CYS1021 3.3 6.8 1.0 CB B:CYS987 3.4 8.9 1.0 N B:CYS974 3.6 9.0 1.0 CA B:CYS1017 3.6 8.3 1.0 ZN B:ZN1203 3.8 10.7 1.0 ZN B:ZN1202 3.8 10.1 1.0 CA B:CYS974 4.0 9.8 1.0 SG B:CYS1023 4.1 8.5 1.0 SG B:CYS985 4.2 10.8 1.0 N B:CYS1017 4.5 8.2 1.0 N B:ASN1018 4.5 6.0 1.0 C B:HIS973 4.6 9.1 1.0 CA B:CYS1021 4.6 9.1 1.0 C B:CYS1017 4.6 10.2 1.0 N B:CYS987 4.7 10.5 1.0 CA B:CYS987 4.7 8.9 1.0 SG B:CYS980 4.7 9.2 1.0 CA B:HIS973 4.7 11.3 1.0 C B:CYS974 4.8 9.4 1.0 O B:CYS974 5.0 11.8 1.0

Zinc binding site 6 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:10.1 occ:1.00 SG B:CYS1027 2.3 8.3 1.0 SG B:CYS1023 2.3 8.5 1.0 SG B:CYS980 2.3 9.2 1.0 SG B:CYS1017 2.4 8.3 1.0 CB B:CYS1017 3.1 7.5 1.0 CB B:CYS1023 3.2 10.0 1.0 CB B:CYS1027 3.2 9.1 1.0 CB B:CYS980 3.3 11.7 1.0 ZN B:ZN1203 3.8 10.7 1.0 ZN B:ZN1201 3.8 10.4 1.0 SG B:CYS974 4.0 8.4 1.0 NE B:ARG1030 4.3 11.3 1.0 NH2 B:ARG1030 4.4 10.7 1.0 CA B:CYS1017 4.6 8.3 1.0 CB B:ASN1029 4.6 8.4 1.0 CA B:CYS1023 4.6 11.2 1.0 CA B:CYS980 4.7 12.4 1.0 CA B:CYS1027 4.7 12.9 1.0 CZ B:ARG1030 4.8 11.6 1.0 O B:TRP1024 4.8 11.7 1.0 CB B:CYS1021 4.9 6.8 1.0 SG B:CYS985 5.0 10.8 1.0

Zinc binding site 7 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:10.7 occ:1.00 SG B:CYS985 2.3 10.8 1.0 SG B:CYS976 2.3 9.7 1.0 SG B:CYS974 2.4 8.4 1.0 SG B:CYS980 2.4 9.2 1.0 CB B:CYS974 3.1 10.8 1.0 CB B:CYS985 3.2 11.0 1.0 CB B:CYS976 3.3 11.0 1.0 CB B:CYS980 3.3 11.7 1.0 ZN B:ZN1201 3.8 10.4 1.0 ZN B:ZN1202 3.8 10.1 1.0 CA B:CYS985 3.9 11.9 1.0 CA B:CYS980 3.9 12.4 1.0 SG B:CYS1017 4.0 8.3 1.0 N B:CYS976 4.3 9.7 1.0 CA B:CYS976 4.4 9.8 1.0 O B:HOH1376 4.5 9.4 1.0 CA B:CYS974 4.6 9.8 1.0 C B:CYS985 4.7 13.1 1.0 SG B:CYS1023 4.7 8.5 1.0 N B:LEU986 4.8 11.9 1.0 N B:CYS980 4.8 9.7 1.0 O B:HOH1465 4.8 17.4 1.0 CB B:CYS1023 4.9 10.0 1.0 O B:HOH1531 5.0 11.2 1.0

Zinc binding site 8 out of 8 in the Structure of G9A in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1204 b:19.5 occ:1.00 SG B:CYS1168 2.3 17.5 1.0 SG B:CYS1170 2.3 20.6 1.0 SG B:CYS1175 2.3 20.0 1.0 SG B:CYS1115 2.3 19.4 1.0 CB B:CYS1175 3.1 24.7 1.0 CB B:CYS1168 3.3 17.2 1.0 CB B:CYS1115 3.4 18.9 1.0 CB B:CYS1170 3.4 20.0 1.0 CA B:CYS1175 3.6 29.2 1.0 N B:CYS1170 4.0 21.7 1.0 O B:HOH1490 4.0 23.4 1.0 N B:CYS1115 4.1 17.1 1.0 N B:LYS1176 4.2 21.8 1.0 CA B:CYS1170 4.3 23.7 1.0 C B:CYS1175 4.3 25.8 1.0 CA B:CYS1115 4.4 20.3 1.0 NE2 B:HIS1113 4.5 16.0 1.0 N B:HIS1177 4.5 20.5 1.0 CD2 B:HIS1113 4.5 14.4 1.0 CA B:CYS1168 4.6 19.3 1.0 C B:CYS1168 4.7 21.6 1.0 N B:CYS1175 4.8 30.8 1.0 N B:GLY1171 4.8 24.2 1.0 C B:CYS1170 4.9 26.9 1.0 O B:CYS1168 4.9 24.0 1.0 CB B:HIS1177 5.0 19.2 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