Zinc in PDB 7xub: Structure of G9A in Complex with Compound 10D

The structure of Structure of G9A in Complex with Compound 10D, PDB code: 7xub 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)	38.05 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.571, 77.464, 68.111, 90, 90.44, 90
R / Rfree (%)	17.8 / 21.5

The binding sites of Zinc atom in the Structure of G9A in Complex with Compound 10D (pdb code 7xub). 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 10D, PDB code: 7xub:
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 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:36.6 occ:1.00 SG A:CYS987 2.3 42.2 1.0 SG A:CYS1017 2.3 38.7 1.0 SG A:CYS1021 2.3 33.6 1.0 SG A:CYS974 2.4 41.9 1.0 CB A:CYS1017 3.2 35.3 1.0 CB A:CYS974 3.2 43.9 1.0 CB A:CYS1021 3.2 35.2 1.0 CB A:CYS987 3.5 41.4 1.0 N A:CYS974 3.5 40.9 1.0 CA A:CYS1017 3.6 33.5 1.0 ZN A:ZN1203 3.7 38.9 1.0 ZN A:ZN1202 3.9 34.5 1.0 CA A:CYS974 4.0 46.7 1.0 SG A:CYS1023 4.1 35.1 1.0 SG A:CYS985 4.3 49.7 1.0 C A:HIS973 4.5 44.2 1.0 N A:CYS1017 4.5 31.8 1.0 CA A:CYS1021 4.5 36.5 1.0 N A:ASN1018 4.6 32.2 1.0 C A:CYS1017 4.6 36.7 1.0 CA A:HIS973 4.6 41.3 1.0 N A:CYS987 4.7 48.3 1.0 SG A:CYS980 4.7 43.6 1.0 CA A:CYS987 4.7 46.9 1.0 C A:CYS974 4.8 44.8 1.0 O A:HOH1398 4.9 35.9 1.0 O A:CYS974 4.9 48.6 1.0 ND2 A:ASN1029 5.0 38.8 1.0

Zinc binding site 2 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:34.5 occ:1.00 SG A:CYS1027 2.3 36.7 1.0 SG A:CYS1023 2.3 35.1 1.0 SG A:CYS1017 2.3 38.7 1.0 SG A:CYS980 2.4 43.6 1.0 CB A:CYS1017 3.1 35.3 1.0 CB A:CYS1023 3.1 36.6 1.0 CB A:CYS1027 3.3 44.0 1.0 CB A:CYS980 3.3 44.6 1.0 ZN A:ZN1203 3.8 38.9 1.0 ZN A:ZN1201 3.9 36.6 1.0 SG A:CYS974 4.2 41.9 1.0 NE A:ARG1030 4.3 38.0 1.0 NH2 A:ARG1030 4.4 35.5 1.0 CB A:ASN1029 4.5 35.0 1.0 CA A:CYS1023 4.6 35.4 1.0 CA A:CYS1017 4.6 33.5 1.0 CA A:CYS980 4.7 55.4 1.0 CA A:CYS1027 4.7 44.5 1.0 CZ A:ARG1030 4.8 39.4 1.0 O A:TRP1024 4.8 36.1 1.0 N A:ASN1029 5.0 41.8 1.0 CB A:CYS1021 5.0 35.2 1.0 SG A:CYS985 5.0 49.7 1.0

Zinc binding site 3 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:38.9 occ:1.00 SG A:CYS980 2.3 43.6 1.0 SG A:CYS974 2.3 41.9 1.0 SG A:CYS976 2.4 49.0 1.0 SG A:CYS985 2.4 49.7 1.0 CB A:CYS974 3.0 43.9 1.0 CB A:CYS985 3.2 50.6 1.0 CB A:CYS976 3.2 57.4 1.0 CB A:CYS980 3.3 44.6 1.0 ZN A:ZN1201 3.7 36.6 1.0 ZN A:ZN1202 3.8 34.5 1.0 CA A:CYS985 3.8 50.4 1.0 SG A:CYS1017 3.8 38.7 1.0 CA A:CYS980 4.0 55.4 1.0 N A:CYS976 4.3 48.5 1.0 CA A:CYS974 4.4 46.7 1.0 CA A:CYS976 4.4 50.1 1.0 C A:CYS985 4.6 51.1 1.0 SG A:CYS1023 4.7 35.1 1.0 O A:HOH1431 4.7 49.6 1.0 CB A:CYS1023 4.8 36.6 1.0 N A:LEU986 4.8 48.4 1.0 O A:HOH1315 4.8 55.2 1.0 C A:CYS974 4.8 44.8 1.0 SG A:CYS987 4.9 42.2 1.0 N A:CYS980 5.0 48.5 1.0 N A:THR975 5.0 47.6 1.0

Zinc binding site 4 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:60.8 occ:1.00 SG A:CYS1170 2.3 60.1 1.0 SG A:CYS1168 2.3 55.7 1.0 SG A:CYS1115 2.3 65.5 1.0 SG A:CYS1175 2.4 63.8 1.0 CB A:CYS1115 3.3 63.9 1.0 CB A:CYS1175 3.3 69.5 1.0 CB A:CYS1170 3.3 60.5 1.0 CB A:CYS1168 3.4 57.9 1.0 CA A:CYS1175 3.7 72.8 1.0 N A:CYS1170 4.0 61.7 1.0 N A:CYS1115 4.1 61.4 1.0 CA A:CYS1170 4.2 66.0 1.0 N A:LYS1176 4.3 68.9 1.0 CA A:CYS1115 4.3 63.2 1.0 C A:CYS1175 4.5 72.6 1.0 N A:GLY1171 4.6 71.0 1.0 C A:CYS1168 4.6 59.1 1.0 NE2 A:HIS1113 4.6 55.7 1.0 CA A:CYS1168 4.6 60.2 1.0 N A:HIS1177 4.6 70.3 1.0 O A:CYS1168 4.7 58.2 1.0 CD2 A:HIS1113 4.7 55.5 1.0 C A:CYS1170 4.8 69.0 1.0 N A:CYS1175 4.9 85.9 1.0 N A:GLN1169 5.0 58.5 1.0

Zinc binding site 5 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:27.2 occ:1.00 SG B:CYS987 2.2 28.5 1.0 SG B:CYS1021 2.3 27.4 1.0 SG B:CYS1017 2.3 30.2 1.0 SG B:CYS974 2.4 25.5 1.0 CB B:CYS1017 3.1 28.5 1.0 CB B:CYS974 3.2 25.9 1.0 CB B:CYS1021 3.3 30.0 1.0 CB B:CYS987 3.3 33.1 1.0 CA B:CYS1017 3.6 29.0 1.0 N B:CYS974 3.6 29.7 1.0 ZN B:ZN1203 3.7 29.4 1.0 ZN B:ZN1202 3.8 28.2 1.0 CA B:CYS974 4.0 33.5 1.0 SG B:CYS1023 4.2 27.8 1.0 SG B:CYS985 4.2 31.8 1.0 N B:CYS1017 4.5 28.2 1.0 C B:HIS973 4.5 33.0 1.0 CA B:CYS987 4.6 30.9 1.0 N B:CYS987 4.6 35.5 1.0 CA B:CYS1021 4.6 29.4 1.0 N B:ASN1018 4.6 30.0 1.0 SG B:CYS980 4.7 32.4 1.0 C B:CYS1017 4.7 30.5 1.0 CA B:HIS973 4.7 29.5 1.0 C B:CYS974 4.8 31.5 1.0

Zinc binding site 6 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:28.2 occ:1.00 SG B:CYS1017 2.3 30.2 1.0 SG B:CYS1023 2.3 27.8 1.0 SG B:CYS1027 2.3 29.9 1.0 SG B:CYS980 2.4 32.4 1.0 CB B:CYS1017 3.2 28.5 1.0 CB B:CYS1023 3.2 28.7 1.0 CB B:CYS1027 3.2 30.0 1.0 CB B:CYS980 3.3 31.6 1.0 ZN B:ZN1203 3.7 29.4 1.0 ZN B:ZN1201 3.8 27.2 1.0 SG B:CYS974 4.0 25.5 1.0 NH2 B:ARG1030 4.3 29.9 1.0 NE B:ARG1030 4.3 28.8 1.0 CB B:ASN1029 4.5 29.8 1.0 CA B:CYS1017 4.6 29.0 1.0 CA B:CYS1023 4.6 33.0 1.0 CA B:CYS980 4.7 33.9 1.0 CA B:CYS1027 4.7 35.5 1.0 CZ B:ARG1030 4.8 30.9 1.0 O B:TRP1024 4.9 31.4 1.0 CB B:CYS1021 4.9 30.0 1.0 SG B:CYS985 5.0 31.8 1.0 N B:ASN1029 5.0 31.1 1.0

Zinc binding site 7 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:29.4 occ:1.00 SG B:CYS985 2.3 31.8 1.0 SG B:CYS974 2.3 25.5 1.0 SG B:CYS980 2.3 32.4 1.0 SG B:CYS976 2.4 28.9 1.0 CB B:CYS974 3.1 25.9 1.0 CB B:CYS976 3.1 29.2 1.0 CB B:CYS980 3.2 31.6 1.0 CB B:CYS985 3.3 34.2 1.0 ZN B:ZN1201 3.7 27.2 1.0 ZN B:ZN1202 3.7 28.2 1.0 CA B:CYS980 3.9 33.9 1.0 CA B:CYS985 4.0 35.1 1.0 SG B:CYS1017 4.0 30.2 1.0 N B:CYS976 4.3 31.3 1.0 CA B:CYS976 4.4 32.3 1.0 O B:HOH1320 4.5 33.1 1.0 CA B:CYS974 4.6 33.5 1.0 O B:HOH1389 4.7 38.2 1.0 C B:CYS985 4.7 36.4 1.0 SG B:CYS1023 4.8 27.8 1.0 N B:CYS980 4.8 35.8 1.0 N B:LEU986 4.8 32.9 1.0 CB B:CYS1023 4.9 28.7 1.0 SG B:CYS987 4.9 28.5 1.0 C B:CYS980 5.0 33.9 1.0 O B:HOH1406 5.0 31.3 1.0 C B:CYS974 5.0 31.5 1.0

Zinc binding site 8 out of 8 in the Structure of G9A in Complex with Compound 10D


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 10D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1204 b:52.3 occ:1.00 SG B:CYS1170 2.3 51.8 1.0 SG B:CYS1168 2.3 56.1 1.0 SG B:CYS1115 2.3 59.8 1.0 SG B:CYS1175 2.3 60.5 1.0 CB B:CYS1175 3.2 60.3 1.0 CB B:CYS1168 3.3 57.4 1.0 CB B:CYS1115 3.4 54.4 1.0 CB B:CYS1170 3.5 57.1 1.0 CA B:CYS1175 3.6 62.3 1.0 N B:LYS1176 3.9 58.5 1.0 O B:HOH1318 4.1 51.8 1.0 N B:CYS1170 4.1 57.3 1.0 N B:CYS1115 4.2 52.5 1.0 C B:CYS1175 4.2 61.2 1.0 N B:HIS1177 4.4 66.9 1.0 CA B:CYS1170 4.4 59.6 1.0 CA B:CYS1115 4.4 50.8 1.0 CA B:CYS1168 4.6 62.9 1.0 C B:CYS1168 4.6 58.9 1.0 CD2 B:HIS1113 4.6 48.3 1.0 NE2 B:HIS1113 4.7 50.0 1.0 O B:CYS1168 4.8 59.4 1.0 N B:CYS1175 4.9 68.9 1.0 N B:SER1178 4.9 65.9 1.0 N B:GLN1169 5.0 58.9 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