Zinc in PDB 7buc: Crystal Structure of EHMT2 Set Domain in Complex with Compound 13

The structure of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13, PDB code: 7buc was solved by M.Suzuki, M.Mizuno, K.Katayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.500, 78.430, 72.990, 90.00, 91.62, 90.00
R / Rfree (%)	21 / 26.2

The binding sites of Zinc atom in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 (pdb code 7buc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13, PDB code: 7buc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:37.4 occ:1.00 SG A:CYS1023 2.2 36.4 1.0 SG A:CYS1017 2.2 39.1 1.0 SG A:CYS980 2.3 44.3 1.0 SG A:CYS1027 2.3 43.1 1.0 CB A:CYS1023 2.8 36.6 1.0 CB A:CYS1017 3.1 36.2 1.0 CB A:CYS1027 3.3 41.0 1.0 CB A:CYS980 3.3 45.8 1.0 ZN A:ZN1502 3.6 46.0 1.0 ZN A:ZN1503 3.8 41.4 1.0 SG A:CYS974 4.1 42.4 1.0 CA A:CYS1023 4.3 37.7 1.0 NH2 A:ARG1030 4.4 39.6 1.0 CA A:CYS1017 4.5 34.7 1.0 CB A:ASN1029 4.5 35.8 1.0 NE A:ARG1030 4.6 37.9 1.0 CA A:CYS980 4.7 48.5 1.0 CA A:CYS1027 4.7 40.9 1.0 CZ A:ARG1030 4.7 39.6 1.0 O A:TRP1024 4.8 44.7 1.0 N A:CYS1023 4.9 38.3 1.0 CB A:CYS1021 5.0 36.9 1.0 C A:CYS1023 5.0 39.0 1.0 SG A:CYS985 5.0 52.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:46.0 occ:1.00 SG A:CYS1017 2.2 39.1 1.0 SG A:CYS1021 2.2 39.2 1.0 SG A:CYS974 2.4 42.4 1.0 SG A:CYS987 2.5 55.4 1.0 CB A:CYS1017 3.0 36.2 1.0 CB A:CYS1021 3.2 36.9 1.0 CB A:CYS974 3.2 43.9 1.0 SG A:CYS1023 3.4 36.4 1.0 CA A:CYS1017 3.4 34.7 1.0 ZN A:ZN1501 3.6 37.4 1.0 ZN A:ZN1503 3.6 41.4 1.0 N A:CYS974 3.6 45.2 1.0 CB A:CYS987 3.7 65.8 1.0 CA A:CYS974 4.0 44.4 1.0 SG A:CYS980 4.3 44.3 1.0 SG A:CYS985 4.3 52.7 1.0 N A:CYS1017 4.4 32.9 1.0 CA A:CYS1021 4.4 36.4 1.0 N A:ASN1018 4.4 36.3 1.0 C A:CYS1017 4.5 34.8 1.0 C A:HIS973 4.6 45.9 1.0 C A:CYS974 4.7 44.5 1.0 O A:CYS974 4.8 42.1 1.0 ND2 A:ASN1029 4.9 37.1 1.0 CB A:CYS1023 4.9 36.6 1.0 CA A:CYS987 5.0 69.5 1.0 CA A:HIS973 5.0 47.3 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:41.4 occ:1.00 SG A:CYS985 2.0 52.7 1.0 SG A:CYS980 2.2 44.3 1.0 SG A:CYS976 2.4 50.1 1.0 SG A:CYS974 2.5 42.4 1.0 CB A:CYS980 3.2 45.8 1.0 CB A:CYS974 3.2 43.9 1.0 CB A:CYS976 3.2 48.1 1.0 CB A:CYS985 3.3 59.6 1.0 ZN A:ZN1502 3.6 46.0 1.0 CA A:CYS980 3.8 48.5 1.0 SG A:CYS1017 3.8 39.1 1.0 ZN A:ZN1501 3.8 37.4 1.0 CA A:CYS985 3.9 62.3 1.0 N A:CYS976 4.5 46.8 1.0 CA A:CYS976 4.5 48.1 1.0 SG A:CYS1023 4.6 36.4 1.0 CA A:CYS974 4.7 44.4 1.0 N A:CYS980 4.8 48.1 1.0 C A:CYS980 4.8 50.6 1.0 SG A:CYS987 4.8 55.4 1.0 C A:CYS985 4.8 63.2 1.0 O A:CYS980 4.8 52.7 1.0 CB A:CYS1023 4.9 36.6 1.0 CB A:CYS987 4.9 65.8 1.0 N A:LEU986 5.0 65.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:55.7 occ:1.00 SG A:CYS1170 2.1 46.7 1.0 SG A:CYS1168 2.2 55.5 1.0 SG A:CYS1115 2.2 53.1 1.0 SG A:CYS1175 2.5 56.3 1.0 CB A:CYS1115 3.0 49.9 1.0 CB A:CYS1168 3.3 54.7 1.0 CB A:CYS1170 3.4 49.5 1.0 CB A:CYS1175 3.7 55.7 1.0 N A:CYS1115 3.9 47.1 1.0 N A:CYS1170 3.9 50.0 1.0 CA A:CYS1115 4.0 49.7 1.0 CA A:CYS1175 4.1 57.9 1.0 CA A:CYS1170 4.2 51.5 1.0 NE2 A:HIS1113 4.5 42.4 1.0 CA A:CYS1168 4.5 52.7 1.0 N A:LYS1176 4.5 56.9 1.0 CD2 A:HIS1113 4.6 41.0 1.0 N A:GLN1169 4.6 53.1 1.0 C A:CYS1168 4.6 52.7 1.0 N A:GLY1171 4.6 54.5 1.0 N A:HIS1177 4.7 56.8 1.0 C A:CYS1175 4.8 58.4 1.0 CB A:HIS1177 4.8 60.0 1.0 C A:CYS1170 4.9 53.0 1.0 N A:SER1178 4.9 59.6 1.0 C A:HIS1177 5.0 60.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1501 b:44.7 occ:1.00 SG B:CYS1023 2.0 43.9 1.0 SG B:CYS1027 2.1 47.1 1.0 SG B:CYS1017 2.2 36.4 1.0 SG B:CYS980 2.7 44.2 1.0 CB B:CYS1023 2.9 44.3 1.0 CB B:CYS1017 3.1 39.1 1.0 CB B:CYS1027 3.1 46.5 1.0 CB B:CYS980 3.7 50.2 1.0 ZN B:ZN1502 3.8 46.2 1.0 ZN B:ZN1503 3.8 62.9 1.0 NH2 B:ARG1030 4.3 37.1 1.0 NE B:ARG1030 4.3 36.9 1.0 CA B:CYS1023 4.4 44.0 1.0 SG B:CYS974 4.4 46.1 1.0 O B:TRP1024 4.5 57.7 1.0 CA B:CYS1017 4.5 39.2 1.0 CA B:CYS1027 4.5 48.3 1.0 CZ B:ARG1030 4.6 37.6 1.0 CB B:ASN1029 4.6 40.6 1.0 N B:CYS1023 4.9 43.3 1.0 C B:CYS1023 4.9 46.2 1.0 N B:ASN1029 5.0 45.6 1.0 CA B:CYS980 5.0 56.8 1.0 CB B:CYS1021 5.0 39.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:46.2 occ:1.00 SG B:CYS1021 2.3 39.9 1.0 SG B:CYS1017 2.3 36.4 1.0 SG B:CYS987 2.5 49.5 1.0 SG B:CYS974 2.5 46.1 1.0 CB B:CYS1017 3.2 39.1 1.0 CB B:CYS987 3.4 52.7 1.0 CB B:CYS1021 3.4 39.6 1.0 CB B:CYS974 3.4 51.5 1.0 CA B:CYS1017 3.4 39.2 1.0 ZN B:ZN1503 3.6 62.9 1.0 SG B:CYS1023 3.8 43.9 1.0 ZN B:ZN1501 3.8 44.7 1.0 N B:CYS974 3.9 57.1 1.0 SG B:CYS985 4.2 73.1 1.0 CA B:CYS974 4.3 55.3 1.0 N B:CYS1017 4.4 39.9 1.0 N B:ASN1018 4.5 39.9 1.0 SG B:CYS980 4.5 44.2 1.0 C B:CYS1017 4.5 39.3 1.0 CA B:CYS1021 4.7 41.9 1.0 CA B:CYS987 4.7 54.7 1.0 C B:HIS973 4.8 58.4 1.0 N B:CYS987 4.9 55.7 1.0 ND2 B:ASN1029 4.9 38.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1503 b:62.9 occ:1.00 SG B:CYS980 2.0 44.2 1.0 SG B:CYS985 2.2 73.1 1.0 SG B:CYS976 2.4 69.6 1.0 SG B:CYS974 2.5 46.1 1.0 CB B:CYS985 3.3 72.2 1.0 CB B:CYS980 3.3 50.2 1.0 CB B:CYS974 3.3 51.5 1.0 CB B:CYS976 3.5 68.0 1.0 ZN B:ZN1502 3.6 46.2 1.0 ZN B:ZN1501 3.8 44.7 1.0 SG B:CYS1017 3.9 36.4 1.0 CA B:CYS980 4.0 56.8 1.0 CA B:CYS985 4.0 69.3 1.0 SG B:CYS1023 4.3 43.9 1.0 N B:CYS976 4.5 62.4 1.0 CA B:CYS976 4.6 65.7 1.0 CB B:CYS1023 4.7 44.3 1.0 CA B:CYS974 4.7 55.3 1.0 C B:CYS985 4.8 66.8 1.0 N B:CYS980 4.9 59.0 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of EHMT2 Set Domain in Complex with Compound 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1504 b:51.5 occ:1.00 SG B:CYS1115 2.1 65.5 1.0 SG B:CYS1168 2.3 49.6 1.0 SG B:CYS1175 2.4 56.8 1.0 SG B:CYS1170 2.4 46.0 1.0 CB B:CYS1170 3.4 50.9 1.0 CB B:CYS1115 3.4 63.9 1.0 CB B:CYS1175 3.4 56.4 1.0 CB B:CYS1168 3.4 52.0 1.0 CA B:CYS1175 3.8 57.3 1.0 N B:CYS1115 4.0 56.7 1.0 N B:LYS1176 4.1 57.8 1.0 N B:CYS1170 4.3 55.2 1.0 CA B:CYS1115 4.3 61.6 1.0 CA B:CYS1170 4.4 54.0 1.0 NE2 B:HIS1113 4.4 41.6 1.0 C B:CYS1175 4.4 58.5 1.0 N B:HIS1177 4.4 54.0 1.0 CD2 B:HIS1113 4.6 42.6 1.0 CA B:CYS1168 4.7 52.6 1.0 CB B:HIS1177 4.8 56.6 1.0 C B:CYS1168 4.9 54.4 1.0

K.Katayama, K.Ishii, E.Tsuda, K.Yotsumoto, K.Hiramoto, M.Suzuki, I.Yasumatsu, W.Igarashi, M.Torihata, T.Ishiyama, T.Katagiri. Discovery of Novel Histone Lysine Methyltransferase G9A/Glp (EHMT2/1) Inhibitors: Design, Synthesis, and Structure-Activity Relationships of 2,4-Diamino-6-Methylpyrimidines. Bioorg.Med.Chem.Lett. V. 30 27475 2020.
ISSN: ESSN 1464-3405
PubMed: 32781218
DOI: 10.1016/J.BMCL.2020.127475