Zinc in PDB 7dcf: Crystal Structure of EHMT2 Set Domain in Complex with Compound 10

The structure of Crystal Structure of EHMT2 Set Domain in Complex with Compound 10, PDB code: 7dcf was solved by M.Suzuki, K.Katayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.59 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.852, 72.73, 63.629, 90, 92.66, 90
R / Rfree (%)	20 / 24.6

The binding sites of Zinc atom in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10 (pdb code 7dcf). 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 10, PDB code: 7dcf:
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 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:18.6 occ:1.00 SG A:CYS1023 2.3 15.9 1.0 SG A:CYS1027 2.3 19.9 1.0 SG A:CYS980 2.4 19.8 1.0 SG A:CYS1017 2.4 17.3 1.0 CB A:CYS1027 3.2 18.7 1.0 CB A:CYS1023 3.2 15.6 1.0 CB A:CYS1017 3.2 18.4 1.0 CB A:CYS980 3.5 21.0 1.0 ZN A:ZN1502 3.8 19.0 1.0 ZN A:ZN1503 3.9 20.6 1.0 SG A:CYS974 4.2 19.8 1.0 NH1 A:ARG1030 4.2 10.4 0.5 NE A:ARG1030 4.2 19.1 0.5 NH2 A:ARG1030 4.4 18.8 0.5 CB A:ASN1029 4.6 15.8 1.0 CZ A:ARG1030 4.6 19.3 0.5 CZ A:ARG1030 4.6 11.3 0.5 CA A:CYS1027 4.7 20.3 1.0 CA A:CYS1023 4.7 15.9 1.0 CA A:CYS1017 4.7 17.5 1.0 CA A:CYS980 4.8 22.4 1.0 O A:TRP1024 4.8 17.5 1.0 N A:ASN1029 4.9 15.7 1.0 CB A:CYS1021 4.9 17.1 1.0 NH2 A:ARG1030 4.9 11.1 0.5 N A:CYS980 5.0 23.0 1.0 CG A:ARG1030 5.0 17.5 0.5

Zinc binding site 2 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:19.0 occ:1.00 SG A:CYS1021 2.2 18.7 1.0 SG A:CYS1017 2.3 17.3 1.0 SG A:CYS987 2.3 31.1 1.0 SG A:CYS974 2.4 19.8 1.0 CB A:CYS1017 3.2 18.4 1.0 CB A:CYS1021 3.2 17.1 1.0 CB A:CYS987 3.4 39.9 1.0 CB A:CYS974 3.4 20.7 1.0 N A:CYS974 3.4 21.4 1.0 CA A:CYS1017 3.6 17.5 1.0 ZN A:ZN1501 3.8 18.6 1.0 ZN A:ZN1503 3.8 20.6 1.0 CA A:CYS974 4.0 22.7 1.0 SG A:CYS1023 4.2 15.9 1.0 O A:HOH1651 4.2 29.1 1.0 SG A:CYS985 4.4 24.8 1.0 N A:CYS1017 4.4 15.3 1.0 CA A:CYS1021 4.4 17.6 1.0 C A:HIS973 4.5 25.4 1.0 N A:ASN1018 4.6 17.2 1.0 SG A:CYS980 4.6 19.8 1.0 CA A:CYS987 4.7 47.6 1.0 N A:CYS987 4.7 41.9 1.0 C A:CYS1017 4.7 20.2 1.0 CA A:HIS973 4.7 24.7 1.0 C A:CYS974 4.8 22.9 1.0 ND2 A:ASN1029 4.8 19.4 1.0 O A:CYS974 4.8 21.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:20.6 occ:1.00 SG A:CYS974 2.3 19.8 1.0 SG A:CYS985 2.3 24.8 1.0 SG A:CYS980 2.3 19.8 1.0 SG A:CYS976 2.3 19.1 1.0 CB A:CYS974 3.1 20.7 1.0 CB A:CYS976 3.2 19.7 1.0 CB A:CYS980 3.2 21.0 1.0 CB A:CYS985 3.3 28.2 1.0 ZN A:ZN1502 3.8 19.0 1.0 CA A:CYS985 3.8 34.2 1.0 ZN A:ZN1501 3.9 18.6 1.0 CA A:CYS980 3.9 22.4 1.0 SG A:CYS1017 4.1 17.3 1.0 N A:CYS976 4.4 21.3 1.0 CA A:CYS976 4.4 19.6 1.0 CA A:CYS974 4.6 22.7 1.0 C A:CYS985 4.7 35.7 1.0 O A:HOH1695 4.7 23.3 1.0 N A:CYS980 4.8 23.0 1.0 N A:LEU986 4.8 37.4 1.0 SG A:CYS1023 4.8 15.9 1.0 CB A:CYS1023 4.8 15.6 1.0 SG A:CYS987 5.0 31.1 1.0 N A:CYS985 5.0 36.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:20.2 occ:1.00 SG A:CYS1168 2.2 18.8 1.0 SG A:CYS1170 2.3 20.9 1.0 SG A:CYS1115 2.4 18.0 1.0 SG A:CYS1175 2.4 19.4 1.0 CB A:CYS1170 3.1 20.1 1.0 CB A:CYS1175 3.2 22.8 1.0 CB A:CYS1168 3.3 18.4 1.0 CB A:CYS1115 3.4 17.7 1.0 CA A:CYS1175 3.8 25.4 1.0 O A:HOH1669 4.0 17.9 1.0 N A:CYS1115 4.0 16.8 1.0 N A:CYS1170 4.0 23.0 1.0 CA A:CYS1170 4.1 22.2 1.0 NE2 A:HIS1113 4.2 17.1 1.0 N A:LYS1176 4.3 25.5 1.0 CA A:CYS1115 4.3 17.0 1.0 CD2 A:HIS1113 4.4 16.8 1.0 C A:CYS1175 4.4 25.4 1.0 N A:HIS1177 4.6 23.6 1.0 CA A:CYS1168 4.6 20.8 1.0 C A:CYS1168 4.8 21.9 1.0 C A:CYS1170 4.8 24.4 1.0 N A:GLY1171 4.8 25.0 1.0 CB A:HIS1177 4.9 24.4 1.0 CB A:SER1172 4.9 32.8 1.0 O A:HOH1715 5.0 31.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1501 b:17.1 occ:1.00 SG B:CYS1017 2.3 16.1 1.0 SG B:CYS980 2.3 16.9 1.0 SG B:CYS1023 2.3 15.6 1.0 SG B:CYS1027 2.3 18.7 1.0 CB B:CYS1027 3.1 19.8 1.0 CB B:CYS1023 3.2 17.3 1.0 CB B:CYS1017 3.2 15.2 1.0 CB B:CYS980 3.3 18.0 1.0 ZN B:ZN1503 3.8 18.1 1.0 ZN B:ZN1502 3.9 19.1 1.0 SG B:CYS974 4.1 18.3 1.0 NE B:ARG1030 4.3 25.4 1.0 NH2 B:ARG1030 4.6 23.9 1.0 CB B:ASN1029 4.6 14.9 1.0 CA B:CYS1027 4.6 19.4 1.0 CA B:CYS1023 4.6 17.7 1.0 CA B:CYS1017 4.7 16.9 1.0 CA B:CYS980 4.7 19.7 1.0 O B:TRP1024 4.8 20.7 1.0 CZ B:ARG1030 4.9 21.7 1.0 CB B:CYS1021 4.9 17.0 1.0 N B:ASN1029 4.9 15.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:19.1 occ:1.00 SG B:CYS1021 2.3 19.0 1.0 SG B:CYS987 2.3 19.9 1.0 SG B:CYS1017 2.4 16.1 1.0 SG B:CYS974 2.5 18.3 1.0 CB B:CYS1017 3.2 15.2 1.0 CB B:CYS974 3.2 20.3 1.0 CB B:CYS1021 3.3 17.0 1.0 CB B:CYS987 3.4 20.4 1.0 CA B:CYS1017 3.5 16.9 1.0 N B:CYS974 3.5 20.5 1.0 ZN B:ZN1503 3.8 18.1 1.0 ZN B:ZN1501 3.9 17.1 1.0 CA B:CYS974 4.0 21.1 1.0 SG B:CYS1023 4.2 15.6 1.0 SG B:CYS985 4.3 20.9 1.0 N B:CYS1017 4.4 14.4 1.0 C B:HIS973 4.5 21.2 1.0 CA B:CYS1021 4.5 16.7 1.0 N B:ASN1018 4.6 18.7 1.0 C B:CYS1017 4.6 19.2 1.0 SG B:CYS980 4.7 16.9 1.0 CA B:CYS987 4.7 22.1 1.0 N B:CYS987 4.7 23.7 1.0 CA B:HIS973 4.7 22.2 1.0 C B:CYS974 4.8 22.1 1.0 O B:CYS974 4.9 20.0 1.0 O B:HOH1673 5.0 21.5 1.0 ND2 B:ASN1029 5.0 16.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1503 b:18.1 occ:1.00 SG B:CYS985 2.3 20.9 1.0 SG B:CYS980 2.3 16.9 1.0 SG B:CYS976 2.3 18.6 1.0 SG B:CYS974 2.3 18.3 1.0 CB B:CYS974 3.2 20.3 1.0 CB B:CYS980 3.3 18.0 1.0 CB B:CYS976 3.3 19.4 1.0 CB B:CYS985 3.3 21.6 1.0 ZN B:ZN1501 3.8 17.1 1.0 ZN B:ZN1502 3.8 19.1 1.0 CA B:CYS985 3.9 24.8 1.0 CA B:CYS980 3.9 19.7 1.0 SG B:CYS1017 4.1 16.1 1.0 N B:CYS976 4.4 18.4 1.0 CA B:CYS976 4.4 19.7 1.0 CA B:CYS974 4.6 21.1 1.0 C B:CYS985 4.6 22.9 1.0 O B:HOH1638 4.7 18.1 1.0 N B:LEU986 4.7 25.6 1.0 N B:CYS980 4.8 19.5 1.0 SG B:CYS1023 4.8 15.6 1.0 CB B:CYS1023 4.8 17.3 1.0 C B:CYS980 5.0 22.0 1.0 O B:HOH1730 5.0 22.6 1.0 C B:CYS974 5.0 22.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of EHMT2 Set Domain in Complex with Compound 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1504 b:19.6 occ:1.00 SG B:CYS1168 2.3 17.5 1.0 SG B:CYS1170 2.3 20.4 1.0 SG B:CYS1115 2.3 22.9 1.0 SG B:CYS1175 2.4 23.7 1.0 CB B:CYS1170 3.2 21.7 1.0 CB B:CYS1175 3.2 23.5 1.0 CB B:CYS1168 3.3 18.4 1.0 CB B:CYS1115 3.4 20.9 1.0 CA B:CYS1175 3.7 25.0 1.0 N B:CYS1170 4.0 21.1 1.0 O B:HOH1708 4.0 17.8 1.0 N B:CYS1115 4.1 18.7 1.0 CA B:CYS1170 4.1 22.6 1.0 N B:LYS1176 4.3 23.4 1.0 CA B:CYS1115 4.4 20.6 1.0 N B:HIS1177 4.4 21.4 1.0 C B:CYS1175 4.4 25.2 1.0 CD2 B:HIS1113 4.6 16.1 1.0 NE2 B:HIS1113 4.6 14.6 1.0 CA B:CYS1168 4.6 18.9 1.0 C B:CYS1168 4.7 21.0 1.0 N B:GLY1171 4.7 27.3 1.0 C B:CYS1170 4.9 26.3 1.0 CB B:HIS1177 4.9 20.3 1.0 O B:CYS1168 4.9 21.4 1.0 N B:SER1178 4.9 18.8 1.0 N B:CYS1175 5.0 26.0 1.0

K.Katayama, K.Ishii, H.Terashima, E.Tsuda, M.Suzuki, K.Yotsumoto, K.Hiramoto, I.Yasumatsu, M.Torihata, T.Ishiyama, T.Muto, T.Katagiri. Discovery of DS79932728: A Potent, Orally Available G9A/Glp Inhibitor For Treating Beta-Thalassemia and Sickle Cell Disease. Acs Med.Chem.Lett. V. 12 121 2021.
ISSN: ISSN 1948-5875
PubMed: 33488973
DOI: 10.1021/ACSMEDCHEMLETT.0C00572