Zinc in PDB 7t7m: Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1):
2.1.1.43;

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1), PDB code: 7t7m was solved by K.-S.Park, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.69 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.49, 128.73, 132.5, 90, 90, 90
R / Rfree (%)	19.9 / 24.4

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) (pdb code 7t7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1), PDB code: 7t7m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1301 b:37.3 occ:1.00 SG A:CYS1075 2.3 38.9 1.0 SG A:CYS1109 2.4 41.6 1.0 SG A:CYS1105 2.4 28.2 1.0 SG A:CYS1062 2.5 39.0 1.0 CB A:CYS1062 3.1 39.6 1.0 CB A:CYS1105 3.2 29.7 1.0 CB A:CYS1109 3.3 37.5 1.0 CB A:CYS1075 3.5 34.0 1.0 N A:CYS1062 3.5 39.9 1.0 CA A:CYS1105 3.7 31.1 1.0 ZN A:ZN1303 3.8 38.4 1.0 CA A:CYS1062 3.8 39.9 1.0 ZN A:ZN1302 3.9 33.5 1.0 SG A:CYS1111 3.9 33.2 1.0 SG A:CYS1073 4.3 40.4 1.0 C A:TYR1061 4.6 42.5 1.0 N A:CYS1075 4.6 42.5 1.0 N A:CYS1105 4.6 27.8 1.0 C A:CYS1062 4.6 42.3 1.0 CA A:CYS1075 4.6 37.1 1.0 CA A:CYS1109 4.7 35.7 1.0 N A:ASN1106 4.7 31.6 1.0 SG A:CYS1068 4.7 31.0 1.0 O A:CYS1062 4.7 41.2 1.0 C A:CYS1105 4.8 35.0 1.0 CA A:TYR1061 4.8 33.1 1.0

Zinc binding site 2 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:33.5 occ:1.00 SG A:CYS1115 2.2 29.4 1.0 SG A:CYS1111 2.2 33.2 1.0 SG A:CYS1105 2.3 28.2 1.0 SG A:CYS1068 2.4 31.0 1.0 CB A:CYS1111 2.9 26.1 1.0 CB A:CYS1115 3.2 32.4 1.0 CB A:CYS1105 3.2 29.7 1.0 CB A:CYS1068 3.4 28.6 1.0 ZN A:ZN1303 3.7 38.4 1.0 ZN A:ZN1301 3.9 37.3 1.0 SG A:CYS1062 4.0 39.0 1.0 NE A:ARG1118 4.3 31.4 1.0 CA A:CYS1111 4.4 26.5 1.0 CB A:ASN1117 4.5 26.1 1.0 CA A:CYS1115 4.7 26.9 1.0 CA A:CYS1105 4.7 31.1 1.0 NH2 A:ARG1118 4.7 33.7 1.0 CA A:CYS1068 4.8 40.0 1.0 O A:TRP1112 4.9 41.0 1.0 N A:CYS1111 4.9 32.1 1.0 N A:ASN1117 4.9 31.4 1.0 CZ A:ARG1118 5.0 31.5 1.0

Zinc binding site 3 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:38.4 occ:1.00 SG A:CYS1068 2.2 31.0 1.0 SG A:CYS1062 2.3 39.0 1.0 SG A:CYS1064 2.4 45.4 1.0 SG A:CYS1073 2.4 40.4 1.0 CB A:CYS1062 3.1 39.6 1.0 CB A:CYS1073 3.1 35.9 1.0 CB A:CYS1068 3.2 28.6 1.0 CB A:CYS1064 3.6 38.3 1.0 ZN A:ZN1302 3.7 33.5 1.0 ZN A:ZN1301 3.8 37.3 1.0 CA A:CYS1073 3.8 28.7 1.0 CA A:CYS1068 3.9 40.0 1.0 SG A:CYS1105 4.0 28.2 1.0 N A:CYS1064 4.5 31.9 1.0 CA A:CYS1062 4.6 39.9 1.0 C A:CYS1073 4.6 37.6 1.0 SG A:CYS1111 4.7 33.2 1.0 CA A:CYS1064 4.7 37.4 1.0 N A:MET1074 4.7 42.5 1.0 N A:CYS1068 4.8 41.7 1.0 CB A:CYS1111 4.9 26.1 1.0

Zinc binding site 4 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1304 b:42.8 occ:1.00 SG A:CYS1258 2.3 42.3 1.0 SG A:CYS1256 2.3 33.5 1.0 SG A:CYS1263 2.5 43.4 1.0 SG A:CYS1203 2.5 40.5 1.0 CB A:CYS1203 3.4 38.2 1.0 CB A:CYS1263 3.4 39.6 1.0 CB A:CYS1258 3.4 41.5 1.0 CB A:CYS1256 3.5 49.4 1.0 N A:CYS1203 3.8 36.3 1.0 CA A:CYS1263 3.8 34.2 1.0 CA A:CYS1203 4.2 35.7 1.0 NE2 A:HIS1201 4.2 32.4 1.0 CD2 A:HIS1201 4.2 34.0 1.0 N A:CYS1258 4.3 37.8 1.0 N A:ARG1264 4.4 39.0 1.0 CA A:CYS1258 4.5 31.8 1.0 C A:CYS1263 4.5 38.8 1.0 N A:HIS1265 4.8 43.2 1.0 C A:HIS1202 4.8 39.9 1.0 CA A:CYS1256 4.8 51.4 1.0 C A:CYS1256 4.9 45.2 1.0

Zinc binding site 5 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:28.9 occ:1.00 SG B:CYS1075 2.3 25.0 1.0 SG B:CYS1109 2.3 37.5 1.0 SG B:CYS1105 2.4 27.0 1.0 SG B:CYS1062 2.5 36.4 1.0 CB B:CYS1105 3.1 33.3 1.0 CB B:CYS1062 3.1 31.8 1.0 CB B:CYS1109 3.3 30.5 1.0 N B:CYS1062 3.4 36.3 1.0 CB B:CYS1075 3.5 33.3 1.0 CA B:CYS1105 3.6 26.7 1.0 ZN B:ZN1302 3.8 30.8 1.0 CA B:CYS1062 3.8 36.5 1.0 ZN B:ZN1303 3.9 34.2 1.0 SG B:CYS1111 4.0 32.0 1.0 SG B:CYS1073 4.4 33.5 1.0 N B:CYS1105 4.5 26.1 1.0 C B:TYR1061 4.5 44.7 1.0 N B:ASN1106 4.5 24.6 1.0 CA B:CYS1109 4.6 34.7 1.0 C B:CYS1105 4.6 28.6 1.0 C B:CYS1062 4.6 37.7 1.0 O B:CYS1062 4.7 34.7 1.0 SG B:CYS1068 4.7 32.2 1.0 CA B:CYS1075 4.8 34.5 1.0 N B:CYS1075 4.8 35.1 1.0 CA B:TYR1061 4.8 30.7 1.0

Zinc binding site 6 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:30.8 occ:1.00 SG B:CYS1111 2.1 32.0 1.0 SG B:CYS1105 2.3 27.0 1.0 SG B:CYS1115 2.4 35.8 1.0 SG B:CYS1068 2.5 32.2 1.0 CB B:CYS1111 2.8 25.5 1.0 CB B:CYS1105 3.2 33.3 1.0 CB B:CYS1115 3.4 22.8 1.0 CB B:CYS1068 3.4 34.0 1.0 ZN B:ZN1303 3.7 34.2 1.0 ZN B:ZN1301 3.8 28.9 1.0 SG B:CYS1062 3.8 36.4 1.0 CA B:CYS1111 4.3 23.4 1.0 CB B:ASN1117 4.5 19.1 1.0 NE B:ARG1118 4.7 32.1 1.0 NH2 B:ARG1118 4.7 32.0 1.0 CA B:CYS1105 4.7 26.7 1.0 CA B:CYS1068 4.8 40.2 1.0 CA B:CYS1115 4.8 26.5 1.0 N B:CYS1111 4.9 26.6 1.0 O B:TRP1112 4.9 36.0 1.0 CB B:CYS1109 5.0 30.5 1.0 C B:CYS1111 5.0 32.1 1.0 SG B:CYS1073 5.0 33.5 1.0

Zinc binding site 7 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:34.2 occ:1.00 SG B:CYS1073 2.2 33.5 1.0 SG B:CYS1068 2.2 32.2 1.0 SG B:CYS1062 2.4 36.4 1.0 SG B:CYS1064 2.5 35.4 1.0 CB B:CYS1062 3.0 31.8 1.0 CB B:CYS1073 3.1 33.7 1.0 CB B:CYS1068 3.3 34.0 1.0 CB B:CYS1064 3.6 34.6 1.0 ZN B:ZN1302 3.7 30.8 1.0 CA B:CYS1073 3.8 36.6 1.0 ZN B:ZN1301 3.9 28.9 1.0 SG B:CYS1105 4.0 27.0 1.0 CA B:CYS1068 4.0 40.2 1.0 CA B:CYS1062 4.5 36.5 1.0 N B:CYS1064 4.5 31.6 1.0 C B:CYS1073 4.6 40.3 1.0 CA B:CYS1064 4.7 31.8 1.0 N B:MET1074 4.8 40.0 1.0 SG B:CYS1111 4.9 32.0 1.0 CB B:CYS1111 4.9 25.5 1.0 SG B:CYS1075 4.9 25.0 1.0 N B:CYS1068 4.9 38.5 1.0 O B:HOH3101 4.9 34.5 1.0 C B:CYS1062 5.0 37.7 1.0

Zinc binding site 8 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1304 b:66.1 occ:1.00 SG B:CYS1258 2.2 76.4 1.0 SG B:CYS1256 2.4 62.5 1.0 SG B:CYS1263 2.5 83.8 1.0 SG B:CYS1203 2.7 68.5 1.0 CB B:CYS1203 3.3 78.0 1.0 CB B:CYS1263 3.6 79.1 1.0 CB B:CYS1256 3.6 82.0 1.0 CB B:CYS1258 3.6 58.0 1.0 N B:CYS1203 3.7 61.7 1.0 CA B:CYS1263 3.9 77.5 1.0 CA B:CYS1203 4.2 68.8 1.0 CD2 B:HIS1201 4.3 48.7 1.0 N B:CYS1258 4.3 89.7 1.0 NE2 B:HIS1201 4.4 60.7 1.0 OG B:SER1260 4.5 76.0 1.0 N B:ARG1264 4.6 78.3 1.0 CA B:CYS1258 4.6 80.9 1.0 C B:CYS1263 4.7 79.9 1.0 C B:HIS1202 4.7 62.0 1.0 N B:HIS1265 4.8 80.6 1.0 CA B:CYS1256 4.9 77.4 1.0 C B:CYS1256 4.9 74.5 1.0 CA B:HIS1202 4.9 59.5 1.0

Zinc binding site 9 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1301 b:38.6 occ:1.00 SG C:CYS1075 2.2 25.7 1.0 SG C:CYS1109 2.2 35.3 1.0 SG C:CYS1105 2.3 29.2 1.0 SG C:CYS1062 2.4 28.7 1.0 CB C:CYS1105 2.9 28.1 1.0 CB C:CYS1062 3.2 36.4 1.0 CB C:CYS1109 3.3 34.1 1.0 CB C:CYS1075 3.5 27.5 1.0 N C:CYS1062 3.5 38.0 1.0 CA C:CYS1105 3.5 29.2 1.0 ZN C:ZN1302 3.8 33.1 1.0 SG C:CYS1111 3.8 29.7 1.0 ZN C:ZN1303 3.8 37.6 1.0 CA C:CYS1062 3.9 36.0 1.0 N C:ASN1106 4.4 28.2 1.0 N C:CYS1105 4.5 26.8 1.0 C C:CYS1105 4.5 31.6 1.0 C C:TYR1061 4.6 39.9 1.0 SG C:CYS1073 4.6 33.0 1.0 CA C:CYS1109 4.6 37.1 1.0 SG C:CYS1068 4.7 38.5 1.0 CA C:CYS1075 4.7 24.6 1.0 C C:CYS1062 4.7 38.6 1.0 N C:CYS1075 4.8 37.5 1.0 CA C:TYR1061 4.8 39.3 1.0 O C:CYS1062 4.8 35.0 1.0

Zinc binding site 10 out of 16 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Covalent Inhibitor (Compound 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1302 b:33.1 occ:1.00 SG C:CYS1111 2.1 29.7 1.0 SG C:CYS1115 2.4 39.5 1.0 SG C:CYS1068 2.4 38.5 1.0 SG C:CYS1105 2.5 29.2 1.0 CB C:CYS1111 2.9 37.1 1.0 CB C:CYS1115 3.2 30.2 1.0 CB C:CYS1105 3.3 28.1 1.0 CB C:CYS1068 3.3 27.9 1.0 ZN C:ZN1303 3.8 37.6 1.0 ZN C:ZN1301 3.8 38.6 1.0 SG C:CYS1062 3.9 28.7 1.0 CA C:CYS1111 4.3 33.8 1.0 NE C:ARG1118 4.4 30.8 1.0 CB C:ASN1117 4.6 39.9 1.0 CA C:CYS1115 4.7 31.6 1.0 CA C:CYS1068 4.7 38.0 1.0 NH2 C:ARG1118 4.7 38.4 1.0 CA C:CYS1105 4.8 29.2 1.0 N C:CYS1111 4.9 30.2 1.0 O C:TRP1112 5.0 33.4 1.0 N C:CYS1068 5.0 35.4 1.0 CZ C:ARG1118 5.0 33.7 1.0

K.S.Park, Y.Xiong, H.Yim, J.Velez, N.Babault, P.Kumar, J.Liu, J.Jin. Discovery of the First-in-Class G9A/Glp Covalent Inhibitors. J.Med.Chem. V. 65 10506 2022.
ISSN: ISSN 0022-2623
PubMed: 35763668
DOI: 10.1021/ACS.JMEDCHEM.2C00652