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Zinc in PDB 5vsd: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13

Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13, PDB code: 5vsd was solved by N.Babault, Y.Xiong, J.Liu, J.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.864, 96.594, 102.478, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 (pdb code 5vsd). 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 Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13, PDB code: 5vsd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vsd

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Zinc binding site 1 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:22.3
occ:1.00
 SG A:CYS1109 2.3 19.2 1.0
SG A:CYS1075 2.4 23.4 1.0
SG A:CYS1105 2.4 19.8 1.0
SG A:CYS1062 2.4 19.0 1.0
CB A:CYS1105 3.2 13.4 1.0
CB A:CYS1109 3.2 15.1 1.0
CB A:CYS1062 3.2 19.6 1.0
CB A:CYS1075 3.4 18.9 1.0
N A:CYS1062 3.6 26.0 1.0
CA A:CYS1105 3.6 26.5 1.0
ZN A:ZN3003 3.8 22.1 1.0
ZN A:ZN3004 3.8 21.6 1.0
CA A:CYS1062 4.0 26.8 1.0
SG A:CYS1111 4.0 19.3 1.0
SG A:CYS1073 4.4 20.9 1.0
C A:TYR1061 4.5 19.6 1.0
N A:CYS1105 4.6 22.8 1.0
CA A:CYS1109 4.6 15.8 1.0
N A:ASN1106 4.6 21.4 1.0
CA A:CYS1075 4.6 20.4 1.0
SG A:CYS1068 4.6 22.2 1.0
N A:CYS1075 4.7 20.0 1.0
C A:CYS1105 4.7 24.7 1.0
CA A:TYR1061 4.8 21.7 1.0
C A:CYS1062 4.8 26.3 1.0
O A:CYS1062 4.9 19.7 1.0
O A:HOH3262 4.9 24.3 1.0
ND2 A:ASN1117 4.9 17.2 1.0

Zinc binding site 2 out of 8 in 5vsd

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Zinc binding site 2 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:22.1
occ:1.00
 SG A:CYS1111 2.3 19.3 1.0
SG A:CYS1115 2.3 19.5 1.0
SG A:CYS1105 2.3 19.8 1.0
SG A:CYS1068 2.4 22.2 1.0
CB A:CYS1111 3.1 19.1 1.0
CB A:CYS1105 3.2 13.4 1.0
CB A:CYS1115 3.2 24.1 1.0
CB A:CYS1068 3.4 22.7 1.0
ZN A:ZN3004 3.7 21.6 1.0
ZN A:ZN3002 3.8 22.3 1.0
SG A:CYS1062 3.9 19.0 1.0
NH2 A:ARG1118 4.2 21.5 1.0
NE A:ARG1118 4.3 25.7 1.0
CA A:CYS1111 4.5 24.8 1.0
CB A:ASN1117 4.6 19.6 1.0
CZ A:ARG1118 4.7 26.4 1.0
CA A:CYS1105 4.7 26.5 1.0
CA A:CYS1115 4.7 23.1 1.0
O A:TRP1112 4.8 23.1 1.0
CA A:CYS1068 4.8 20.2 1.0
CB A:CYS1109 4.9 15.1 1.0
N A:ASN1117 5.0 23.3 1.0

Zinc binding site 3 out of 8 in 5vsd

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Zinc binding site 3 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:21.6
occ:1.00
 SG A:CYS1068 2.2 22.2 1.0
SG A:CYS1062 2.4 19.0 1.0
SG A:CYS1064 2.4 21.9 1.0
SG A:CYS1073 2.4 20.9 1.0
CB A:CYS1062 3.1 19.6 1.0
CB A:CYS1064 3.2 20.4 1.0
CB A:CYS1073 3.2 21.3 1.0
CB A:CYS1068 3.2 22.7 1.0
ZN A:ZN3003 3.7 22.1 1.0
ZN A:ZN3002 3.8 22.3 1.0
CA A:CYS1073 3.9 21.2 1.0
CA A:CYS1068 3.9 20.2 1.0
SG A:CYS1105 4.0 19.8 1.0
N A:CYS1064 4.4 20.6 1.0
CA A:CYS1064 4.4 20.8 1.0
O A:HOH3216 4.4 24.2 1.0
O A:HOH3213 4.5 17.6 1.0
N A:MET1074 4.5 25.7 1.0
C A:CYS1073 4.6 27.2 1.0
CA A:CYS1062 4.6 26.8 1.0
SG A:CYS1111 4.7 19.3 1.0
N A:CYS1068 4.8 20.4 1.0
CB A:CYS1111 4.8 19.1 1.0
O A:HOH3289 4.8 32.1 1.0
C A:CYS1062 5.0 26.3 1.0

Zinc binding site 4 out of 8 in 5vsd

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Zinc binding site 4 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:22.8
occ:1.00
 SG A:CYS1203 2.3 23.2 1.0
SG A:CYS1258 2.3 24.1 1.0
SG A:CYS1263 2.4 22.0 1.0
SG A:CYS1256 2.4 25.5 1.0
CB A:CYS1263 3.2 24.7 1.0
CB A:CYS1256 3.4 22.2 1.0
CB A:CYS1203 3.4 29.9 1.0
CB A:CYS1258 3.4 19.7 1.0
CA A:CYS1263 3.8 31.6 1.0
O A:HOH3236 4.1 20.8 1.0
N A:CYS1203 4.1 22.1 1.0
N A:ARG1264 4.1 24.3 1.0
N A:CYS1258 4.2 21.3 1.0
NE2 A:HIS1201 4.3 19.2 1.0
CA A:CYS1258 4.4 20.5 1.0
CA A:CYS1203 4.4 22.0 1.0
C A:CYS1263 4.4 22.1 1.0
CD2 A:HIS1201 4.5 21.6 1.0
N A:HIS1265 4.5 27.3 1.0
CA A:CYS1256 4.7 26.8 1.0
N A:GLY1259 4.8 28.9 1.0
C A:CYS1256 4.8 33.0 1.0
CB A:SER1260 4.9 20.2 1.0
C A:CYS1258 4.9 30.8 1.0
N A:SER1260 5.0 25.0 1.0

Zinc binding site 5 out of 8 in 5vsd

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Zinc binding site 5 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:23.2
occ:1.00
 SG B:CYS1075 2.4 24.5 1.0
SG B:CYS1062 2.4 18.9 1.0
SG B:CYS1109 2.4 23.0 1.0
SG B:CYS1105 2.4 22.3 1.0
CB B:CYS1105 3.1 18.5 1.0
CB B:CYS1062 3.2 23.7 1.0
CB B:CYS1109 3.2 24.8 1.0
CB B:CYS1075 3.4 29.6 1.0
CA B:CYS1105 3.6 24.2 1.0
N B:CYS1062 3.6 19.8 1.0
ZN B:ZN3003 3.7 21.5 1.0
ZN B:ZN3004 3.8 23.3 1.0
CA B:CYS1062 4.0 22.2 1.0
SG B:CYS1111 4.2 20.8 1.0
SG B:CYS1073 4.2 24.4 1.0
N B:ASN1106 4.5 21.1 1.0
N B:CYS1105 4.5 16.4 1.0
CA B:CYS1109 4.6 20.8 1.0
C B:TYR1061 4.6 29.6 1.0
C B:CYS1105 4.6 22.2 1.0
CA B:CYS1075 4.6 20.8 1.0
N B:CYS1075 4.7 24.6 1.0
SG B:CYS1068 4.7 23.3 1.0
C B:CYS1062 4.8 24.2 1.0
CA B:TYR1061 4.8 23.2 1.0
O B:HOH3260 4.8 29.5 1.0
O B:CYS1062 4.9 26.0 1.0

Zinc binding site 6 out of 8 in 5vsd

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Zinc binding site 6 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:21.5
occ:1.00
 SG B:CYS1105 2.3 22.3 1.0
SG B:CYS1111 2.3 20.8 1.0
SG B:CYS1068 2.3 23.3 1.0
SG B:CYS1115 2.4 21.5 1.0
CB B:CYS1105 3.1 18.5 1.0
CB B:CYS1111 3.2 23.0 1.0
CB B:CYS1068 3.3 18.3 1.0
CB B:CYS1115 3.3 20.1 1.0
ZN B:ZN3004 3.7 23.3 1.0
ZN B:ZN3002 3.7 23.2 1.0
SG B:CYS1062 3.9 18.9 1.0
NH2 B:ARG1118 4.3 25.7 1.0
NE B:ARG1118 4.4 25.2 1.0
CB B:ASN1117 4.5 21.4 1.0
CA B:CYS1105 4.6 24.2 1.0
CA B:CYS1111 4.6 21.3 1.0
CA B:CYS1068 4.7 25.8 1.0
CZ B:ARG1118 4.7 17.7 1.0
CA B:CYS1115 4.8 21.4 1.0
O B:TRP1112 4.9 21.9 1.0
SG B:CYS1073 4.9 24.4 1.0
CB B:CYS1109 4.9 24.8 1.0
N B:ASN1117 4.9 19.5 1.0

Zinc binding site 7 out of 8 in 5vsd

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Zinc binding site 7 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:23.3
occ:1.00
 SG B:CYS1073 2.3 24.4 1.0
SG B:CYS1068 2.3 23.3 1.0
SG B:CYS1064 2.4 24.7 1.0
SG B:CYS1062 2.4 18.9 1.0
CB B:CYS1062 3.1 23.7 1.0
CB B:CYS1073 3.1 24.4 1.0
CB B:CYS1068 3.2 18.3 1.0
CB B:CYS1064 3.2 27.8 1.0
ZN B:ZN3003 3.7 21.5 1.0
ZN B:ZN3002 3.8 23.2 1.0
CA B:CYS1068 3.8 25.8 1.0
CA B:CYS1073 3.9 24.3 1.0
SG B:CYS1105 4.0 22.3 1.0
N B:CYS1064 4.4 30.2 1.0
CA B:CYS1064 4.4 31.1 1.0
O B:HOH3157 4.5 31.2 1.0
CA B:CYS1062 4.6 22.2 1.0
SG B:CYS1111 4.7 20.8 1.0
N B:CYS1068 4.7 27.5 1.0
C B:CYS1073 4.7 29.6 1.0
O B:HOH3133 4.7 23.1 1.0
N B:MET1074 4.9 22.5 1.0
C B:CYS1068 4.9 30.2 1.0
CB B:CYS1111 4.9 23.0 1.0
O B:CYS1068 5.0 33.4 1.0
C B:CYS1062 5.0 24.2 1.0

Zinc binding site 8 out of 8 in 5vsd

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Zinc binding site 8 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


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 Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:30.3
occ:1.00
 SG B:CYS1256 2.3 27.3 1.0
SG B:CYS1258 2.3 28.4 1.0
SG B:CYS1263 2.4 32.6 1.0
SG B:CYS1203 2.5 29.7 1.0
CB B:CYS1263 3.2 36.0 1.0
CB B:CYS1258 3.3 26.0 1.0
CB B:CYS1256 3.3 30.4 1.0
CB B:CYS1203 3.5 30.9 1.0
CA B:CYS1263 3.8 32.2 1.0
O B:HOH3190 4.0 32.7 1.0
N B:CYS1258 4.0 29.9 1.0
N B:CYS1203 4.1 26.9 1.0
CA B:CYS1258 4.2 30.4 1.0
N B:ARG1264 4.2 39.0 1.0
NE2 B:HIS1201 4.3 23.7 1.0
CA B:CYS1203 4.4 23.7 1.0
C B:CYS1263 4.4 36.9 1.0
CD2 B:HIS1201 4.5 23.7 1.0
N B:HIS1265 4.6 38.3 1.0
CA B:CYS1256 4.6 37.9 1.0
C B:CYS1256 4.7 33.2 1.0
N B:GLY1259 4.7 30.3 1.0
C B:CYS1258 4.8 36.2 1.0
O B:CYS1256 5.0 34.8 1.0

Reference:

Y.Xiong, F.Li, N.Babault, H.Wu, A.Dong, H.Zeng, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Structure-Activity Relationship Studies of G9A-Like Protein (Glp) Inhibitors. Bioorg. Med. Chem. V. 25 4414 2017.
ISSN: ESSN 1464-3391
PubMed: 28662962
DOI: 10.1016/J.BMC.2017.06.021
Page generated: Mon Oct 28 13:21:03 2024

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