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Zinc in PDB 5tuz: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124

Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124, PDB code: 5tuz 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) 59.02 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.940, 95.780, 102.360, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 (pdb code 5tuz). 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 MS0124, PDB code: 5tuz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5tuz

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Zinc binding site 1 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:16.1
occ:1.00
 SG A:CYS1105 2.3 15.1 1.0
SG A:CYS1109 2.3 15.5 1.0
SG A:CYS1075 2.3 15.8 1.0
SG A:CYS1062 2.4 13.4 1.0
CB A:CYS1105 3.2 14.2 1.0
CB A:CYS1062 3.2 18.4 1.0
CB A:CYS1109 3.3 11.8 1.0
CB A:CYS1075 3.4 15.2 1.0
CA A:CYS1105 3.6 12.1 1.0
N A:CYS1062 3.6 13.5 1.0
ZN A:ZN3003 3.8 14.6 1.0
ZN A:ZN3004 3.8 15.2 1.0
CA A:CYS1062 4.0 17.0 1.0
SG A:CYS1111 4.2 13.6 1.0
SG A:CYS1073 4.3 14.2 1.0
N A:CYS1105 4.5 11.7 1.0
C A:TYR1061 4.5 18.0 1.0
N A:ASN1106 4.6 11.1 1.0
CA A:CYS1109 4.6 17.1 1.0
C A:CYS1105 4.6 14.1 1.0
CA A:CYS1075 4.7 14.9 1.0
N A:CYS1075 4.7 16.2 1.0
SG A:CYS1068 4.7 14.1 1.0
CA A:TYR1061 4.8 16.1 1.0
C A:CYS1062 4.8 18.1 1.0
O A:CYS1062 4.9 13.6 1.0
O A:HOH3222 4.9 18.1 1.0
ND2 A:ASN1117 5.0 13.6 1.0

Zinc binding site 2 out of 8 in 5tuz

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Zinc binding site 2 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:14.6
occ:1.00
 SG A:CYS1111 2.3 13.6 1.0
SG A:CYS1115 2.3 14.9 1.0
SG A:CYS1105 2.3 15.1 1.0
SG A:CYS1068 2.4 14.1 1.0
CB A:CYS1105 3.1 14.2 1.0
CB A:CYS1111 3.2 11.4 1.0
CB A:CYS1115 3.2 14.2 1.0
CB A:CYS1068 3.3 15.6 1.0
ZN A:ZN3004 3.7 15.2 1.0
ZN A:ZN3002 3.8 16.1 1.0
SG A:CYS1062 4.0 13.4 1.0
NH2 A:ARG1118 4.4 18.4 1.0
NE A:ARG1118 4.4 15.8 1.0
CB A:ASN1117 4.5 15.0 1.0
CA A:CYS1105 4.6 12.1 1.0
CA A:CYS1111 4.6 15.1 1.0
CA A:CYS1115 4.7 16.4 1.0
CA A:CYS1068 4.7 15.3 1.0
CZ A:ARG1118 4.8 15.1 1.0
O A:TRP1112 4.8 11.4 1.0
N A:ASN1117 4.9 14.4 1.0
CB A:CYS1109 5.0 11.8 1.0

Zinc binding site 3 out of 8 in 5tuz

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Zinc binding site 3 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:15.2
occ:1.00
 SG A:CYS1068 2.3 14.1 1.0
SG A:CYS1073 2.3 14.2 1.0
SG A:CYS1062 2.3 13.4 1.0
SG A:CYS1064 2.4 16.3 1.0
CB A:CYS1062 3.2 18.4 1.0
CB A:CYS1064 3.2 15.7 1.0
CB A:CYS1068 3.3 15.6 1.0
CB A:CYS1073 3.3 21.2 1.0
ZN A:ZN3003 3.7 14.6 1.0
ZN A:ZN3002 3.8 16.1 1.0
CA A:CYS1073 3.9 15.3 1.0
CA A:CYS1068 3.9 15.3 1.0
SG A:CYS1105 4.0 15.1 1.0
N A:CYS1064 4.4 15.5 1.0
CA A:CYS1064 4.4 17.7 1.0
O A:HOH3131 4.6 23.2 1.0
CA A:CYS1062 4.6 17.0 1.0
C A:CYS1073 4.7 17.1 1.0
N A:MET1074 4.8 17.9 1.0
SG A:CYS1111 4.8 13.6 1.0
N A:CYS1068 4.8 15.7 1.0
O A:HOH3217 4.8 20.0 1.0
O A:HOH3170 4.8 35.8 1.0
CB A:CYS1111 4.8 11.4 1.0

Zinc binding site 4 out of 8 in 5tuz

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Zinc binding site 4 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:20.2
occ:1.00
 SG A:CYS1256 2.3 19.8 1.0
SG A:CYS1258 2.3 18.9 1.0
SG A:CYS1203 2.3 21.0 1.0
SG A:CYS1263 2.4 20.4 1.0
CB A:CYS1263 3.3 19.7 1.0
CB A:CYS1256 3.3 21.7 1.0
CB A:CYS1258 3.3 17.7 1.0
CB A:CYS1203 3.4 23.4 1.0
CA A:CYS1263 3.8 25.4 1.0
O A:HOH3188 3.9 21.2 1.0
N A:CYS1203 4.1 18.1 1.0
N A:CYS1258 4.1 20.9 1.0
N A:ARG1264 4.2 22.0 1.0
NE2 A:HIS1201 4.2 21.5 1.0
CA A:CYS1258 4.2 20.1 1.0
CD2 A:HIS1201 4.3 18.7 1.0
CA A:CYS1203 4.3 19.6 1.0
C A:CYS1263 4.5 20.1 1.0
N A:HIS1265 4.6 21.9 1.0
CA A:CYS1256 4.6 25.2 1.0
N A:GLY1259 4.7 22.9 1.0
C A:CYS1256 4.7 28.5 1.0
C A:CYS1258 4.8 22.2 1.0
CB A:HIS1265 5.0 26.0 1.0
O A:CYS1256 5.0 26.6 1.0

Zinc binding site 5 out of 8 in 5tuz

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Zinc binding site 5 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:17.1
occ:1.00
 SG B:CYS1075 2.3 15.7 1.0
SG B:CYS1109 2.3 16.2 1.0
SG B:CYS1105 2.4 15.4 1.0
SG B:CYS1062 2.4 15.3 1.0
CB B:CYS1105 3.2 14.8 1.0
CB B:CYS1062 3.2 18.4 1.0
CB B:CYS1109 3.3 16.9 1.0
CB B:CYS1075 3.4 12.9 1.0
CA B:CYS1105 3.6 13.3 1.0
N B:CYS1062 3.6 17.2 1.0
ZN B:ZN3004 3.8 17.6 1.0
ZN B:ZN3003 3.8 15.7 1.0
CA B:CYS1062 4.0 18.1 1.0
SG B:CYS1111 4.1 16.4 1.0
SG B:CYS1073 4.3 16.9 1.0
N B:ASN1106 4.5 12.1 1.0
N B:CYS1105 4.5 10.5 1.0
CA B:CYS1109 4.6 16.0 1.0
C B:TYR1061 4.6 20.4 1.0
C B:CYS1105 4.6 14.5 1.0
SG B:CYS1068 4.7 16.8 1.0
CA B:CYS1075 4.7 14.6 1.0
N B:CYS1075 4.7 15.4 1.0
C B:CYS1062 4.8 19.0 1.0
CA B:TYR1061 4.9 17.7 1.0
O B:CYS1062 4.9 18.5 1.0

Zinc binding site 6 out of 8 in 5tuz

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Zinc binding site 6 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:15.7
occ:1.00
 SG B:CYS1068 2.3 16.8 1.0
SG B:CYS1115 2.3 15.0 1.0
SG B:CYS1111 2.3 16.4 1.0
SG B:CYS1105 2.4 15.4 1.0
CB B:CYS1111 3.2 14.7 1.0
CB B:CYS1105 3.2 14.8 1.0
CB B:CYS1115 3.2 13.3 1.0
CB B:CYS1068 3.3 13.4 1.0
ZN B:ZN3004 3.7 17.6 1.0
ZN B:ZN3002 3.8 17.1 1.0
SG B:CYS1062 4.0 15.3 1.0
NE B:ARG1118 4.3 13.4 1.0
NH2 B:ARG1118 4.4 17.4 1.0
CB B:ASN1117 4.6 13.6 1.0
CA B:CYS1111 4.6 15.7 1.0
CA B:CYS1105 4.7 13.3 1.0
CA B:CYS1068 4.7 15.8 1.0
CA B:CYS1115 4.7 15.0 1.0
CZ B:ARG1118 4.8 17.6 1.0
O B:TRP1112 4.8 15.4 1.0
N B:ASN1117 4.9 11.8 1.0
SG B:CYS1073 5.0 16.9 1.0

Zinc binding site 7 out of 8 in 5tuz

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Zinc binding site 7 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:17.6
occ:1.00
 SG B:CYS1068 2.3 16.8 1.0
SG B:CYS1073 2.4 16.9 1.0
SG B:CYS1062 2.4 15.3 1.0
SG B:CYS1064 2.4 17.6 1.0
CB B:CYS1062 3.1 18.4 1.0
CB B:CYS1064 3.2 22.8 1.0
CB B:CYS1073 3.2 15.5 1.0
CB B:CYS1068 3.3 13.4 1.0
ZN B:ZN3003 3.7 15.7 1.0
ZN B:ZN3002 3.8 17.1 1.0
CA B:CYS1068 3.9 15.8 1.0
CA B:CYS1073 3.9 20.0 1.0
SG B:CYS1105 4.0 15.4 1.0
N B:CYS1064 4.4 20.5 1.0
CA B:CYS1064 4.4 25.5 1.0
CA B:CYS1062 4.6 18.1 1.0
O B:HOH3141 4.6 22.2 1.0
C B:CYS1073 4.7 22.1 1.0
SG B:CYS1111 4.7 16.4 1.0
N B:CYS1068 4.7 15.3 1.0
CB B:CYS1111 4.8 14.7 1.0
O B:HOH3134 4.8 20.5 1.0
N B:MET1074 4.8 19.0 1.0
C B:CYS1062 4.9 19.0 1.0

Zinc binding site 8 out of 8 in 5tuz

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Zinc binding site 8 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


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 MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:25.2
occ:1.00
 SG B:CYS1256 2.3 23.8 1.0
SG B:CYS1258 2.3 23.8 1.0
SG B:CYS1203 2.4 23.9 1.0
SG B:CYS1263 2.4 27.8 1.0
CB B:CYS1263 3.3 33.7 1.0
CB B:CYS1258 3.3 21.6 1.0
CB B:CYS1256 3.3 27.7 1.0
CB B:CYS1203 3.6 22.2 1.0
CA B:CYS1263 3.7 33.4 1.0
O B:HOH3221 4.0 23.6 1.0
N B:CYS1258 4.0 24.9 1.0
N B:CYS1203 4.1 22.3 1.0
CA B:CYS1258 4.2 24.6 1.0
N B:ARG1264 4.2 33.8 1.0
NE2 B:HIS1201 4.3 20.5 1.0
CD2 B:HIS1201 4.4 20.7 1.0
C B:CYS1263 4.4 33.0 1.0
CA B:CYS1203 4.5 19.9 1.0
N B:HIS1265 4.6 32.8 1.0
CA B:CYS1256 4.6 32.9 1.0
C B:CYS1256 4.7 30.8 1.0
N B:GLY1259 4.8 26.6 1.0
O B:CYS1256 4.8 31.0 1.0
C B:CYS1258 4.9 30.3 1.0
N B:CYS1263 5.0 32.3 1.0
CB B:HIS1265 5.0 32.9 1.0

Reference:

Y.Xiong, F.Li, N.Babault, A.Dong, H.Zeng, H.Wu, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Discovery of Potent and Selective Inhibitors For G9A-Like Protein (Glp) Lysine Methyltransferase. J. Med. Chem. V. 60 1876 2017.
ISSN: ISSN 1520-4804
PubMed: 28135087
DOI: 10.1021/ACS.JMEDCHEM.6B01645
Page generated: Mon Oct 28 08:48:18 2024

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