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Zinc in PDB 5vse: Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine

Enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine

All present enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine, PDB code: 5vse 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) 45.88 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.491, 78.691, 72.610, 90.00, 91.35, 90.00
R / Rfree (%) 16.8 / 19.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine (pdb code 5vse). 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine, PDB code: 5vse:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vse

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Zinc binding site 1 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:24.9
occ:1.00
 SG A:CYS1027 2.3 25.2 1.0
SG A:CYS980 2.3 28.2 1.0
SG A:CYS1023 2.3 24.9 1.0
SG A:CYS1017 2.4 23.4 1.0
CB A:CYS1017 3.2 23.7 1.0
CB A:CYS1023 3.2 28.0 1.0
CB A:CYS1027 3.2 27.2 1.0
CB A:CYS980 3.3 31.4 1.0
ZN A:ZN1502 3.8 27.2 1.0
ZN A:ZN1503 3.8 27.7 1.0
SG A:CYS974 4.1 26.6 1.0
NH2 A:ARG1030 4.4 31.6 1.0
NE A:ARG1030 4.4 29.6 1.0
CB A:ASN1029 4.5 25.7 1.0
CA A:CYS1023 4.6 28.1 1.0
CA A:CYS1017 4.6 19.5 1.0
CA A:CYS1027 4.7 25.4 1.0
CA A:CYS980 4.7 31.2 1.0
O A:TRP1024 4.8 30.4 1.0
CZ A:ARG1030 4.8 28.2 1.0
N A:ASN1029 4.9 27.1 1.0
CB A:CYS1021 5.0 27.3 1.0

Zinc binding site 2 out of 8 in 5vse

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Zinc binding site 2 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:27.2
occ:1.00
 SG A:CYS1017 2.3 23.4 1.0
SG A:CYS987 2.3 44.6 1.0
SG A:CYS1021 2.3 25.3 1.0
SG A:CYS974 2.4 26.6 1.0
CB A:CYS1017 3.2 23.7 1.0
CB A:CYS974 3.2 33.5 1.0
CB A:CYS1021 3.3 27.3 1.0
CB A:CYS987 3.4 44.4 1.0
CA A:CYS1017 3.6 19.5 1.0
N A:CYS974 3.6 28.8 1.0
ZN A:ZN1503 3.8 27.7 1.0
ZN A:ZN1501 3.8 24.9 1.0
CA A:CYS974 3.9 26.6 1.0
SG A:CYS1023 4.1 24.9 1.0
SG A:CYS985 4.3 35.4 1.0
N A:CYS1017 4.4 23.9 1.0
CA A:CYS1021 4.6 26.1 1.0
C A:HIS973 4.6 29.0 1.0
N A:ASN1018 4.6 23.5 1.0
C A:CYS1017 4.7 24.4 1.0
CA A:CYS987 4.7 50.3 1.0
SG A:CYS980 4.7 28.2 1.0
N A:CYS987 4.7 50.4 1.0
C A:CYS974 4.8 32.4 1.0
CA A:HIS973 4.8 26.9 1.0
O A:HOH1714 4.9 40.6 1.0
O A:CYS974 4.9 28.9 1.0
ND2 A:ASN1029 4.9 26.7 1.0

Zinc binding site 3 out of 8 in 5vse

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Zinc binding site 3 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:27.7
occ:1.00
 SG A:CYS976 2.2 28.4 1.0
SG A:CYS974 2.4 26.6 1.0
SG A:CYS985 2.4 35.4 1.0
SG A:CYS980 2.5 28.2 1.0
CB A:CYS974 3.1 33.5 1.0
CB A:CYS976 3.1 28.3 1.0
CB A:CYS985 3.3 40.0 1.0
CB A:CYS980 3.3 31.4 1.0
ZN A:ZN1502 3.8 27.2 1.0
ZN A:ZN1501 3.8 24.9 1.0
CA A:CYS985 3.9 40.7 1.0
CA A:CYS980 3.9 31.2 1.0
SG A:CYS1017 4.1 23.4 1.0
N A:CYS976 4.3 29.0 1.0
CA A:CYS976 4.4 30.4 1.0
CA A:CYS974 4.6 26.6 1.0
O A:HOH1616 4.6 29.0 1.0
C A:CYS985 4.7 43.5 1.0
SG A:CYS1023 4.8 24.9 1.0
N A:CYS980 4.8 32.9 1.0
N A:LEU986 4.8 59.9 1.0
CB A:CYS1023 4.9 28.0 1.0
O A:HOH1717 4.9 39.1 1.0
O A:HOH1724 5.0 51.7 1.0
SG A:CYS987 5.0 44.6 1.0

Zinc binding site 4 out of 8 in 5vse

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Zinc binding site 4 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:33.5
occ:1.00
 SG A:CYS1175 2.2 38.1 1.0
SG A:CYS1170 2.3 37.8 1.0
SG A:CYS1168 2.3 36.6 1.0
SG A:CYS1115 2.5 38.4 1.0
CB A:CYS1175 3.0 46.3 1.0
CB A:CYS1168 3.3 36.9 1.0
CB A:CYS1170 3.3 40.4 1.0
CB A:CYS1115 3.3 42.5 1.0
CA A:CYS1175 3.6 48.1 1.0
O A:HOH1707 4.0 35.3 1.0
N A:CYS1170 4.0 36.7 1.0
N A:CYS1115 4.1 38.4 1.0
CA A:CYS1170 4.2 41.8 1.0
N A:LYS1176 4.3 40.1 1.0
C A:CYS1175 4.3 39.9 1.0
CA A:CYS1115 4.3 41.9 1.0
N A:HIS1177 4.5 39.2 1.0
NE2 A:HIS1113 4.5 30.1 1.0
CD2 A:HIS1113 4.6 29.0 1.0
CA A:CYS1168 4.6 36.6 1.0
C A:CYS1168 4.7 36.5 1.0
N A:GLY1171 4.8 40.6 1.0
N A:CYS1175 4.8 46.5 1.0
C A:CYS1170 4.9 43.9 1.0
CB A:HIS1177 5.0 38.7 1.0
O A:CYS1168 5.0 39.6 1.0

Zinc binding site 5 out of 8 in 5vse

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Zinc binding site 5 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1501

b:27.6
occ:1.00
 SG B:CYS1017 2.3 28.5 1.0
SG B:CYS1023 2.3 29.2 1.0
SG B:CYS1027 2.3 30.9 1.0
SG B:CYS980 2.4 31.0 1.0
CB B:CYS1017 3.1 26.3 1.0
CB B:CYS1023 3.2 34.3 1.0
CB B:CYS1027 3.3 30.9 1.0
CB B:CYS980 3.4 42.8 1.0
ZN B:ZN1503 3.8 29.8 1.0
ZN B:ZN1502 3.8 27.9 1.0
SG B:CYS974 4.1 28.7 1.0
NH2 B:ARG1030 4.3 33.0 1.0
NE B:ARG1030 4.4 32.2 1.0
CB B:ASN1029 4.6 25.7 1.0
CA B:CYS1017 4.6 22.4 1.0
CA B:CYS1023 4.7 31.3 1.0
CA B:CYS1027 4.7 31.3 1.0
CZ B:ARG1030 4.7 33.0 1.0
CA B:CYS980 4.8 34.6 1.0
O B:TRP1024 4.8 33.9 1.0
CB B:CYS1021 4.9 28.5 1.0

Zinc binding site 6 out of 8 in 5vse

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Zinc binding site 6 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1502

b:27.9
occ:1.00
 SG B:CYS974 2.3 28.7 1.0
SG B:CYS1021 2.3 26.5 1.0
SG B:CYS987 2.3 30.8 1.0
SG B:CYS1017 2.5 28.5 1.0
CB B:CYS1017 3.2 26.3 1.0
CB B:CYS1021 3.3 28.5 1.0
CB B:CYS974 3.3 31.6 1.0
CB B:CYS987 3.5 33.1 1.0
N B:CYS974 3.6 27.6 1.0
CA B:CYS1017 3.6 22.4 1.0
ZN B:ZN1503 3.7 29.8 1.0
ZN B:ZN1501 3.8 27.6 1.0
CA B:CYS974 4.0 30.9 1.0
SG B:CYS1023 4.2 29.2 1.0
SG B:CYS985 4.3 32.1 1.0
N B:CYS1017 4.5 25.6 1.0
N B:ASN1018 4.6 23.3 1.0
CA B:CYS1021 4.6 27.4 1.0
C B:HIS973 4.6 36.7 1.0
SG B:CYS980 4.6 31.0 1.0
C B:CYS1017 4.7 23.8 1.0
N B:CYS987 4.7 31.4 1.0
CA B:CYS987 4.7 30.3 1.0
CA B:HIS973 4.8 29.4 1.0
C B:CYS974 4.9 37.3 1.0
O B:HOH1720 4.9 29.3 1.0
O B:CYS974 4.9 29.5 1.0
ND2 B:ASN1029 5.0 26.9 1.0

Zinc binding site 7 out of 8 in 5vse

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Zinc binding site 7 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:29.8
occ:1.00
 SG B:CYS976 2.3 34.0 1.0
SG B:CYS980 2.3 31.0 1.0
SG B:CYS985 2.3 32.1 1.0
SG B:CYS974 2.5 28.7 1.0
CB B:CYS974 3.1 31.6 1.0
CB B:CYS976 3.1 41.6 1.0
CB B:CYS980 3.2 42.8 1.0
CB B:CYS985 3.2 35.6 1.0
ZN B:ZN1502 3.7 27.9 1.0
ZN B:ZN1501 3.8 27.6 1.0
CA B:CYS985 3.8 34.7 1.0
CA B:CYS980 3.9 34.6 1.0
SG B:CYS1017 4.0 28.5 1.0
N B:CYS976 4.3 37.3 1.0
CA B:CYS976 4.4 38.5 1.0
O B:HOH1616 4.4 35.2 1.0
CA B:CYS974 4.5 30.9 1.0
C B:CYS985 4.6 38.9 1.0
SG B:CYS1023 4.8 29.2 1.0
N B:CYS980 4.8 36.4 1.0
O B:HOH1696 4.8 35.9 1.0
N B:LEU986 4.8 37.8 1.0
CB B:CYS1023 4.9 34.3 1.0
SG B:CYS987 5.0 30.8 1.0
C B:CYS974 5.0 37.3 1.0

Zinc binding site 8 out of 8 in 5vse

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Zinc binding site 8 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 17: N~2~-Cyclopentyl-6,7-Dimethoxy-N~2~-Methyl-N~4~-(1- Methylpiperidin-4-Yl)Quinazoline-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1504

b:33.7
occ:1.00
 SG B:CYS1175 2.2 33.9 1.0
SG B:CYS1168 2.3 32.1 1.0
SG B:CYS1170 2.4 36.5 1.0
SG B:CYS1115 2.4 37.8 1.0
CB B:CYS1175 3.1 39.1 1.0
CB B:CYS1168 3.3 31.9 1.0
CB B:CYS1115 3.4 36.5 1.0
CB B:CYS1170 3.4 38.7 1.0
CA B:CYS1175 3.7 39.1 1.0
N B:CYS1115 4.1 33.7 1.0
N B:CYS1170 4.1 33.6 1.0
O B:HOH1744 4.1 37.9 1.0
CA B:CYS1115 4.3 34.2 1.0
CA B:CYS1170 4.3 41.0 1.0
N B:LYS1176 4.4 40.8 1.0
C B:CYS1175 4.4 42.1 1.0
CD2 B:HIS1113 4.5 27.6 1.0
NE2 B:HIS1113 4.5 29.1 1.0
N B:HIS1177 4.5 34.1 1.0
CA B:CYS1168 4.6 34.5 1.0
C B:CYS1168 4.7 38.5 1.0
CB B:HIS1177 4.9 33.0 1.0
N B:GLY1171 4.9 39.5 1.0
N B:CYS1175 4.9 47.0 1.0
N B:SER1178 5.0 34.3 1.0
O B:CYS1168 5.0 40.4 1.0
C B:CYS1170 5.0 44.0 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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