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Zinc in PDB 4nvq: Human G9A in Complex with Inhibitor A-366

Enzymatic activity of Human G9A in Complex with Inhibitor A-366

All present enzymatic activity of Human G9A in Complex with Inhibitor A-366:
2.1.1.43;

Protein crystallography data

The structure of Human G9A in Complex with Inhibitor A-366, PDB code: 4nvq was solved by R.F.Sweis, M.Pliushchev, P.J.Brown, J.Guo, F.Li, D.Maag, A.M.Petros, N.B.Soni, C.Tse, M.Vedadi, M.R.Michaelides, G.G.Chiang, W.N.Pappano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.59 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.140, 78.250, 71.440, 90.00, 92.61, 90.00
R / Rfree (%) 20.2 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Human G9A in Complex with Inhibitor A-366 (pdb code 4nvq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human G9A in Complex with Inhibitor A-366, PDB code: 4nvq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4nvq

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Zinc binding site 1 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:55.0
occ:1.00
 SG A:CYS1017 2.2 52.0 1.0
SG A:CYS987 2.2 62.6 1.0
SG A:CYS1021 2.3 49.9 1.0
SG A:CYS974 2.6 50.0 1.0
CB A:CYS1017 3.2 47.6 1.0
CB A:CYS1021 3.4 46.6 1.0
CB A:CYS974 3.4 47.6 1.0
CB A:CYS987 3.4 59.5 1.0
CA A:CYS1017 3.6 45.7 1.0
ZN A:ZN1204 3.6 59.0 1.0
N A:CYS974 3.6 50.7 1.0
ZN A:ZN1205 3.8 59.5 1.0
CA A:CYS974 4.1 49.7 1.0
SG A:CYS1023 4.2 53.4 1.0
SG A:CYS985 4.3 63.3 1.0
N A:CYS1017 4.5 43.3 1.0
SG A:CYS980 4.5 39.4 1.0
N A:ASN1018 4.6 47.1 1.0
CA A:CYS1021 4.6 47.1 1.0
C A:HIS973 4.6 57.6 1.0
C A:CYS1017 4.6 48.1 1.0
CA A:CYS987 4.7 60.1 1.0
N A:CYS987 4.7 60.5 1.0
CA A:HIS973 4.8 51.7 1.0
ND2 A:ASN1029 4.8 46.4 1.0
C A:CYS974 4.9 58.2 1.0
O A:HOH1405 5.0 56.4 1.0

Zinc binding site 2 out of 8 in 4nvq

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Zinc binding site 2 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:59.0
occ:1.00
 SG A:CYS974 2.2 50.0 1.0
SG A:CYS980 2.2 39.4 1.0
SG A:CYS985 2.3 63.3 1.0
SG A:CYS976 2.6 63.8 1.0
CB A:CYS974 2.9 47.6 1.0
CB A:CYS980 3.2 41.8 1.0
CB A:CYS976 3.3 60.5 1.0
CB A:CYS985 3.4 59.5 1.0
ZN A:ZN1203 3.6 55.0 1.0
SG A:CYS1017 3.9 52.0 1.0
ZN A:ZN1205 3.9 59.5 1.0
CA A:CYS985 3.9 59.5 1.0
CA A:CYS980 4.1 46.4 1.0
O A:HOH1425 4.3 48.2 1.0
CA A:CYS974 4.4 49.7 1.0
N A:CYS976 4.5 61.8 1.0
CA A:CYS976 4.5 61.0 1.0
SG A:CYS987 4.7 62.6 1.0
C A:CYS985 4.7 60.6 1.0
N A:LEU986 4.8 57.4 1.0
N A:CYS980 4.9 48.4 1.0
SG A:CYS1023 4.9 53.4 1.0
C A:CYS974 4.9 58.2 1.0
CB A:CYS1023 4.9 49.9 1.0

Zinc binding site 3 out of 8 in 4nvq

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Zinc binding site 3 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1205

b:59.5
occ:1.00
 SG A:CYS1027 2.1 49.0 1.0
SG A:CYS1017 2.3 52.0 1.0
SG A:CYS1023 2.4 53.4 1.0
O A:HOH1425 2.5 48.2 1.0
SG A:CYS980 2.6 39.4 1.0
CB A:CYS1017 3.0 47.6 1.0
CB A:CYS1027 3.1 47.5 1.0
CB A:CYS1023 3.3 49.9 1.0
CB A:CYS980 3.6 41.8 1.0
ZN A:ZN1203 3.8 55.0 1.0
ZN A:ZN1204 3.9 59.0 1.0
SG A:CYS974 4.2 50.0 1.0
NE A:ARG1030 4.4 54.6 1.0
NH2 A:ARG1030 4.5 62.6 1.0
CA A:CYS1017 4.5 45.7 1.0
CB A:ASN1029 4.5 46.7 1.0
CA A:CYS1027 4.6 49.5 1.0
CA A:CYS1023 4.7 49.1 1.0
CZ A:ARG1030 4.8 72.6 1.0
CA A:CYS980 4.9 46.4 1.0
O A:TRP1024 4.9 58.1 1.0
CB A:CYS1021 4.9 46.6 1.0
O A:ASP979 4.9 61.4 1.0
N A:ASN1029 5.0 47.8 1.0

Zinc binding site 4 out of 8 in 4nvq

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Zinc binding site 4 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1206

b:61.5
occ:1.00
 SG A:CYS1115 2.2 64.5 1.0
SG A:CYS1168 2.2 62.9 1.0
SG A:CYS1170 2.3 61.4 1.0
SG A:CYS1175 2.5 72.8 1.0
CB A:CYS1175 3.3 69.7 1.0
CB A:CYS1115 3.3 60.9 1.0
O A:HOH1398 3.4 82.6 1.0
CB A:CYS1168 3.4 58.9 1.0
CB A:CYS1170 3.5 58.7 1.0
CA A:CYS1175 3.7 70.4 1.0
N A:CYS1115 4.0 59.5 1.0
CA A:CYS1115 4.2 60.6 1.0
N A:LYS1176 4.3 66.8 1.0
N A:CYS1170 4.3 58.5 1.0
NE2 A:HIS1113 4.4 52.7 1.0
CD2 A:HIS1113 4.4 53.0 1.0
CA A:CYS1170 4.4 59.9 1.0
N A:HIS1177 4.4 60.0 1.0
C A:CYS1175 4.4 73.7 1.0
O A:HOH1389 4.5 56.7 1.0
CA A:CYS1168 4.6 58.7 1.0
C A:CYS1168 4.7 65.0 1.0
O A:CYS1168 4.8 64.8 1.0
CB A:HIS1177 4.9 60.8 1.0
N A:CYS1175 4.9 72.6 1.0
N A:SER1178 4.9 60.7 1.0
CA A:HIS1177 5.0 60.0 1.0

Zinc binding site 5 out of 8 in 4nvq

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Zinc binding site 5 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:44.7
occ:1.00
 SG B:CYS1023 2.2 40.6 1.0
SG B:CYS1017 2.3 45.6 1.0
SG B:CYS1027 2.3 47.2 1.0
SG B:CYS980 2.4 51.7 1.0
CB B:CYS1017 3.1 41.8 1.0
CB B:CYS1023 3.2 37.9 1.0
CB B:CYS1027 3.2 45.5 1.0
CB B:CYS980 3.5 49.9 1.0
ZN B:ZN1205 3.7 48.5 1.0
ZN B:ZN1204 3.8 48.1 1.0
SG B:CYS974 4.0 46.1 1.0
NE B:ARG1030 4.4 43.2 1.0
NH2 B:ARG1030 4.4 58.6 1.0
CA B:CYS1017 4.6 41.3 1.0
CB B:ASN1029 4.6 42.5 1.0
CA B:CYS1023 4.6 39.2 1.0
CA B:CYS1027 4.7 45.7 1.0
CZ B:ARG1030 4.8 57.3 1.0
CB B:CYS1021 4.8 39.8 1.0
CA B:CYS980 4.8 51.8 1.0
O B:TRP1024 4.9 38.4 1.0

Zinc binding site 6 out of 8 in 4nvq

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Zinc binding site 6 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:48.1
occ:1.00
 SG B:CYS974 2.3 46.1 1.0
SG B:CYS980 2.3 51.7 1.0
SG B:CYS985 2.3 58.2 1.0
SG B:CYS976 2.5 51.7 1.0
CB B:CYS974 3.1 43.9 1.0
CB B:CYS976 3.2 48.1 1.0
CB B:CYS980 3.3 49.9 1.0
CB B:CYS985 3.3 57.8 1.0
ZN B:ZN1205 3.8 48.5 1.0
ZN B:ZN1203 3.8 44.7 1.0
CA B:CYS985 3.9 61.5 1.0
SG B:CYS1017 3.9 45.6 1.0
CA B:CYS980 4.1 51.8 1.0
CA B:CYS976 4.4 48.5 1.0
N B:CYS976 4.5 48.5 1.0
CA B:CYS974 4.6 45.7 1.0
O B:HOH1306 4.6 55.6 1.0
SG B:CYS987 4.7 55.9 1.0
C B:CYS985 4.7 70.3 1.0
N B:LEU986 4.9 70.3 1.0
SG B:CYS1023 4.9 40.6 1.0
CB B:CYS1023 4.9 37.9 1.0
N B:CYS980 4.9 52.5 1.0

Zinc binding site 7 out of 8 in 4nvq

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Zinc binding site 7 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1205

b:48.5
occ:1.00
 SG B:CYS1021 2.2 42.7 1.0
SG B:CYS987 2.2 55.9 1.0
SG B:CYS1017 2.3 45.6 1.0
SG B:CYS974 2.5 46.1 1.0
CB B:CYS1017 3.1 41.8 1.0
CB B:CYS1021 3.2 39.8 1.0
CB B:CYS974 3.4 43.9 1.0
N B:CYS974 3.5 47.8 1.0
CA B:CYS1017 3.5 41.3 1.0
CB B:CYS987 3.6 54.4 1.0
ZN B:ZN1203 3.7 44.7 1.0
ZN B:ZN1204 3.8 48.1 1.0
CA B:CYS974 4.0 45.7 1.0
SG B:CYS1023 4.1 40.6 1.0
SG B:CYS985 4.4 58.2 1.0
CA B:CYS1021 4.4 39.2 1.0
O B:HOH1324 4.5 60.4 1.0
N B:CYS1017 4.5 41.5 1.0
N B:ASN1018 4.5 42.8 1.0
C B:HIS973 4.5 53.8 1.0
C B:CYS1017 4.6 44.9 1.0
SG B:CYS980 4.7 51.7 1.0
CA B:HIS973 4.7 49.2 1.0
C B:CYS974 4.8 49.9 1.0
CA B:CYS987 4.8 55.6 1.0
N B:CYS987 4.9 69.4 1.0
O B:CYS974 4.9 46.2 1.0
ND2 B:ASN1029 4.9 47.5 1.0

Zinc binding site 8 out of 8 in 4nvq

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Zinc binding site 8 out of 8 in the Human G9A in Complex with Inhibitor A-366


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human G9A in Complex with Inhibitor A-366 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1206

b:60.1
occ:1.00
 SG B:CYS1170 2.2 62.2 1.0
SG B:CYS1168 2.2 61.4 1.0
SG B:CYS1175 2.4 67.5 1.0
SG B:CYS1115 2.4 60.5 1.0
CB B:CYS1175 3.3 63.5 1.0
CB B:CYS1170 3.3 59.0 1.0
CB B:CYS1168 3.4 56.6 1.0
CB B:CYS1115 3.5 56.5 1.0
CA B:CYS1175 3.8 63.7 1.0
O B:HOH1314 4.0 50.8 1.0
N B:CYS1115 4.0 55.7 1.0
N B:CYS1170 4.1 57.9 1.0
CA B:CYS1170 4.2 58.9 1.0
CA B:CYS1115 4.3 56.0 1.0
N B:LYS1176 4.4 58.9 1.0
CD2 B:HIS1113 4.5 54.4 1.0
NE2 B:HIS1113 4.5 53.8 1.0
C B:CYS1175 4.5 65.3 1.0
CA B:CYS1168 4.6 55.3 1.0
C B:CYS1168 4.6 60.9 1.0
N B:HIS1177 4.6 57.6 1.0
O B:CYS1168 4.7 59.7 1.0
N B:GLY1171 4.9 65.5 1.0
N B:CYS1175 4.9 65.3 1.0
C B:CYS1170 4.9 65.8 1.0

Reference:

R.F.Sweis, M.Pliushchev, P.J.Brown, J.Guo, F.Li, D.Maag, A.M.Petros, N.B.Soni, C.Tse, M.Vedadi, M.R.Michaelides, G.G.Chiang, W.N.Pappano. Discovery and Development of Potent and Selective Inhibitors of Histone Methyltransferase G9A. Acs Med Chem Lett V. 5 205 2014.
ISSN: ISSN 1948-5875
PubMed: 24900801
DOI: 10.1021/ML400496H
Page generated: Wed Dec 16 05:37:43 2020

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