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Zinc in PDB 3k5k: Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A

Enzymatic activity of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A

All present enzymatic activity of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A:
2.1.1.43;

Protein crystallography data

The structure of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A, PDB code: 3k5k was solved by A.Dong, G.A.Wasney, F.Liu, X.Chen, A.Allali-Hassani, G.Senisterra, I.Chau, C.Bountra, J.Weigelt, A.M.Edwards, C.H.Arrowsmith, S.V.Frye, A.Bochkarev, P.J.Brown, J.Jin, M.Vedadi, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.674, 78.074, 72.507, 90.00, 91.81, 90.00
R / Rfree (%) 21 / 26.4

Other elements in 3k5k:

The structure of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A (pdb code 3k5k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A, PDB code: 3k5k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3k5k

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Zinc binding site 1 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1194

b:33.5
occ:1.00
 SG A:CYS987 2.3 36.3 1.0
SG A:CYS1021 2.3 27.1 1.0
SG A:CYS1017 2.4 31.9 1.0
SG A:CYS974 2.4 31.4 1.0
CB A:CYS974 3.3 33.6 1.0
CB A:CYS1017 3.3 27.7 1.0
CB A:CYS1021 3.3 29.9 1.0
CB A:CYS987 3.4 36.8 1.0
N A:CYS974 3.5 33.1 1.0
CA A:CYS1017 3.6 27.2 1.0
ZN A:ZN1196 3.8 35.4 1.0
ZN A:ZN1195 3.9 32.2 1.0
CA A:CYS974 4.0 33.6 1.0
SG A:CYS1023 4.2 29.6 1.0
SG A:CYS985 4.3 37.3 1.0
C A:HIS973 4.5 33.0 1.0
N A:CYS1017 4.5 27.0 1.0
CA A:CYS1021 4.5 29.5 1.0
SG A:CYS980 4.6 31.7 1.0
N A:ASN1018 4.6 25.9 1.0
CA A:CYS987 4.6 36.8 1.0
CA A:HIS973 4.7 32.1 1.0
N A:CYS987 4.7 37.3 1.0
C A:CYS1017 4.7 26.3 1.0
O A:HOH61 4.9 31.4 1.0
C A:CYS974 4.9 34.4 1.0
ND2 A:ASN1029 5.0 29.6 1.0
O A:CYS974 5.0 33.9 1.0

Zinc binding site 2 out of 8 in 3k5k

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Zinc binding site 2 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1195

b:32.2
occ:1.00
 SG A:CYS1027 2.1 36.1 1.0
SG A:CYS1023 2.2 29.6 1.0
SG A:CYS1017 2.4 31.9 1.0
SG A:CYS980 2.6 31.7 1.0
CB A:CYS1017 3.1 27.7 1.0
CB A:CYS1027 3.2 35.5 1.0
CB A:CYS1023 3.2 32.4 1.0
CB A:CYS980 3.4 39.3 1.0
ZN A:ZN1196 3.8 35.4 1.0
ZN A:ZN1194 3.9 33.5 1.0
SG A:CYS974 4.1 31.4 1.0
NE A:ARG1030 4.4 32.0 1.0
NH2 A:ARG1030 4.5 32.2 1.0
CB A:ASN1029 4.5 31.1 1.0
CA A:CYS1017 4.6 27.2 1.0
CA A:CYS1027 4.6 34.8 1.0
CA A:CYS1023 4.6 32.2 1.0
O A:TRP1024 4.8 35.8 1.0
CA A:CYS980 4.8 39.5 1.0
CZ A:ARG1030 4.8 32.7 1.0
CB A:CYS1021 4.9 29.9 1.0
N A:ASN1029 5.0 31.8 1.0

Zinc binding site 3 out of 8 in 3k5k

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Zinc binding site 3 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1196

b:35.4
occ:1.00
 SG A:CYS980 2.0 31.7 1.0
SG A:CYS985 2.3 37.3 1.0
SG A:CYS974 2.4 31.4 1.0
SG A:CYS976 2.4 37.7 1.0
CB A:CYS974 3.1 33.6 1.0
CB A:CYS976 3.1 40.4 1.0
CB A:CYS980 3.2 39.3 1.0
CB A:CYS985 3.4 38.9 1.0
ZN A:ZN1194 3.8 33.5 1.0
ZN A:ZN1195 3.8 32.2 1.0
CA A:CYS980 3.9 39.5 1.0
CA A:CYS985 4.0 38.8 1.0
SG A:CYS1017 4.1 31.9 1.0
CA A:CYS976 4.4 40.1 1.0
N A:CYS976 4.4 39.0 1.0
O A:HOH441 4.5 48.3 1.0
CA A:CYS974 4.6 33.6 1.0
SG A:CYS1023 4.7 29.6 1.0
N A:CYS980 4.8 40.5 1.0
C A:CYS985 4.8 38.3 1.0
O A:HOH237 4.8 35.1 1.0
CB A:CYS1023 4.8 32.4 1.0
SG A:CYS987 4.9 36.3 1.0
C A:CYS980 4.9 40.7 1.0
N A:LEU986 4.9 37.5 1.0

Zinc binding site 4 out of 8 in 3k5k

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Zinc binding site 4 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1197

b:37.8
occ:1.00
 SG A:CYS1115 2.2 38.5 1.0
SG A:CYS1168 2.3 34.4 1.0
SG A:CYS1170 2.3 37.2 1.0
SG A:CYS1175 2.4 35.9 1.0
CB A:CYS1168 3.3 35.0 1.0
CB A:CYS1170 3.3 37.9 1.0
CB A:CYS1115 3.3 36.0 1.0
CB A:CYS1175 3.4 41.2 1.0
CA A:CYS1175 3.8 40.8 1.0
N A:CYS1115 4.0 34.7 1.0
N A:CYS1170 4.1 37.6 1.0
CA A:CYS1170 4.3 38.7 1.0
O A:HOH445 4.3 37.9 1.0
CA A:CYS1115 4.3 36.1 1.0
N A:LYS1176 4.3 39.5 1.0
CD2 A:HIS1113 4.4 28.8 1.0
NE2 A:HIS1113 4.4 30.2 1.0
N A:HIS1177 4.5 36.6 1.0
C A:CYS1175 4.5 40.9 1.0
CA A:CYS1168 4.6 35.8 1.0
C A:CYS1168 4.7 36.5 1.0
CB A:HIS1177 4.9 35.7 1.0
O A:CYS1168 4.9 37.0 1.0
N A:CYS1175 5.0 42.8 1.0
N A:GLY1171 5.0 41.4 1.0
N A:SER1178 5.0 34.7 1.0

Zinc binding site 5 out of 8 in 3k5k

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Zinc binding site 5 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1194

b:27.9
occ:1.00
 SG B:CYS987 2.3 28.8 1.0
SG B:CYS1021 2.3 24.8 1.0
SG B:CYS974 2.4 27.1 1.0
SG B:CYS1017 2.4 27.2 1.0
CB B:CYS1017 3.2 25.4 1.0
CB B:CYS974 3.3 28.5 1.0
CB B:CYS1021 3.3 24.7 1.0
CB B:CYS987 3.4 31.4 1.0
N B:CYS974 3.5 28.7 1.0
CA B:CYS1017 3.5 25.1 1.0
ZN B:ZN1196 3.8 29.2 1.0
ZN B:ZN1195 3.8 27.1 1.0
CA B:CYS974 4.0 28.8 1.0
SG B:CYS1023 4.2 24.6 1.0
SG B:CYS985 4.3 29.7 1.0
N B:CYS1017 4.5 24.5 1.0
C B:HIS973 4.5 29.2 1.0
CA B:CYS1021 4.5 24.6 1.0
N B:ASN1018 4.6 24.2 1.0
CA B:CYS987 4.6 32.0 1.0
C B:CYS1017 4.7 24.6 1.0
N B:CYS987 4.7 32.1 1.0
CA B:HIS973 4.7 29.3 1.0
SG B:CYS980 4.7 27.8 1.0
C B:CYS974 4.8 28.6 1.0
O B:HOH54 4.9 25.6 1.0
O B:CYS974 5.0 28.6 1.0
ND2 B:ASN1029 5.0 23.5 1.0

Zinc binding site 6 out of 8 in 3k5k

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Zinc binding site 6 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1195

b:27.1
occ:1.00
 SG B:CYS1023 2.2 24.6 1.0
SG B:CYS1017 2.3 27.2 1.0
SG B:CYS1027 2.4 27.6 1.0
SG B:CYS980 2.4 27.8 1.0
CB B:CYS1017 3.2 25.4 1.0
CB B:CYS1023 3.2 25.5 1.0
CB B:CYS1027 3.3 29.2 1.0
CB B:CYS980 3.4 30.7 1.0
ZN B:ZN1196 3.7 29.2 1.0
ZN B:ZN1194 3.8 27.9 1.0
SG B:CYS974 4.1 27.1 1.0
NE B:ARG1030 4.4 29.8 1.0
NH2 B:ARG1030 4.4 32.1 1.0
CA B:CYS1017 4.6 25.1 1.0
CB B:ASN1029 4.6 26.0 1.0
CA B:CYS1023 4.6 26.1 1.0
CA B:CYS1027 4.7 29.0 1.0
CA B:CYS980 4.8 30.6 1.0
O B:TRP1024 4.8 31.3 1.0
CZ B:ARG1030 4.8 30.4 1.0
CB B:CYS1021 4.9 24.7 1.0
SG B:CYS985 5.0 29.7 1.0
N B:ASN1029 5.0 27.1 1.0

Zinc binding site 7 out of 8 in 3k5k

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Zinc binding site 7 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1196

b:29.2
occ:1.00
 SG B:CYS980 2.2 27.8 1.0
SG B:CYS985 2.3 29.7 1.0
SG B:CYS974 2.4 27.1 1.0
SG B:CYS976 2.4 28.4 1.0
CB B:CYS980 3.2 30.7 1.0
CB B:CYS976 3.2 28.6 1.0
CB B:CYS974 3.2 28.5 1.0
CB B:CYS985 3.3 34.0 1.0
ZN B:ZN1195 3.7 27.1 1.0
ZN B:ZN1194 3.8 27.9 1.0
CA B:CYS985 3.9 33.3 1.0
CA B:CYS980 3.9 30.6 1.0
SG B:CYS1017 4.1 27.2 1.0
N B:CYS976 4.4 28.7 1.0
CA B:CYS976 4.4 29.1 1.0
O B:HOH45 4.5 32.4 1.0
CA B:CYS974 4.6 28.8 1.0
C B:CYS985 4.7 33.5 1.0
SG B:CYS1023 4.7 24.6 1.0
O B:HOH59 4.8 32.0 1.0
N B:CYS980 4.8 30.8 1.0
N B:LEU986 4.8 33.0 1.0
CB B:CYS1023 4.8 25.5 1.0
O B:HOH89 4.9 31.3 1.0
SG B:CYS987 4.9 28.8 1.0

Zinc binding site 8 out of 8 in 3k5k

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Zinc binding site 8 out of 8 in the Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Discovery of A 2,4-Diamino-7-Aminoalkoxy-Quinazoline As A Potent Inhibitor of Histone Lysine Methyltransferase, G9A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1197

b:37.1
occ:1.00
 SG B:CYS1170 2.1 38.6 1.0
SG B:CYS1168 2.3 34.7 1.0
SG B:CYS1175 2.4 38.7 1.0
SG B:CYS1115 2.5 36.8 1.0
CB B:CYS1170 3.2 38.9 1.0
CB B:CYS1115 3.3 34.5 1.0
CB B:CYS1168 3.4 36.3 1.0
CB B:CYS1175 3.4 41.8 1.0
CA B:CYS1175 3.8 42.0 1.0
N B:CYS1170 4.0 38.1 1.0
N B:CYS1115 4.0 33.2 1.0
O B:HOH134 4.1 42.9 1.0
CA B:CYS1170 4.1 39.0 1.0
CA B:CYS1115 4.3 34.6 1.0
N B:LYS1176 4.5 40.9 1.0
CD2 B:HIS1113 4.5 30.2 1.0
N B:GLY1171 4.5 40.9 1.0
NE2 B:HIS1113 4.5 32.4 1.0
CA B:CYS1168 4.6 36.4 1.0
C B:CYS1175 4.6 41.8 1.0
C B:CYS1168 4.6 37.2 1.0
N B:HIS1177 4.7 39.2 1.0
C B:CYS1170 4.8 39.9 1.0
O B:CYS1168 4.8 36.6 1.0
CB B:HIS1177 4.9 38.5 1.0
N B:CYS1175 5.0 43.3 1.0

Reference:

F.Liu, X.Chen, A.Allali-Hassani, A.M.Quinn, G.A.Wasney, A.Dong, D.Barsyte, I.Kozieradzki, G.Senisterra, I.Chau, A.Siarheyeva, D.B.Kireev, A.Jadhav, J.M.Herold, S.V.Frye, C.H.Arrowsmith, P.J.Brown, A.Simeonov, M.Vedadi, J.Jin. Discovery of A 2,4-Diamino-7-Aminoalkoxyquinazoline As A Potent and Selective Inhibitor of Histone Lysine Methyltransferase G9A. J.Med.Chem. V. 52 7950 2009.
ISSN: ISSN 0022-2623
PubMed: 19891491
DOI: 10.1021/JM901543M
Page generated: Sat Oct 26 07:40:30 2024

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