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Zinc in PDB 5i8b: Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One)

Enzymatic activity of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One)

All present enzymatic activity of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One):
2.3.1.48;

Protein crystallography data

The structure of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One), PDB code: 5i8b was solved by J.M.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.87 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.236, 60.576, 54.138, 90.00, 102.75, 90.00
R / Rfree (%) 19 / 20

Other elements in 5i8b:

The structure of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One) (pdb code 5i8b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One), PDB code: 5i8b:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5i8b

Go back to Zinc Binding Sites List in 5i8b
Zinc binding site 1 out of 3 in the Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:22.3
occ:1.00
 ND1 A:HIS1291 2.1 21.4 1.0
SG A:CYS1199 2.3 21.9 1.0
SG A:CYS1200 2.3 22.1 1.0
SG A:CYS1294 2.3 22.6 1.0
CE1 A:HIS1291 3.1 19.2 1.0
CG A:HIS1291 3.2 21.5 1.0
CB A:CYS1199 3.3 26.7 1.0
CB A:CYS1294 3.3 21.9 1.0
CB A:CYS1200 3.5 22.3 1.0
CB A:HIS1291 3.5 23.4 1.0
N A:CYS1200 3.6 23.7 1.0
C A:CYS1199 3.9 24.4 1.0
CA A:CYS1200 4.0 22.2 1.0
CA A:CYS1199 4.2 22.2 1.0
NE2 A:HIS1291 4.2 23.0 1.0
CD2 A:HIS1291 4.3 22.2 1.0
N A:HIS1291 4.3 20.8 1.0
O A:HOH1582 4.3 29.5 1.0
C A:CYS1200 4.4 24.8 1.0
O A:CYS1199 4.5 24.0 1.0
O A:CYS1200 4.5 22.6 1.0
CA A:HIS1291 4.5 20.4 1.0
O A:HOH1693 4.6 34.7 1.0
CA A:CYS1294 4.7 23.4 1.0
NH2 A:ARG1202 4.9 29.2 1.0
N A:CYS1199 4.9 22.1 1.0

Zinc binding site 2 out of 3 in 5i8b

Go back to Zinc Binding Sites List in 5i8b
Zinc binding site 2 out of 3 in the Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:25.2
occ:1.00
 SG A:CYS1311 2.3 25.4 1.0
SG A:CYS1286 2.4 24.9 1.0
SG A:CYS1308 2.4 25.8 1.0
SG A:CYS1283 2.4 23.9 1.0
CB A:CYS1283 3.2 26.2 1.0
CB A:CYS1286 3.2 26.1 1.0
CB A:CYS1311 3.3 26.1 1.0
CB A:CYS1308 3.5 25.7 1.0
N A:CYS1286 3.7 28.6 1.0
N A:CYS1308 4.0 23.8 1.0
CA A:CYS1286 4.0 27.9 1.0
CA A:CYS1308 4.2 23.7 1.0
N A:CYS1311 4.3 28.0 1.0
CA A:CYS1311 4.4 28.9 1.0
O A:HOH1503 4.6 28.6 1.0
O A:HOH1672 4.6 40.6 1.0
CB A:GLU1285 4.6 28.2 1.0
CA A:CYS1283 4.7 23.4 1.0
O A:CYS1308 4.7 29.7 1.0
C A:CYS1308 4.7 30.1 1.0
C A:GLU1285 4.8 29.0 1.0
NH1 A:ARG1288 4.8 26.2 1.0
C A:CYS1286 4.8 27.7 1.0
N A:GLY1287 4.9 23.8 1.0

Zinc binding site 3 out of 3 in 5i8b

Go back to Zinc Binding Sites List in 5i8b
Zinc binding site 3 out of 3 in the Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cbp in Complex with CPD23 ((R)-6-(3-(Benzyloxy)Phenyl)-4-Methyl-1,3,4, 5-Tetrahydro-2H-Benzo[B][1,4]Diazepin-2-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1403

b:72.2
occ:0.89
 SG A:CYS1213 2.0 77.1 1.0
SG A:CYS1219 2.3 68.8 1.0
SG A:CYS1237 2.4 72.4 1.0
CE2 A:PHE1236 3.0 82.6 1.0
CB A:CYS1219 3.2 79.5 1.0
CB A:CYS1213 3.3 72.2 1.0
CB A:CYS1237 3.6 67.0 1.0
CD2 A:PHE1236 3.6 79.2 1.0
SG A:CYS1240 3.8 95.0 1.0
CZ A:PHE1236 3.9 82.4 1.0
CB A:CYS1240 4.2 81.9 1.0
N A:CYS1237 4.3 71.5 1.0
CA A:CYS1237 4.5 71.2 1.0
CA A:CYS1219 4.6 84.5 1.0
CA A:CYS1213 4.6 71.2 1.0
O A:CYS1237 4.7 73.9 1.0
N A:LYS1216 4.8 88.5 1.0
C A:CYS1213 4.8 73.7 1.0
C A:CYS1219 4.9 80.3 1.0
CG A:PHE1236 5.0 79.0 1.0
C A:CYS1237 5.0 75.3 1.0

Reference:

A.M.Taylor, A.Cote, M.C.Hewitt, R.Pastor, Y.Leblanc, C.G.Nasveschuk, F.A.Romero, T.D.Crawford, N.Cantone, H.Jayaram, J.Setser, J.Murray, M.H.Beresini, G.De Leon Boenig, Z.Chen, A.R.Conery, R.T.Cummings, L.A.Dakin, E.M.Flynn, O.W.Huang, S.Kaufman, P.J.Keller, J.R.Kiefer, T.Lai, Y.Li, J.Liao, W.Liu, H.Lu, E.Pardo, V.Tsui, J.Wang, Y.Wang, Z.Xu, F.Yan, D.Yu, L.Zawadzke, X.Zhu, X.Zhu, R.J.Sims, A.G.Cochran, S.Bellon, J.E.Audia, S.Magnuson, B.K.Albrecht. Fragment-Based Discovery of A Selective and Cell-Active Benzodiazepinone Cbp/EP300 Bromodomain Inhibitor (Cpi-637). Acs Med.Chem.Lett. V. 7 531 2016.
ISSN: ISSN 1948-5875
PubMed: 27190605
DOI: 10.1021/ACSMEDCHEMLETT.6B00075
Page generated: Sun Oct 27 18:00:07 2024

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