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Sodium in PDB 6ay3: Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide)

Enzymatic activity of Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide)

All present enzymatic activity of Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide):
2.3.1.48;

Protein crystallography data

The structure of Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide), PDB code: 6ay3 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) 29.78 / 1.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.910, 80.448, 48.522, 90.00, 109.06, 90.00
R / Rfree (%) 20.2 / 23.7

Other elements in 6ay3:

The structure of Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide) also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide) (pdb code 6ay3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide), PDB code: 6ay3:

Sodium binding site 1 out of 1 in 6ay3

Go back to Sodium Binding Sites List in 6ay3
Sodium binding site 1 out of 1 in the Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crebbp Bromodomain in Complex with CPD16 (5-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1H- Indole-3-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1203

b:28.5
occ:1.00
 O A:HOH1454 2.1 28.4 1.0
O A:HOH1337 2.1 26.5 1.0
O A:HOH1329 2.1 30.5 1.0
O A:HOH1415 2.1 27.7 1.0
O A:HOH1414 2.2 26.2 1.0
O A:HOH1356 2.2 24.6 1.0
NH2 A:ARG1103 4.0 33.5 1.0
OE2 A:GLU1188 4.1 38.0 0.4
OE1 A:GLU1099 4.2 18.1 0.4
OE1 A:GLU1188 4.3 16.2 0.6
O A:HOH1422 4.3 25.8 1.0
CB A:PRO1096 4.3 11.8 1.0
NH1 A:ARG1103 4.3 30.8 1.0
O A:HOH1458 4.4 31.2 1.0
OE2 A:GLU1188 4.4 37.5 0.6
O A:PRO1096 4.5 10.9 1.0
CZ A:ARG1103 4.6 27.2 1.0
CD A:GLU1188 4.8 14.9 0.6
C A:PRO1096 4.9 10.8 1.0
CA A:PRO1096 5.0 10.3 1.0

Reference:

S.M.Bronner, J.Murray, F.A.Romero, K.W.Lai, V.Tsui, P.Cyr, M.H.Beresini, G.De Leon Boenig, Z.Chen, E.F.Choo, K.R.Clark, T.D.Crawford, H.Jayaram, S.Kaufman, R.Li, Y.Li, J.Liao, X.Liang, W.Liu, J.Ly, J.Maher, J.Wai, F.Wang, A.Zheng, X.Zhu, S.Magnuson. A Unique Approach to Design Potent and Selective Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (Cbp) Inhibitors. J. Med. Chem. V. 60 10151 2017.
ISSN: ISSN 1520-4804
PubMed: 29155580
DOI: 10.1021/ACS.JMEDCHEM.7B01372
Page generated: Tue Dec 15 11:58:00 2020

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