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Fluorine 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:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where 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:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ay3

Go back to Fluorine Binding Sites List in 6ay3
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F1201

b:18.8
occ:1.00
 F32 A:C3J1201 0.0 18.8 1.0
C31 A:C3J1201 1.4 17.3 1.0
F33 A:C3J1201 2.2 18.2 1.0
C22 A:C3J1201 2.4 12.7 1.0
C26 A:C3J1201 3.0 16.1 1.0
C23 A:C3J1201 3.2 12.0 1.0
C21 A:C3J1201 3.3 9.4 1.0
CG A:PRO1110 3.3 11.6 1.0
C25 A:C3J1201 3.5 9.8 1.0
CE2 A:PHE1177 3.6 7.8 1.0
CB A:ARG1173 3.6 8.1 1.0
CD2 A:PHE1177 3.8 11.5 1.0
CD A:ARG1173 4.0 13.0 1.0
NE A:ARG1173 4.1 12.5 1.0
CG2 A:VAL1174 4.2 9.8 1.0
N27 A:C3J1201 4.2 16.7 1.0
CZ A:ARG1173 4.2 13.6 1.0
CD A:PRO1110 4.3 11.3 1.0
NH1 A:ARG1173 4.4 17.1 1.0
CB A:PRO1110 4.4 11.4 1.0
CG A:ARG1173 4.4 11.4 1.0
C24 A:C3J1201 4.5 11.7 1.0
C20 A:C3J1201 4.5 8.7 1.0
N A:VAL1174 4.6 9.8 1.0
CZ A:PHE1177 4.7 10.0 1.0
C A:ARG1173 4.7 8.6 1.0
C29 A:C3J1201 4.8 13.1 1.0
CA A:ARG1173 4.8 10.4 1.0
O B:HOH1339 4.8 12.4 1.0
NH2 A:ARG1173 4.9 12.9 1.0
CA A:VAL1174 4.9 10.7 1.0
C19 A:C3J1201 5.0 8.9 1.0

Fluorine binding site 2 out of 4 in 6ay3

Go back to Fluorine Binding Sites List in 6ay3
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F binding site number 2 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:F1201

b:18.2
occ:1.00
 F33 A:C3J1201 0.0 18.2 1.0
C31 A:C3J1201 1.4 17.3 1.0
F32 A:C3J1201 2.2 18.8 1.0
C22 A:C3J1201 2.4 12.7 1.0
C21 A:C3J1201 2.7 9.4 1.0
CZ A:ARG1173 3.0 13.6 1.0
NH2 A:ARG1173 3.1 12.9 1.0
O B:HOH1397 3.3 26.6 1.0
NE A:ARG1173 3.4 12.5 1.0
NH1 A:ARG1173 3.5 17.1 1.0
C23 A:C3J1201 3.7 12.0 1.0
O B:HOH1339 4.0 12.4 1.0
C20 A:C3J1201 4.1 8.7 1.0
CD A:ARG1173 4.1 13.0 1.0
CG2 A:VAL1174 4.2 9.8 1.0
CB A:ARG1173 4.3 8.1 1.0
C25 A:C3J1201 4.3 9.8 1.0
C13 A:C3J1201 4.4 10.9 1.0
C26 A:C3J1201 4.4 16.1 1.0
OE1 B:GLU1186 4.6 10.9 1.0
O A:HOH1393 4.6 30.3 1.0
C12 A:C3J1201 4.7 9.7 1.0
C24 A:C3J1201 4.7 11.7 1.0
CG A:PRO1110 4.8 11.6 1.0
CG A:ARG1173 4.8 11.4 1.0
C14 A:C3J1201 4.8 11.9 1.0
OE2 B:GLU1186 4.8 16.3 1.0
N15 A:C3J1201 4.9 12.2 1.0
C19 A:C3J1201 4.9 8.9 1.0
C1 A:EDO1202 5.0 30.0 1.0

Fluorine binding site 3 out of 4 in 6ay3

Go back to Fluorine Binding Sites List in 6ay3
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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
B:F1201

b:21.2
occ:1.00
 F32 B:C3J1201 0.0 21.2 1.0
C31 B:C3J1201 1.4 14.1 1.0
F33 B:C3J1201 2.2 22.6 1.0
C22 B:C3J1201 2.4 10.6 1.0
C26 B:C3J1201 3.2 20.4 1.0
C21 B:C3J1201 3.2 12.8 1.0
CG B:PRO1110 3.3 14.4 1.0
C23 B:C3J1201 3.3 13.0 1.0
CB B:ARG1173 3.5 8.9 1.0
C25 B:C3J1201 3.6 12.2 1.0
CE2 B:PHE1177 3.7 11.6 1.0
CD2 B:PHE1177 3.9 10.3 1.0
CG2 B:VAL1174 4.0 12.9 1.0
NE B:ARG1173 4.1 14.4 1.0
CD B:ARG1173 4.1 9.8 1.0
CD B:PRO1110 4.1 11.1 1.0
CZ B:ARG1173 4.2 15.9 1.0
CB B:PRO1110 4.3 11.2 1.0
N27 B:C3J1201 4.3 15.8 1.0
N B:VAL1174 4.3 8.2 1.0
NH1 B:ARG1173 4.4 14.7 1.0
CG B:ARG1173 4.4 9.7 1.0
C20 B:C3J1201 4.5 11.6 1.0
C B:ARG1173 4.5 8.5 1.0
C24 B:C3J1201 4.5 16.1 1.0
CA B:ARG1173 4.6 8.6 1.0
CA B:VAL1174 4.7 8.8 1.0
NH2 B:ARG1173 4.8 13.6 1.0
CZ B:PHE1177 4.8 10.9 1.0
C29 B:C3J1201 4.9 15.6 1.0
O B:ARG1173 5.0 10.3 1.0
C19 B:C3J1201 5.0 10.6 1.0

Fluorine binding site 4 out of 4 in 6ay3

Go back to Fluorine Binding Sites List in 6ay3
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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
B:F1201

b:22.6
occ:1.00
 F33 B:C3J1201 0.0 22.6 1.0
C31 B:C3J1201 1.4 14.1 1.0
F32 B:C3J1201 2.2 21.2 1.0
C22 B:C3J1201 2.3 10.6 1.0
C21 B:C3J1201 2.6 12.8 1.0
CZ B:ARG1173 3.1 15.9 1.0
NH2 B:ARG1173 3.1 13.6 1.0
NE B:ARG1173 3.5 14.4 1.0
NH1 B:ARG1173 3.5 14.7 1.0
C23 B:C3J1201 3.6 13.0 1.0
C20 B:C3J1201 4.0 11.6 1.0
CG2 B:VAL1174 4.2 12.9 1.0
CB B:ARG1173 4.3 8.9 1.0
CD B:ARG1173 4.3 9.8 1.0
C25 B:C3J1201 4.3 12.2 1.0
C26 B:C3J1201 4.4 20.4 1.0
C13 B:C3J1201 4.5 14.3 1.0
C24 B:C3J1201 4.7 16.1 1.0
C12 B:C3J1201 4.7 13.0 1.0
CG B:PRO1110 4.8 14.4 1.0
N15 B:C3J1201 4.9 12.6 1.0
C19 B:C3J1201 4.9 10.6 1.0
CG B:ARG1173 4.9 9.7 1.0
C14 B:C3J1201 5.0 11.8 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 Jul 15 09:48:50 2025

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