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Fluorine in PDB 5w0e: Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide)

Enzymatic activity of Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide)

All present enzymatic activity of Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide):
2.3.1.48;

Protein crystallography data

The structure of Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide), PDB code: 5w0e 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) 26.34 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.815, 49.386, 79.819, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 26

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide) (pdb code 5w0e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide), PDB code: 5w0e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5w0e

Go back to Fluorine Binding Sites List in 5w0e
Fluorine binding site 1 out of 2 in the Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-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 CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:28.5
occ:1.00
 F36 A:9U41201 0.0 28.5 1.0
C35 A:9U41201 1.4 25.9 1.0
F37 A:9U41201 2.2 29.1 1.0
C26 A:9U41201 2.4 19.4 1.0
C25 A:9U41201 2.6 15.7 1.0
CZ A:ARG1173 3.0 17.1 1.0
NH2 A:ARG1173 3.2 17.9 1.0
NE A:ARG1173 3.2 15.0 1.0
NH1 A:ARG1173 3.4 16.4 1.0
C27 A:9U41201 3.7 16.5 1.0
CG2 A:VAL1174 3.9 15.1 1.0
CB A:ARG1173 3.9 13.3 1.0
CD A:ARG1173 3.9 17.5 1.0
C24 A:9U41201 4.0 16.4 1.0
C14 A:9U41201 4.1 18.6 1.0
N11 A:9U41201 4.3 18.4 1.0
C29 A:9U41201 4.3 19.9 1.0
C30 A:9U41201 4.5 23.3 1.0
CG A:ARG1173 4.6 16.0 1.0
C10 A:9U41201 4.6 17.8 1.0
CG A:PRO1110 4.7 18.8 1.0
N A:VAL1174 4.7 13.6 1.0
N12 A:9U41201 4.7 17.6 1.0
C28 A:9U41201 4.8 17.2 1.0
N19 A:9U41201 4.8 17.1 1.0
C23 A:9U41201 4.9 15.5 1.0

Fluorine binding site 2 out of 2 in 5w0e

Go back to Fluorine Binding Sites List in 5w0e
Fluorine binding site 2 out of 2 in the Crebbp Bromodomain in Complex with CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-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 CPD19 (3-(7-(Difluoromethyl)-6-(1- Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-N-Methyl-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:29.1
occ:1.00
 F37 A:9U41201 0.0 29.1 1.0
C35 A:9U41201 1.4 25.9 1.0
F36 A:9U41201 2.2 28.5 1.0
C26 A:9U41201 2.4 19.4 1.0
C30 A:9U41201 3.1 23.3 1.0
C27 A:9U41201 3.2 16.5 1.0
CG A:PRO1110 3.2 18.8 1.0
C25 A:9U41201 3.2 15.7 1.0
CE2 A:PHE1177 3.4 15.2 1.0
C29 A:9U41201 3.4 19.9 1.0
CB A:ARG1173 3.5 13.3 1.0
CD2 A:PHE1177 3.6 15.2 1.0
CG2 A:VAL1174 4.1 15.1 1.0
CD A:ARG1173 4.1 17.5 1.0
NE A:ARG1173 4.1 15.0 1.0
CD A:PRO1110 4.2 15.7 1.0
CB A:PRO1110 4.3 15.4 1.0
N31 A:9U41201 4.3 21.8 1.0
N A:VAL1174 4.3 13.6 1.0
CZ A:ARG1173 4.3 17.1 1.0
CG A:ARG1173 4.4 16.0 1.0
NH1 A:ARG1173 4.4 16.4 1.0
C A:ARG1173 4.4 14.3 1.0
C28 A:9U41201 4.4 17.2 1.0
C24 A:9U41201 4.5 16.4 1.0
CZ A:PHE1177 4.6 15.4 1.0
CA A:ARG1173 4.6 13.5 1.0
CA A:VAL1174 4.7 12.7 1.0
C33 A:9U41201 4.7 25.0 1.0
CG A:PHE1177 4.8 13.2 1.0
O A:ARG1173 4.9 14.5 1.0
NH2 A:ARG1173 5.0 17.9 1.0
C23 A:9U41201 5.0 15.5 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 08:45:32 2025

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