Fluorine in PDB 5w0i: Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)

Enzymatic activity of Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)

All present enzymatic activity of Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One):
2.3.1.48;

Protein crystallography data

The structure of Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One), PDB code: 5w0i 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) 31.06 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.879, 48.602, 80.763, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One) (pdb code 5w0i). 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 CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One), PDB code: 5w0i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w0i

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Fluorine binding site 1 out of 4 in the Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)


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 CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:29.6
occ:0.49
 F34 A:9UA1201 0.0 29.6 0.5
F34 A:9UA1201 0.4 29.8 0.5
C33 A:9UA1201 1.4 25.6 0.5
C33 A:9UA1201 1.6 25.4 0.5
F35 A:9UA1201 2.2 28.0 0.5
F35 A:9UA1201 2.3 28.4 0.5
C24 A:9UA1201 2.4 21.6 0.5
C24 A:9UA1201 2.5 21.7 0.5
C23 A:9UA1201 2.6 19.1 0.5
C23 A:9UA1201 2.6 19.3 0.5
CZ A:ARG1173 3.1 19.7 1.0
NH2 A:ARG1173 3.2 20.5 1.0
NE A:ARG1173 3.3 18.3 1.0
NH1 A:ARG1173 3.6 21.4 1.0
CG2 A:VAL1174 3.6 18.1 1.0
C25 A:9UA1201 3.7 21.4 0.5
C16 A:9UA1201 3.8 20.5 0.5
CB A:ARG1173 3.8 17.7 1.0
C25 A:9UA1201 3.8 21.9 0.5
C16 A:9UA1201 3.9 20.4 0.5
CD A:ARG1173 3.9 19.9 1.0
C22 A:9UA1201 4.0 18.6 0.5
C22 A:9UA1201 4.0 18.5 0.5
N10 A:9UA1201 4.0 18.9 0.5
N10 A:9UA1201 4.0 18.8 0.5
O15 A:9UA1201 4.1 23.8 0.5
C27 A:9UA1201 4.3 23.0 0.5
O15 A:9UA1201 4.5 23.9 0.5
CG A:ARG1173 4.5 18.6 1.0
C28 A:9UA1201 4.5 24.3 0.5
N A:VAL1174 4.5 15.5 1.0
C9 A:9UA1201 4.6 17.8 0.5
N11 A:9UA1201 4.6 19.3 0.5
C9 A:9UA1201 4.6 18.0 0.5
O A:HOH1391 4.6 30.5 1.0
N11 A:9UA1201 4.6 19.1 0.5
C27 A:9UA1201 4.6 23.1 0.5
CG A:PRO1110 4.7 17.7 1.0
C26 A:9UA1201 4.7 21.2 0.5
N17 A:9UA1201 4.8 19.1 0.5
N17 A:9UA1201 4.8 19.0 0.5
C31 A:9UA1201 4.8 24.1 0.5
C26 A:9UA1201 4.8 21.1 0.5
C12 A:9UA1201 4.9 20.9 0.5
C12 A:9UA1201 4.9 21.0 0.5
C21 A:9UA1201 4.9 18.3 0.5
C21 A:9UA1201 4.9 18.4 0.5
CA A:ARG1173 4.9 16.9 1.0
CB A:VAL1174 4.9 17.0 1.0
C A:ARG1173 5.0 17.2 1.0

Fluorine binding site 2 out of 4 in 5w0i

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Fluorine binding site 2 out of 4 in the Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)


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 CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:29.8
occ:0.51
 F34 A:9UA1201 0.0 29.8 0.5
F34 A:9UA1201 0.4 29.6 0.5
C33 A:9UA1201 1.2 25.6 0.5
C33 A:9UA1201 1.4 25.4 0.5
F35 A:9UA1201 2.2 28.0 0.5
C24 A:9UA1201 2.2 21.6 0.5
F35 A:9UA1201 2.3 28.4 0.5
C24 A:9UA1201 2.3 21.7 0.5
C23 A:9UA1201 2.7 19.1 0.5
C23 A:9UA1201 2.7 19.3 0.5
CZ A:ARG1173 2.8 19.7 1.0
NH2 A:ARG1173 3.1 20.5 1.0
NE A:ARG1173 3.1 18.3 1.0
NH1 A:ARG1173 3.2 21.4 1.0
C25 A:9UA1201 3.5 21.4 0.5
C25 A:9UA1201 3.6 21.9 0.5
CD A:ARG1173 3.8 19.9 1.0
CB A:ARG1173 3.9 17.7 1.0
C16 A:9UA1201 4.0 20.5 0.5
CG2 A:VAL1174 4.0 18.1 1.0
C22 A:9UA1201 4.0 18.6 0.5
C27 A:9UA1201 4.0 23.0 0.5
C16 A:9UA1201 4.1 20.4 0.5
C22 A:9UA1201 4.1 18.5 0.5
O15 A:9UA1201 4.2 23.8 0.5
N10 A:9UA1201 4.2 18.9 0.5
C28 A:9UA1201 4.2 24.3 0.5
N10 A:9UA1201 4.2 18.8 0.5
C27 A:9UA1201 4.3 23.1 0.5
CG A:ARG1173 4.4 18.6 1.0
O A:HOH1391 4.5 30.5 1.0
C31 A:9UA1201 4.5 24.1 0.5
O15 A:9UA1201 4.5 23.9 0.5
C26 A:9UA1201 4.6 21.2 0.5
C26 A:9UA1201 4.7 21.1 0.5
C9 A:9UA1201 4.8 17.8 0.5
C9 A:9UA1201 4.8 18.0 0.5
N A:VAL1174 4.8 15.5 1.0
CG A:PRO1110 4.8 17.7 1.0
C21 A:9UA1201 4.8 18.3 0.5
N11 A:9UA1201 4.9 19.3 0.5
N11 A:9UA1201 4.9 19.1 0.5
C21 A:9UA1201 4.9 18.4 0.5
N17 A:9UA1201 4.9 19.1 0.5
N17 A:9UA1201 4.9 19.0 0.5

Fluorine binding site 3 out of 4 in 5w0i

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Fluorine binding site 3 out of 4 in the Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)


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 CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:28.0
occ:0.49
 F35 A:9UA1201 0.0 28.0 0.5
F35 A:9UA1201 0.2 28.4 0.5
C33 A:9UA1201 1.4 25.6 0.5
C33 A:9UA1201 1.4 25.4 0.5
F34 A:9UA1201 2.2 29.8 0.5
F34 A:9UA1201 2.2 29.6 0.5
C24 A:9UA1201 2.4 21.6 0.5
C24 A:9UA1201 2.4 21.7 0.5
C28 A:9UA1201 3.0 24.3 0.5
C25 A:9UA1201 3.1 21.4 0.5
C23 A:9UA1201 3.2 19.1 0.5
C23 A:9UA1201 3.3 19.3 0.5
CE2 A:PHE1177 3.3 20.1 1.0
C25 A:9UA1201 3.3 21.9 0.5
C27 A:9UA1201 3.3 23.0 0.5
CB A:ARG1173 3.4 17.7 1.0
CG A:PRO1110 3.5 17.7 1.0
C31 A:9UA1201 3.5 24.1 0.5
CD2 A:PHE1177 3.5 19.5 1.0
C27 A:9UA1201 3.7 23.1 0.5
CD A:ARG1173 4.0 19.9 1.0
CG2 A:VAL1174 4.2 18.1 1.0
N29 A:9UA1201 4.2 25.6 0.5
NE A:ARG1173 4.2 18.3 1.0
CG A:ARG1173 4.3 18.6 1.0
CZ A:PHE1177 4.3 18.7 1.0
CZ A:ARG1173 4.3 19.7 1.0
CD A:PRO1110 4.4 17.9 1.0
C26 A:9UA1201 4.4 21.2 0.5
NH1 A:ARG1173 4.4 21.4 1.0
N A:VAL1174 4.4 15.5 1.0
C A:ARG1173 4.5 17.2 1.0
C22 A:9UA1201 4.5 18.6 0.5
C22 A:9UA1201 4.5 18.5 0.5
C26 A:9UA1201 4.5 21.1 0.5
CB A:PRO1110 4.6 18.4 1.0
CA A:ARG1173 4.6 16.9 1.0
C31 A:9UA1201 4.6 24.5 0.5
CG A:PHE1177 4.7 18.2 1.0
N30 A:9UA1201 4.8 25.4 0.5
CA A:VAL1174 4.8 16.2 1.0
O A:ARG1173 4.8 16.5 1.0
C21 A:9UA1201 5.0 18.3 0.5

Fluorine binding site 4 out of 4 in 5w0i

Go back to Fluorine Binding Sites List in 5w0i
Fluorine binding site 4 out of 4 in the Crebbp Bromodomain in Complex with CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One)


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 CPD8 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydrofuran-3-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3-C]Pyridin- 5-Yl)Ethan-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:28.4
occ:0.51
 F35 A:9UA1201 0.0 28.4 0.5
F35 A:9UA1201 0.2 28.0 0.5
C33 A:9UA1201 1.4 25.6 0.5
C33 A:9UA1201 1.4 25.4 0.5
F34 A:9UA1201 2.3 29.8 0.5
F34 A:9UA1201 2.3 29.6 0.5
C24 A:9UA1201 2.4 21.6 0.5
C24 A:9UA1201 2.4 21.7 0.5
C28 A:9UA1201 2.8 24.3 0.5
C25 A:9UA1201 3.1 21.4 0.5
C27 A:9UA1201 3.2 23.0 0.5
C25 A:9UA1201 3.2 21.9 0.5
CE2 A:PHE1177 3.2 20.1 1.0
C23 A:9UA1201 3.3 19.1 0.5
C31 A:9UA1201 3.3 24.1 0.5
C23 A:9UA1201 3.3 19.3 0.5
CB A:ARG1173 3.5 17.7 1.0
CG A:PRO1110 3.5 17.7 1.0
CD2 A:PHE1177 3.5 19.5 1.0
C27 A:9UA1201 3.6 23.1 0.5
CD A:ARG1173 4.0 19.9 1.0
N29 A:9UA1201 4.0 25.6 0.5
NE A:ARG1173 4.2 18.3 1.0
CZ A:PHE1177 4.3 18.7 1.0
CG A:ARG1173 4.3 18.6 1.0
CG2 A:VAL1174 4.3 18.1 1.0
CZ A:ARG1173 4.3 19.7 1.0
C26 A:9UA1201 4.3 21.2 0.5
NH1 A:ARG1173 4.3 21.4 1.0
CD A:PRO1110 4.4 17.9 1.0
C26 A:9UA1201 4.5 21.1 0.5
C31 A:9UA1201 4.5 24.5 0.5
C22 A:9UA1201 4.5 18.6 0.5
C22 A:9UA1201 4.5 18.5 0.5
N A:VAL1174 4.6 15.5 1.0
C A:ARG1173 4.6 17.2 1.0
N30 A:9UA1201 4.6 25.4 0.5
CB A:PRO1110 4.7 18.4 1.0
CA A:ARG1173 4.7 16.9 1.0
CG A:PHE1177 4.7 18.2 1.0
N30 A:9UA1201 4.9 26.0 0.5
C21 A:9UA1201 4.9 18.3 0.5
O A:ARG1173 4.9 16.5 1.0
C28 A:9UA1201 5.0 24.9 0.5
O A:HOH1357 5.0 22.0 1.0
CA A:VAL1174 5.0 16.2 1.0
C21 A:9UA1201 5.0 18.4 0.5

Reference:

F.A.Romero, J.Murray, K.W.Lai, V.Tsui, B.K.Albrecht, L.An, M.H.Beresini, G.De Leon Boenig, S.M.Bronner, E.W.Chan, K.X.Chen, Z.Chen, E.F.Choo, K.Clagg, K.Clark, T.D.Crawford, P.Cyr, D.De Almeida Nagata, K.E.Gascoigne, J.L.Grogan, G.Hatzivassiliou, W.Huang, T.L.Hunsaker, S.Kaufman, S.G.Koenig, R.Li, Y.Li, X.Liang, J.Liao, W.Liu, J.Ly, J.Maher, C.Masui, M.Merchant, Y.Ran, A.M.Taylor, J.Wai, F.Wang, X.Wei, D.Yu, B.Y.Zhu, X.Zhu, S.Magnuson. Gne-781, A Highly Advanced Potent and Selective Bromodomain Inhibitor of Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (Cbp). J. Med. Chem. V. 60 9162 2017.
ISSN: ISSN 1520-4804
PubMed: 28892380
DOI: 10.1021/ACS.JMEDCHEM.7B00796
Page generated: Sun Dec 13 12:41:14 2020

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