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Fluorine in PDB 5w0l: Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridin-5-Yl)Ethan-1-One), PDB code: 5w0l 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) 28.08 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.648, 34.055, 80.887, 90.00, 90.01, 90.00
R / Rfree (%) 19.3 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridin-5-Yl)Ethan-1-One) (pdb code 5w0l). 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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-Yl)-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridin-5-Yl)Ethan-1-One), PDB code: 5w0l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5w0l

Go back to Fluorine Binding Sites List in 5w0l
Fluorine binding site 1 out of 4 in the Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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:49.4
occ:1.00
 F A:9UD1201 0.0 49.4 1.0
C10 A:9UD1201 1.4 33.4 1.0
F1 A:9UD1201 2.2 55.6 1.0
C9 A:9UD1201 2.4 21.1 1.0
C8 A:9UD1201 2.7 17.0 1.0
CZ A:ARG1173 3.2 22.7 1.0
NE A:ARG1173 3.4 18.9 1.0
NH2 A:ARG1173 3.5 24.4 1.0
CG2 A:VAL1174 3.6 17.2 1.0
NH1 A:ARG1173 3.7 21.0 1.0
C4 A:9UD1201 3.7 19.6 1.0
CB A:ARG1173 3.8 14.1 1.0
O A:HOH1392 3.9 46.1 1.0
CD A:ARG1173 4.0 17.4 1.0
C7 A:9UD1201 4.0 15.9 1.0
C16 A:9UD1201 4.2 22.4 1.0
N3 A:9UD1201 4.3 18.1 1.0
C2 A:9UD1201 4.3 24.0 1.0
CG A:PRO1110 4.4 15.9 1.0
N A:VAL1174 4.5 15.8 1.0
CG A:ARG1173 4.5 16.3 1.0
C3 A:9UD1201 4.5 39.4 1.0
C14 A:9UD1201 4.7 16.9 1.0
C5 A:9UD1201 4.8 14.6 1.0
O A:HOH1361 4.8 27.8 1.0
N4 A:9UD1201 4.8 17.5 1.0
N2 A:9UD1201 4.9 18.3 1.0
C A:ARG1173 4.9 16.5 1.0
CB A:VAL1174 4.9 16.6 1.0
CA A:ARG1173 4.9 14.2 1.0
C6 A:9UD1201 4.9 17.8 1.0
CA A:VAL1174 5.0 18.2 1.0

Fluorine binding site 2 out of 4 in 5w0l

Go back to Fluorine Binding Sites List in 5w0l
Fluorine binding site 2 out of 4 in the Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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:55.6
occ:1.00
 F1 A:9UD1201 0.0 55.6 1.0
C10 A:9UD1201 1.4 33.4 1.0
F A:9UD1201 2.2 49.4 1.0
C9 A:9UD1201 2.4 21.1 1.0
NH1 A:ARG1173 2.6 21.0 1.0
C3 A:9UD1201 2.8 39.4 1.0
C2 A:9UD1201 2.9 24.0 1.0
C4 A:9UD1201 2.9 19.6 1.0
CZ A:ARG1173 3.0 22.7 1.0
O A:HOH1392 3.3 46.1 1.0
NE A:ARG1173 3.4 18.9 1.0
CD A:ARG1173 3.5 17.4 1.0
C8 A:9UD1201 3.5 17.0 1.0
N1 A:9UD1201 3.7 34.7 1.0
C1 A:9UD1201 3.8 29.3 1.0
NH2 A:ARG1173 3.8 24.4 1.0
N A:9UD1201 4.2 31.4 1.0
C5 A:9UD1201 4.3 14.6 1.0
CB A:ARG1173 4.3 14.1 1.0
CE2 A:PHE1177 4.4 18.4 1.0
CG A:ARG1173 4.5 16.3 1.0
C7 A:9UD1201 4.7 15.9 1.0

Fluorine binding site 3 out of 4 in 5w0l

Go back to Fluorine Binding Sites List in 5w0l
Fluorine binding site 3 out of 4 in the Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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
B:F1201

b:49.3
occ:1.00
 F B:9UD1201 0.0 49.3 1.0
C10 B:9UD1201 1.4 34.7 1.0
F1 B:9UD1201 2.2 56.7 1.0
C9 B:9UD1201 2.4 26.6 1.0
C8 B:9UD1201 2.7 20.1 1.0
CZ B:ARG1173 3.2 19.8 1.0
NH1 B:ARG1173 3.3 24.6 1.0
NE B:ARG1173 3.3 15.2 1.0
CG2 B:VAL1174 3.6 14.9 1.0
C4 B:9UD1201 3.7 25.0 1.0
CB B:ARG1173 3.7 13.0 1.0
NH2 B:ARG1173 3.7 23.6 1.0
CD B:ARG1173 4.0 16.6 1.0
C7 B:9UD1201 4.1 17.9 1.0
C16 B:9UD1201 4.2 19.2 1.0
O B:HOH1392 4.2 42.2 1.0
C2 B:9UD1201 4.3 28.3 1.0
CG B:PRO1110 4.4 15.8 1.0
N3 B:9UD1201 4.4 17.7 1.0
N B:VAL1174 4.4 13.6 1.0
CG B:ARG1173 4.5 14.0 1.0
C3 B:9UD1201 4.5 32.4 1.0
C14 B:9UD1201 4.8 18.2 1.0
C5 B:9UD1201 4.8 19.6 1.0
C B:ARG1173 4.8 16.1 1.0
CA B:ARG1173 4.8 12.7 1.0
O B:HOH1366 4.8 30.4 1.0
CB B:VAL1174 4.9 13.0 1.0
CE2 B:PHE1177 4.9 18.4 1.0
N4 B:9UD1201 4.9 16.3 1.0
CA B:VAL1174 4.9 14.6 1.0
N2 B:9UD1201 4.9 19.6 1.0
C6 B:9UD1201 5.0 18.1 1.0
CB B:PRO1110 5.0 16.4 1.0

Fluorine binding site 4 out of 4 in 5w0l

Go back to Fluorine Binding Sites List in 5w0l
Fluorine binding site 4 out of 4 in the Crebbp Bromodomain in Complex with CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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 CPD10 (1-(3-(7-(Difluoromethyl)-6- (1-Methyl-1H-Pyrazol-4-Yl)-3,4-Dihydroquinolin-1(2H)-Yl)-1- (Tetrahydro-2H-Pyran-4-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
B:F1201

b:56.7
occ:1.00
 F1 B:9UD1201 0.0 56.7 1.0
C10 B:9UD1201 1.4 34.7 1.0
F B:9UD1201 2.2 49.3 1.0
C9 B:9UD1201 2.3 26.6 1.0
NH2 B:ARG1173 2.6 23.6 1.0
C2 B:9UD1201 2.8 28.3 1.0
C4 B:9UD1201 2.9 25.0 1.0
CZ B:ARG1173 2.9 19.8 1.0
C3 B:9UD1201 3.0 32.4 1.0
O B:HOH1392 3.2 42.2 1.0
NE B:ARG1173 3.4 15.2 1.0
C8 B:9UD1201 3.5 20.1 1.0
NH1 B:ARG1173 3.6 24.6 1.0
C1 B:9UD1201 3.6 28.6 1.0
CD B:ARG1173 3.7 16.6 1.0
N1 B:9UD1201 3.8 33.7 1.0
N B:9UD1201 4.1 29.8 1.0
C5 B:9UD1201 4.2 19.6 1.0
O B:HOH1397 4.4 34.0 1.0
CB B:ARG1173 4.4 13.0 1.0
CE2 B:PHE1177 4.6 18.4 1.0
C7 B:9UD1201 4.6 17.9 1.0
CG B:ARG1173 4.7 14.0 1.0
O B:HOH1362 4.8 20.2 1.0
C6 B:9UD1201 4.9 18.1 1.0

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: Thu Aug 1 16:22:10 2024

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