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Fluorine in PDB 5ktx: Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone)

Enzymatic activity of Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone)

All present enzymatic activity of Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone):
2.3.1.48;

Protein crystallography data

The structure of Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone), PDB code: 5ktx was solved by J.M.Murray, C.Noland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.66 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.255, 49.320, 80.253, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone) (pdb code 5ktx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone), PDB code: 5ktx:

Fluorine binding site 1 out of 1 in 5ktx

Go back to Fluorine Binding Sites List in 5ktx
Fluorine binding site 1 out of 1 in the Crebbp Bromodomain in Complex with CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone)


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 CPD59 ((S)-1-(3-((2-Fluoro-4-(1- Methyl-1H-Pyrazol-4-Yl)Phenyl)Amino)-1-(Tetrahydrofuran-3-Yl)-6,7- Dihydro-1H-Pyrazolo[4,3-C]Pyridin-5(4H)-Yl)Ethanone) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:12.5
occ:1.00
 F25 A:6XH1201 0.0 12.5 1.0
C24 A:6XH1201 1.3 10.8 1.0
C19 A:6XH1201 2.4 10.2 1.0
C23 A:6XH1201 2.4 11.7 1.0
N18 A:6XH1201 2.7 11.7 1.0
CA A:PRO1110 3.4 7.8 1.0
O A:HOH1499 3.4 44.5 1.0
O A:HOH1469 3.4 28.2 1.0
O A:LEU1109 3.5 9.4 1.0
C20 A:6XH1201 3.6 11.3 1.0
C22 A:6XH1201 3.6 12.2 1.0
O A:HOH1448 3.7 17.0 1.0
N A:PRO1110 3.8 7.5 1.0
C A:LEU1109 3.9 8.5 1.0
NE2 A:GLN1113 4.0 14.2 1.0
O A:HOH1506 4.1 34.3 1.0
CB A:PRO1110 4.1 9.5 1.0
O A:HOH1480 4.1 46.9 1.0
C21 A:6XH1201 4.1 11.3 1.0
C9 A:6XH1201 4.1 10.1 1.0
O A:HOH1525 4.4 41.8 1.0
CG A:PRO1110 4.4 9.7 1.0
C A:PRO1110 4.4 8.1 1.0
CD A:PRO1110 4.7 8.4 1.0
O A:HOH1395 4.7 22.5 1.0
O A:PRO1110 4.7 9.1 1.0
CB A:LEU1109 4.9 10.1 1.0
C26 A:6XH1201 4.9 11.0 1.0
N10 A:6XH1201 4.9 11.6 1.0
O A:HOH1400 4.9 17.1 1.0
CA A:LEU1109 5.0 8.5 1.0
CD A:GLN1113 5.0 17.7 1.0

Reference:

T.D.Crawford, F.A.Romero, K.W.Lai, V.Tsui, A.M.Taylor, G.De Leon Boenig, C.L.Noland, J.Murray, J.Ly, E.F.Choo, T.L.Hunsaker, E.W.Chan, M.Merchant, S.Kharbanda, K.E.Gascoigne, S.Kaufman, M.H.Beresini, J.Liao, W.Liu, K.X.Chen, Z.Chen, A.R.Conery, A.Cote, H.Jayaram, Y.Jiang, J.R.Kiefer, T.Kleinheinz, Y.Li, J.Maher, E.Pardo, F.Poy, K.L.Spillane, F.Wang, J.Wang, X.Wei, Z.Xu, Z.Xu, I.Yen, L.Zawadzke, X.Zhu, S.Bellon, R.Cummings, A.G.Cochran, B.K.Albrecht, S.Magnuson. Discovery of A Potent and Selective in Vivo Probe (Gne-272) For the Bromodomains of Cbp/EP300. J. Med. Chem. V. 59 10549 2016.
ISSN: ISSN 1520-4804
PubMed: 27682507
DOI: 10.1021/ACS.JMEDCHEM.6B01022
Page generated: Tue Jul 15 04:53:36 2025

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