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Fluorine in PDB 4uiy: N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide

Protein crystallography data

The structure of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide, PDB code: 4uiy was solved by C.Chung, N.T.Theodoulou, P.Bamborough, P.G.Humphreys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.32 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.350, 44.240, 78.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.643 / 18.47

Fluorine Binding Sites:

The binding sites of Fluorine atom in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide (pdb code 4uiy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide, PDB code: 4uiy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4uiy

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Fluorine binding site 1 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:10.2
occ:0.50
 F20 A:5V21172 0.0 10.2 0.5
F20 A:5V21172 0.9 12.6 0.5
C19 A:5V21172 1.3 12.0 0.5
C19 A:5V21172 1.4 9.7 0.5
F22 A:5V21172 1.6 13.8 0.5
F21 A:5V21172 2.1 11.4 0.5
F22 A:5V21172 2.2 9.8 0.5
C16 A:5V21172 2.3 11.2 0.5
C16 A:5V21172 2.3 9.9 0.5
F21 A:5V21172 2.4 11.8 0.5
C17 A:5V21172 2.8 10.4 0.5
C17 A:5V21172 3.0 8.8 0.5
CD2 A:LEU92 3.3 15.0 1.0
C14 A:5V21172 3.4 10.0 0.5
C14 A:5V21172 3.5 11.1 0.5
C09 A:5V21172 4.1 9.0 0.5
O A:HOH2263 4.2 44.6 1.0
O A:HOH2147 4.2 19.1 1.0
S24 A:5V21172 4.2 8.2 0.5
S24 A:5V21172 4.2 8.7 0.5
O1 A:EDO1171 4.2 33.1 1.0
C09 A:5V21172 4.2 8.4 0.5
C12 A:5V21172 4.5 9.2 0.5
C12 A:5V21172 4.6 10.2 0.5
CG A:LEU92 4.7 12.3 1.0
C10 A:5V21172 4.9 8.4 0.5
C10 A:5V21172 4.9 9.3 0.5
C1 A:EDO1171 4.9 29.1 1.0
CD1 A:LEU92 4.9 14.5 1.0

Fluorine binding site 2 out of 6 in 4uiy

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Fluorine binding site 2 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:11.4
occ:0.50
 F21 A:5V21172 0.0 11.4 0.5
C19 A:5V21172 1.3 9.7 0.5
F21 A:5V21172 1.4 11.8 0.5
F20 A:5V21172 1.4 12.6 0.5
C19 A:5V21172 1.6 12.0 0.5
F22 A:5V21172 2.1 9.8 0.5
F20 A:5V21172 2.1 10.2 0.5
C16 A:5V21172 2.3 9.9 0.5
C16 A:5V21172 2.4 11.2 0.5
F22 A:5V21172 2.7 13.8 0.5
C17 A:5V21172 2.9 8.8 0.5
C17 A:5V21172 2.9 10.4 0.5
O1 A:EDO1171 3.1 33.1 1.0
C1 A:EDO1171 3.2 29.1 1.0
CH2 A:TRP81 3.4 12.2 1.0
C14 A:5V21172 3.4 10.0 0.5
C14 A:5V21172 3.5 11.1 0.5
CZ3 A:TRP81 3.6 12.6 1.0
C2 A:EDO1171 3.9 33.6 1.0
O A:HOH2263 4.0 44.6 1.0
C09 A:5V21172 4.2 8.4 0.5
C09 A:5V21172 4.2 9.0 0.5
O2 A:EDO1171 4.5 38.0 1.0
C12 A:5V21172 4.6 9.2 0.5
CZ2 A:TRP81 4.6 11.6 1.0
C12 A:5V21172 4.7 10.2 0.5
S24 A:5V21172 4.8 8.2 0.5
CE3 A:TRP81 4.9 12.0 1.0
C10 A:5V21172 4.9 8.4 0.5
C10 A:5V21172 4.9 9.3 0.5
S24 A:5V21172 5.0 8.7 0.5

Fluorine binding site 3 out of 6 in 4uiy

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Fluorine binding site 3 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:9.8
occ:0.50
 F22 A:5V21172 0.0 9.8 0.5
F21 A:5V21172 0.9 11.8 0.5
C19 A:5V21172 1.2 12.0 0.5
F22 A:5V21172 1.2 13.8 0.5
C19 A:5V21172 1.3 9.7 0.5
F21 A:5V21172 2.1 11.4 0.5
F20 A:5V21172 2.2 10.2 0.5
C16 A:5V21172 2.3 11.2 0.5
F20 A:5V21172 2.3 12.6 0.5
C16 A:5V21172 2.4 9.9 0.5
C14 A:5V21172 2.7 10.0 0.5
C14 A:5V21172 2.8 11.1 0.5
C17 A:5V21172 3.5 10.4 0.5
CZ3 A:TRP81 3.5 12.6 1.0
C17 A:5V21172 3.6 8.8 0.5
CH2 A:TRP81 3.9 12.2 1.0
C12 A:5V21172 4.1 9.2 0.5
C12 A:5V21172 4.1 10.2 0.5
CD2 A:LEU92 4.3 15.0 1.0
C09 A:5V21172 4.7 9.0 0.5
CE3 A:TRP81 4.7 12.0 1.0
C09 A:5V21172 4.8 8.4 0.5
O1 A:EDO1170 4.8 22.8 1.0
C10 A:5V21172 4.9 9.3 0.5
C10 A:5V21172 4.9 8.4 0.5

Fluorine binding site 4 out of 6 in 4uiy

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Fluorine binding site 4 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:12.6
occ:0.50
 F20 A:5V21172 0.0 12.6 0.5
F20 A:5V21172 0.9 10.2 0.5
C19 A:5V21172 1.2 9.7 0.5
C19 A:5V21172 1.4 12.0 0.5
F21 A:5V21172 1.4 11.4 0.5
F21 A:5V21172 2.1 11.8 0.5
F22 A:5V21172 2.2 13.8 0.5
F22 A:5V21172 2.3 9.8 0.5
C16 A:5V21172 2.3 9.9 0.5
C16 A:5V21172 2.4 11.2 0.5
C17 A:5V21172 2.7 10.4 0.5
C17 A:5V21172 2.8 8.8 0.5
O1 A:EDO1171 3.5 33.1 1.0
C14 A:5V21172 3.6 10.0 0.5
O A:HOH2263 3.6 44.6 1.0
C14 A:5V21172 3.7 11.1 0.5
C1 A:EDO1171 4.1 29.1 1.0
S24 A:5V21172 4.1 8.2 0.5
C09 A:5V21172 4.1 9.0 0.5
CD2 A:LEU92 4.1 15.0 1.0
S24 A:5V21172 4.2 8.7 0.5
C09 A:5V21172 4.2 8.4 0.5
O A:HOH2147 4.6 19.1 1.0
C12 A:5V21172 4.7 9.2 0.5
C2 A:EDO1171 4.8 33.6 1.0
C12 A:5V21172 4.8 10.2 0.5
CH2 A:TRP81 4.8 12.2 1.0
CZ3 A:TRP81 4.8 12.6 1.0
C10 A:5V21172 4.9 8.4 0.5
C10 A:5V21172 5.0 9.3 0.5

Fluorine binding site 5 out of 6 in 4uiy

Go back to Fluorine Binding Sites List in 4uiy
Fluorine binding site 5 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:11.8
occ:0.50
 F21 A:5V21172 0.0 11.8 0.5
F22 A:5V21172 0.9 9.8 0.5
C19 A:5V21172 1.3 9.7 0.5
C19 A:5V21172 1.3 12.0 0.5
F21 A:5V21172 1.4 11.4 0.5
F22 A:5V21172 2.0 13.8 0.5
F20 A:5V21172 2.1 12.6 0.5
C16 A:5V21172 2.4 9.9 0.5
C16 A:5V21172 2.4 11.2 0.5
F20 A:5V21172 2.4 10.2 0.5
CZ3 A:TRP81 3.0 12.6 1.0
C14 A:5V21172 3.0 10.0 0.5
C14 A:5V21172 3.0 11.1 0.5
CH2 A:TRP81 3.1 12.2 1.0
C17 A:5V21172 3.4 10.4 0.5
C17 A:5V21172 3.5 8.8 0.5
CE3 A:TRP81 4.3 12.0 1.0
C12 A:5V21172 4.3 9.2 0.5
C12 A:5V21172 4.3 10.2 0.5
C1 A:EDO1171 4.4 29.1 1.0
CZ2 A:TRP81 4.5 11.6 1.0
O1 A:EDO1171 4.5 33.1 1.0
C09 A:5V21172 4.6 9.0 0.5
C09 A:5V21172 4.7 8.4 0.5
CD2 A:LEU92 4.9 15.0 1.0
C10 A:5V21172 5.0 9.3 0.5
C10 A:5V21172 5.0 8.4 0.5

Fluorine binding site 6 out of 6 in 4uiy

Go back to Fluorine Binding Sites List in 4uiy
Fluorine binding site 6 out of 6 in the N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of N-Terminal Bromodomain of Human BRD4 with N-(1,1-Dioxo-1- Thian-4-Yl)-5-Methyl-4-Oxo-7-3-(Trifluoromethyl)Phenyl-4H, 5H-Thieno-3,2-C-Pyridine-2-Carboximidamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1172

b:13.8
occ:0.50
 F22 A:5V21172 0.0 13.8 0.5
F22 A:5V21172 1.2 9.8 0.5
C19 A:5V21172 1.3 12.0 0.5
C19 A:5V21172 1.6 9.7 0.5
F20 A:5V21172 1.6 10.2 0.5
F21 A:5V21172 2.0 11.8 0.5
F20 A:5V21172 2.2 12.6 0.5
C16 A:5V21172 2.3 11.2 0.5
C16 A:5V21172 2.5 9.9 0.5
F21 A:5V21172 2.7 11.4 0.5
C14 A:5V21172 2.9 10.0 0.5
C14 A:5V21172 2.9 11.1 0.5
CD2 A:LEU92 3.2 15.0 1.0
C17 A:5V21172 3.5 10.4 0.5
C17 A:5V21172 3.7 8.8 0.5
C12 A:5V21172 4.2 9.2 0.5
C12 A:5V21172 4.2 10.2 0.5
C09 A:5V21172 4.7 9.0 0.5
CZ3 A:TRP81 4.7 12.6 1.0
CG A:LEU92 4.7 12.3 1.0
C09 A:5V21172 4.8 8.4 0.5
O1 A:EDO1170 4.9 22.8 1.0
O A:HOH2144 4.9 32.0 1.0
C10 A:5V21172 4.9 9.3 0.5
C10 A:5V21172 5.0 8.4 0.5

Reference:

N.H.Theodoulou, P.Bamborough, A.J.Bannister, I.Becher, R.A.Bit, K.H.Che, C.Chung, A.Dittmann, G.Drewes, D.H.Drewry, L.Gordon, P.Grandi, M.Leveridge, M.Lindon, A.Michon, J.Molnar, S.C.Robson, N.C.O.Tomkinson, T.Kouzarides, R.K.Prinjha, P.G.Humphreys. The Discovery of I-BRD9, A Selective Cell Active Chemical Probe For Bromodomain Containing Protein 9 Inhibition. J.Med.Chem. 2015.
ISSN: ESSN 1520-4804
PubMed: 25856009
DOI: 10.1021/ACS.JMEDCHEM.5B00256
Page generated: Thu Aug 1 06:05:35 2024

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