Fluorine in PDB 5vzs: BRD4-BD1 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)

Protein crystallography data

The structure of BRD4-BD1 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: 5vzs 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) 29.23 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 29.986, 41.878, 59.895, 102.08, 106.79, 89.36
R / Rfree (%) 19.2 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BRD4-BD1 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 5vzs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the BRD4-BD1 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: 5vzs:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5vzs

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Fluorine binding site 1 out of 4 in the BRD4-BD1 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 BRD4-BD1 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:F202

b:59.8
occ:1.00
 F36 A:9U4202 0.0 59.8 1.0
C35 A:9U4202 1.4 52.7 1.0
F37 A:9U4202 2.3 62.1 1.0
C26 A:9U4202 2.4 34.4 1.0
C27 A:9U4202 3.0 34.1 1.0
C30 A:9U4202 3.1 41.7 1.0
C29 A:9U4202 3.1 41.8 1.0
O A:LEU92 3.3 42.4 1.0
C25 A:9U4202 3.4 30.3 1.0
CA A:LEU92 3.7 35.2 1.0
C A:LEU92 3.9 42.4 1.0
N31 A:9U4202 4.0 45.8 1.0
C33 A:9U4202 4.0 36.4 1.0
CB A:LEU92 4.1 35.5 1.0
CD2 A:LEU92 4.1 37.8 1.0
C28 A:9U4202 4.3 33.1 1.0
N32 A:9U4202 4.5 44.9 1.0
C24 A:9U4202 4.6 29.0 1.0
O A:LYS91 4.7 51.2 1.0
CG A:LEU92 4.7 35.9 1.0
C23 A:9U4202 5.0 36.2 1.0
N A:LEU92 5.0 38.6 1.0

Fluorine binding site 2 out of 4 in 5vzs

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Fluorine binding site 2 out of 4 in the BRD4-BD1 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 BRD4-BD1 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:F202

b:62.1
occ:1.00
 F37 A:9U4202 0.0 62.1 1.0
C35 A:9U4202 1.4 52.7 1.0
F36 A:9U4202 2.3 59.8 1.0
C26 A:9U4202 2.4 34.4 1.0
C25 A:9U4202 2.6 30.3 1.0
O A:LEU92 3.5 42.4 1.0
C27 A:9U4202 3.7 34.1 1.0
C18 A:9U4202 3.9 33.8 1.0
C24 A:9U4202 4.0 29.0 1.0
N11 A:9U4202 4.0 30.2 1.0
CB A:LEU92 4.3 35.5 1.0
C29 A:9U4202 4.4 41.8 1.0
C A:LEU92 4.4 42.4 1.0
C30 A:9U4202 4.5 41.7 1.0
CD2 A:LEU94 4.5 37.9 1.0
C10 A:9U4202 4.6 24.3 1.0
CA A:LEU92 4.6 35.2 1.0
N12 A:9U4202 4.7 28.1 1.0
C28 A:9U4202 4.7 33.1 1.0
N19 A:9U4202 4.8 28.4 1.0
CG A:LEU94 4.8 42.8 1.0
C23 A:9U4202 4.9 36.2 1.0
CD2 A:LEU92 4.9 37.8 1.0
C17 A:9U4202 4.9 32.9 1.0
C13 A:9U4202 4.9 25.8 1.0

Fluorine binding site 3 out of 4 in 5vzs

Go back to Fluorine Binding Sites List in 5vzs
Fluorine binding site 3 out of 4 in the BRD4-BD1 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 3 of BRD4-BD1 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
B:F203

b:46.3
occ:1.00
 F36 B:9U4203 0.0 46.3 1.0
C35 B:9U4203 1.4 40.7 1.0
F37 B:9U4203 2.3 48.5 1.0
C26 B:9U4203 2.4 30.2 1.0
C25 B:9U4203 2.7 24.3 1.0
C27 B:9U4203 3.7 27.6 1.0
CB B:ILE146 3.8 27.0 1.0
CD1 B:ILE146 4.0 27.9 1.0
C24 B:9U4203 4.1 22.9 1.0
C14 B:9U4203 4.1 33.4 1.0
CG1 B:ILE146 4.1 19.3 1.0
N11 B:9U4203 4.2 29.4 1.0
O B:HOH349 4.3 26.3 1.0
C29 B:9U4203 4.4 30.5 1.0
CA B:ILE146 4.6 25.7 1.0
C10 B:9U4203 4.6 23.5 1.0
N12 B:9U4203 4.7 27.1 1.0
C30 B:9U4203 4.7 27.2 1.0
C28 B:9U4203 4.8 26.7 1.0
CG2 B:ILE146 4.9 21.6 1.0
N B:ILE146 4.9 20.1 1.0
N19 B:9U4203 4.9 28.4 1.0
C23 B:9U4203 4.9 30.5 1.0

Fluorine binding site 4 out of 4 in 5vzs

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Fluorine binding site 4 out of 4 in the BRD4-BD1 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 4 of BRD4-BD1 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
B:F203

b:48.5
occ:1.00
 F37 B:9U4203 0.0 48.5 1.0
C35 B:9U4203 1.4 40.7 1.0
F36 B:9U4203 2.3 46.3 1.0
C26 B:9U4203 2.4 30.2 1.0
CE B:MET149 3.2 44.8 1.0
C27 B:9U4203 3.2 27.6 1.0
C30 B:9U4203 3.2 27.2 1.0
C25 B:9U4203 3.2 24.3 1.0
SD B:MET149 3.3 47.2 1.0
C29 B:9U4203 3.5 30.5 1.0
CG B:PRO82 3.6 25.2 1.0
CG1 B:ILE146 3.9 19.3 1.0
CB B:PRO82 4.0 22.8 1.0
CD B:PRO82 4.0 20.9 1.0
CB B:ILE146 4.0 27.0 1.0
CA B:ILE146 4.2 25.7 1.0
CD1 B:ILE146 4.3 27.9 1.0
N31 B:9U4203 4.4 27.8 1.0
C28 B:9U4203 4.4 26.7 1.0
C24 B:9U4203 4.5 22.9 1.0
C33 B:9U4203 4.7 29.7 1.0
CG B:MET149 4.8 32.5 1.0
N B:ILE146 4.9 20.1 1.0
C23 B:9U4203 4.9 30.5 1.0

Reference:

J.M.Murray, J.M.Murray. N/A N/A.
Page generated: Sun Dec 13 12:41:11 2020

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