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Fluorine in PDB 3qgf: Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide

Enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide, PDB code: 3qgf was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.44 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.900, 90.100, 231.300, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.9

Other elements in 3qgf:

The structure of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide (pdb code 3qgf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide, PDB code: 3qgf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 1 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:25.3
occ:1.00
 F35 A:46F602 0.0 25.3 1.0
C24 A:46F602 1.3 24.3 1.0
F36 A:46F602 2.1 20.3 1.0
F37 A:46F602 2.2 27.7 1.0
O34 A:46F602 2.3 26.0 1.0
C13 A:46F602 2.7 18.4 1.0
C5 A:46F602 3.0 16.8 1.0
CG2 A:ILE462 3.2 18.9 1.0
C6 A:46F602 3.8 12.8 1.0
CD1 A:LEU466 4.0 17.9 1.0
CG1 A:ILE462 4.0 14.2 1.0
C7 A:46F602 4.1 16.5 1.0
CG2 A:ILE413 4.2 19.8 1.0
CB A:ILE462 4.2 15.5 1.0
CG A:LEU547 4.4 46.6 1.0
CD1 A:ILE462 4.5 22.6 1.0
CD1 A:ILE454 4.5 25.6 1.0
CD1 A:LEU547 4.6 47.0 1.0
CD1 A:ILE413 4.6 13.1 1.0
CG A:LEU466 4.7 17.7 1.0
C8 A:46F602 4.8 14.7 1.0
C14 A:46F602 4.9 16.3 1.0

Fluorine binding site 2 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 2 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:20.3
occ:1.00
 F36 A:46F602 0.0 20.3 1.0
C24 A:46F602 1.3 24.3 1.0
F35 A:46F602 2.1 25.3 1.0
O34 A:46F602 2.2 26.0 1.0
F37 A:46F602 2.3 27.7 1.0
CB A:TRP550 3.2 22.3 1.0
C13 A:46F602 3.5 18.4 1.0
CG A:TRP550 3.6 22.6 1.0
CD2 A:TRP550 3.9 22.3 1.0
CD1 A:ILE454 4.0 25.6 1.0
CG1 A:ILE454 4.0 21.6 1.0
CE3 A:TRP550 4.0 23.7 1.0
CD1 A:TYR452 4.0 22.4 1.0
O A:LEU547 4.2 45.8 1.0
CG1 A:ILE462 4.2 14.2 1.0
C5 A:46F602 4.2 16.8 1.0
CD1 A:ILE462 4.3 22.6 1.0
CG A:TYR452 4.3 19.7 1.0
C6 A:46F602 4.4 12.8 1.0
CD1 A:TRP550 4.4 25.1 1.0
CE1 A:TYR452 4.5 22.7 1.0
CG2 A:ILE462 4.6 18.9 1.0
CB A:TYR452 4.6 18.4 1.0
CA A:TRP550 4.6 24.5 1.0
CG A:LEU547 4.6 46.6 1.0
CD1 A:LEU547 4.7 47.0 1.0
CE2 A:TRP550 4.8 25.7 1.0
CZ3 A:TRP550 5.0 25.1 1.0
CB A:LEU547 5.0 42.3 1.0

Fluorine binding site 3 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 3 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:27.7
occ:1.00
 F37 A:46F602 0.0 27.7 1.0
C24 A:46F602 1.3 24.3 1.0
F35 A:46F602 2.2 25.3 1.0
O34 A:46F602 2.2 26.0 1.0
F36 A:46F602 2.3 20.3 1.0
C13 A:46F602 2.9 18.4 1.0
C5 A:46F602 2.9 16.8 1.0
CD1 A:ILE454 3.2 25.6 1.0
CG A:TYR452 3.4 19.7 1.0
CD2 A:TYR452 3.5 19.6 1.0
CD1 A:TYR452 3.7 22.4 1.0
CB A:TYR452 3.7 18.4 1.0
CE2 A:TYR452 4.0 19.3 1.0
CG1 A:ILE454 4.1 21.6 1.0
CD1 A:ILE447 4.1 22.7 1.0
CE1 A:TYR452 4.1 22.7 1.0
C6 A:46F602 4.2 12.8 1.0
CD1 A:ILE413 4.3 13.1 1.0
CZ A:TYR452 4.3 24.3 1.0
C7 A:46F602 4.3 16.5 1.0
CG2 A:ILE413 4.7 19.8 1.0
CB A:TRP550 4.8 22.3 1.0
CG2 A:ILE462 5.0 18.9 1.0

Fluorine binding site 4 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 4 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:37.0
occ:1.00
 F35 B:46F602 0.0 37.0 1.0
C24 B:46F602 1.4 38.5 1.0
F36 B:46F602 2.2 35.6 1.0
F37 B:46F602 2.2 40.6 1.0
O34 B:46F602 2.3 38.2 1.0
C13 B:46F602 2.8 31.5 1.0
CG2 B:ILE462 3.1 29.9 1.0
C5 B:46F602 3.1 30.0 1.0
CD1 B:LEU547 3.2 98.0 1.0
C6 B:46F602 3.7 28.4 1.0
CG1 B:ILE462 3.8 30.4 1.0
CB B:ILE462 4.0 28.9 1.0
CD1 B:LEU466 4.0 17.3 1.0
C7 B:46F602 4.3 29.2 1.0
CG2 B:ILE413 4.3 27.9 1.0
CD1 B:ILE462 4.3 40.9 1.0
CG B:LEU547 4.6 98.0 1.0
O B:LEU547 4.7 94.8 1.0
CG B:LEU466 4.7 19.7 1.0
C8 B:46F602 4.8 31.2 1.0
CD1 B:ILE413 4.8 24.5 1.0
CD2 B:LEU547 4.8 0.7 1.0
C14 B:46F602 4.9 32.2 1.0
CA B:ILE462 5.0 25.3 1.0

Fluorine binding site 5 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 5 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:35.6
occ:1.00
 F36 B:46F602 0.0 35.6 1.0
C24 B:46F602 1.4 38.5 1.0
O34 B:46F602 2.2 38.2 1.0
F35 B:46F602 2.2 37.0 1.0
F37 B:46F602 2.2 40.6 1.0
CB B:TRP550 3.2 78.7 1.0
C13 B:46F602 3.5 31.5 1.0
CG1 B:ILE454 3.8 40.3 1.0
CG B:TRP550 3.9 79.7 1.0
CD2 B:TYR452 3.9 30.5 1.0
O B:LEU547 4.0 94.8 1.0
CG B:TYR452 4.0 31.5 1.0
CD1 B:ILE454 4.1 49.7 1.0
CB B:TYR452 4.2 33.0 1.0
CD1 B:LEU547 4.2 98.0 1.0
C5 B:46F602 4.2 30.0 1.0
CD2 B:TRP550 4.3 79.5 1.0
C6 B:46F602 4.4 28.4 1.0
CG1 B:ILE462 4.4 30.4 1.0
CD1 B:ILE462 4.4 40.9 1.0
CE2 B:TYR452 4.5 30.9 1.0
CE3 B:TRP550 4.5 80.8 1.0
CA B:TRP550 4.5 79.8 1.0
CD1 B:TYR452 4.7 32.9 1.0
CD1 B:TRP550 4.8 82.8 1.0
CG2 B:ILE462 4.8 29.9 1.0
C B:TRP550 4.9 79.7 1.0

Fluorine binding site 6 out of 6 in 3qgf

Go back to Fluorine Binding Sites List in 3qgf
Fluorine binding site 6 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Complex with (2E)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7- Dihydro-5H-Indolo[1,2-D][1,4]Benzodiazepin-10-Yl) Carbonyl]Amino}Cyclopentyl)Carbonyl]Amino}Phenyl)Prop-2-Enoic Acid and (2R)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:40.6
occ:1.00
 F37 B:46F602 0.0 40.6 1.0
C24 B:46F602 1.4 38.5 1.0
F36 B:46F602 2.2 35.6 1.0
F35 B:46F602 2.2 37.0 1.0
O34 B:46F602 2.3 38.2 1.0
C13 B:46F602 2.9 31.5 1.0
C5 B:46F602 2.9 30.0 1.0
CD1 B:ILE454 3.6 49.7 1.0
CG B:TYR452 3.8 31.5 1.0
CD1 B:TYR452 3.8 32.9 1.0
CD1 B:ILE413 3.9 24.5 1.0
CD1 B:ILE447 3.9 32.8 1.0
CG1 B:ILE454 4.1 40.3 1.0
CD2 B:TYR452 4.2 30.5 1.0
CB B:TYR452 4.2 33.0 1.0
CG2 B:ILE413 4.2 27.9 1.0
CE1 B:TYR452 4.2 31.9 1.0
C6 B:46F602 4.3 28.4 1.0
C7 B:46F602 4.3 29.2 1.0
CE2 B:TYR452 4.5 30.9 1.0
CZ B:TYR452 4.5 37.6 1.0
CG2 B:ILE462 4.7 29.9 1.0
CG1 B:ILE413 4.8 24.2 1.0

Reference:

R.G.Gentles, S.Sheriff, B.R.Beno, C.Wan, K.Kish, M.Ding, X.Zheng, L.Chupak, M.A.Poss, M.R.Witmer, P.Morin, Y.K.Wang, K.Rigat, J.Lemm, S.Voss, M.Liu, L.Pelosi, S.B.Roberts, M.Gao, J.F.Kadow. Investigation of the Mode of Binding of A Novel Series of N-Benzyl-4-Heteroaryl-1-(Phenylsulfonyl)Piperazine-2- Carboxamides to the Hepatitis C Virus Polymerase. Bioorg.Med.Chem.Lett. V. 21 2212 2011.
ISSN: ISSN 0960-894X
PubMed: 21441029
DOI: 10.1016/J.BMCL.2011.03.011
Page generated: Wed Jul 31 22:01:46 2024

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