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Fluorine in PDB 3qge: 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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide, PDB code: 3qge was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.61 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.700, 91.400, 232.100, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27.2

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-(2,6-Dimethoxypyrimidin-4-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide (pdb code 3qge). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 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-(2,6-Dimethoxypyrimidin-4-Yl)-N-(4-Methoxybenzyl)-1-{[4- (Trifluoromethoxy)Phenyl]Sulfonyl}Piperazine-2-Carboxamide, PDB code: 3qge:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3qge

Go back to Fluorine Binding Sites List in 3qge
Fluorine binding site 1 out of 3 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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-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:64.1
occ:1.00
 F39 B:26F602 0.0 64.1 1.0
C26 B:26F602 1.4 61.5 1.0
F41 B:26F602 2.2 62.5 1.0
F40 B:26F602 2.2 62.7 1.0
O36 B:26F602 2.3 55.2 1.0
C12 B:26F602 2.7 51.9 1.0
C5 B:26F602 3.0 48.5 1.0
CG2 B:ILE462 3.2 30.1 1.0
C6 B:26F602 3.6 53.4 1.0
CG B:LEU547 3.6 0.0 1.0
CD1 B:LEU547 3.9 1.0 1.0
CD1 B:LEU466 3.9 32.5 1.0
CG1 B:ILE462 4.1 30.1 1.0
C7 B:26F602 4.2 48.2 1.0
CB B:ILE462 4.2 30.0 1.0
CD2 B:LEU547 4.4 0.9 1.0
CG B:LEU466 4.4 33.5 1.0
CD2 B:LEU466 4.4 35.7 1.0
CD1 B:ILE462 4.6 30.6 1.0
CB B:LEU547 4.6 0.8 1.0
C8 B:26F602 4.6 53.9 1.0
CG2 B:ILE413 4.6 29.5 1.0
C13 B:26F602 4.8 50.9 1.0
CA B:ILE462 4.9 28.0 1.0

Fluorine binding site 2 out of 3 in 3qge

Go back to Fluorine Binding Sites List in 3qge
Fluorine binding site 2 out of 3 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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-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:62.7
occ:1.00
 F40 B:26F602 0.0 62.7 1.0
C26 B:26F602 1.3 61.5 1.0
F41 B:26F602 2.2 62.5 1.0
F39 B:26F602 2.2 64.1 1.0
O36 B:26F602 2.2 55.2 1.0
CD1 B:ILE454 3.1 57.2 1.0
CG1 B:ILE454 3.5 49.5 1.0
C12 B:26F602 3.5 51.9 1.0
CD1 B:ILE462 3.8 30.6 1.0
CB B:TRP550 3.9 1.0 1.0
CG2 B:ILE462 4.0 30.1 1.0
CG1 B:ILE462 4.1 30.1 1.0
CD2 B:TYR452 4.2 45.8 1.0
C5 B:26F602 4.3 48.5 1.0
CG B:TYR452 4.3 46.0 1.0
CB B:TYR452 4.4 46.3 1.0
CG B:TRP550 4.4 0.8 1.0
C6 B:26F602 4.4 53.4 1.0
CD1 B:ILE413 4.4 34.6 1.0
CB B:ILE462 4.7 30.0 1.0
CB B:ILE454 4.8 48.2 1.0
CE2 B:TYR452 4.8 46.1 1.0
CD1 B:LEU547 4.9 1.0 1.0
CG2 B:ILE454 4.9 47.9 1.0
CD1 B:TYR452 4.9 47.2 1.0
CD1 B:TRP550 4.9 0.9 1.0
CD2 B:TRP550 5.0 0.1 1.0
CG2 B:ILE413 5.0 29.5 1.0

Fluorine binding site 3 out of 3 in 3qge

Go back to Fluorine Binding Sites List in 3qge
Fluorine binding site 3 out of 3 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-(2,6-Dimethoxypyrimidin-4-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-(2,6-Dimethoxypyrimidin-4-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:62.5
occ:1.00
 F41 B:26F602 0.0 62.5 1.0
C26 B:26F602 1.4 61.5 1.0
F39 B:26F602 2.2 64.1 1.0
F40 B:26F602 2.2 62.7 1.0
O36 B:26F602 2.3 55.2 1.0
C12 B:26F602 2.9 51.9 1.0
C5 B:26F602 3.0 48.5 1.0
CD2 B:TYR452 3.3 45.8 1.0
CD1 B:LEU547 3.4 1.0 1.0
CE2 B:TYR452 3.5 46.1 1.0
CB B:TRP550 3.7 1.0 1.0
CG B:LEU547 4.0 0.0 1.0
CG B:TYR452 4.1 46.0 1.0
C6 B:26F602 4.3 53.4 1.0
CZ B:TYR452 4.3 51.9 1.0
C7 B:26F602 4.3 48.2 1.0
CG B:TRP550 4.6 0.8 1.0
CA B:TRP550 4.6 0.4 1.0
CB B:TYR452 4.7 46.3 1.0
N B:PHE551 4.7 0.5 1.0
C B:TRP550 4.7 0.8 1.0
CD1 B:TYR452 4.8 47.2 1.0
CD1 B:ILE454 4.9 57.2 1.0
CE1 B:TYR452 4.9 46.8 1.0
N B:TRP550 4.9 0.2 1.0
CB B:LEU547 5.0 0.8 1.0
CE3 B:TRP550 5.0 0.7 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 22:01:08 2024

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