Atomistry » Fluorine » PDB 3ptm-3qri » 3qge
Atomistry »
  Fluorine »
    PDB 3ptm-3qri »
      3qge »

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: Mon Jul 14 18:54:55 2025

Last articles

Mn in 5ZAC
Mn in 5Z30
Mn in 5Z2P
Mn in 5Z6W
Mn in 5Z5Y
Mn in 5Z5P
Mn in 5Z5N
Mn in 5Z5L
Mn in 5Z2R
Mn in 5Z2K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy