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Chlorine 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:

Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3qgf

Go back to Chlorine Binding Sites List in 3qgf
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl602

b:31.5
occ:1.00
 CL39 A:46F602 0.0 31.5 1.0
C16 A:46F602 1.7 33.3 1.0
N26 A:46F602 2.5 35.6 1.0
C10 A:46F602 2.7 31.6 1.0
O A:HOH788 3.3 34.5 1.0
OH A:TYR191 3.5 16.5 1.0
CB A:SER556 3.5 67.6 1.0
O A:HOH759 3.5 19.2 1.0
O A:TYR555 3.6 57.3 1.0
C A:TYR555 3.8 58.4 1.0
N25 A:46F602 3.8 32.6 1.0
CB A:PHE193 4.0 17.5 1.0
CG A:PHE193 4.0 18.7 1.0
OG A:SER288 4.0 25.5 1.0
C9 A:46F602 4.0 29.1 1.0
CD2 A:PHE193 4.1 17.7 1.0
N A:SER556 4.2 59.9 1.0
OG A:SER556 4.3 77.3 1.0
C15 A:46F602 4.4 28.7 1.0
CA A:TYR555 4.4 50.4 1.0
CA A:SER556 4.5 62.1 1.0
CD1 A:PHE193 4.6 21.6 1.0
CB A:TYR555 4.7 53.4 1.0
CZ A:TYR191 4.8 18.5 1.0
CE2 A:PHE193 4.8 21.9 1.0
O A:TYR448 4.8 26.9 1.0
CB A:SER288 4.9 21.4 1.0

Chlorine binding site 2 out of 2 in 3qgf

Go back to Chlorine Binding Sites List in 3qgf
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
B:Cl602

b:41.3
occ:1.00
 CL39 B:46F602 0.0 41.3 1.0
C16 B:46F602 1.7 39.1 1.0
N26 B:46F602 2.5 36.7 1.0
C10 B:46F602 2.7 38.8 1.0
O B:HOH770 3.6 20.3 1.0
OH B:TYR191 3.7 22.8 1.0
OG B:SER288 3.8 28.5 1.0
N25 B:46F602 3.8 34.0 1.0
CG B:PHE193 3.9 17.6 1.0
CB B:PHE193 4.0 18.2 1.0
C9 B:46F602 4.0 35.2 1.0
CD2 B:PHE193 4.0 16.1 1.0
O B:TYR555 4.1 86.1 1.0
C B:TYR555 4.2 87.1 1.0
CD1 B:PHE193 4.4 19.6 1.0
C15 B:46F602 4.4 33.8 1.0
N B:SER556 4.5 85.0 1.0
CE2 B:PHE193 4.6 17.1 1.0
CA B:TYR555 4.7 81.7 1.0
CB B:SER288 4.7 20.3 1.0
O B:TYR448 4.7 35.1 1.0
CA B:SER556 4.8 85.2 1.0
CG B:TYR555 4.9 85.9 1.0
CZ B:TYR191 5.0 22.4 1.0
CD2 B:TYR555 5.0 86.8 1.0
CE1 B:PHE193 5.0 19.0 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: Fri Jul 11 09:23:54 2025

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