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

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy