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Fluorine in PDB 3qgh: Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide

Enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide

All present enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide, PDB code: 3qgh was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.93 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.300, 84.700, 132.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide (pdb code 3qgh). 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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide, PDB code: 3qgh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 1 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:24.7
occ:1.00
 F41 A:63F601 0.0 24.7 1.0
C27 A:63F601 1.3 22.8 1.0
F42 A:63F601 2.2 21.3 1.0
O39 A:63F601 2.2 19.6 1.0
F43 A:63F601 2.2 23.9 1.0
OG A:SER368 3.0 17.5 1.0
CZ A:PHE415 3.1 9.9 1.0
CB A:SER368 3.2 9.4 1.0
CE1 A:PHE415 3.3 11.0 1.0
C12 A:63F601 3.5 14.3 1.0
O A:HOH1055 3.8 34.9 1.0
O A:CYS366 3.9 13.8 1.0
CG A:LEU384 4.2 14.9 1.0
CD2 A:LEU384 4.2 15.0 1.0
CE2 A:PHE415 4.2 12.3 1.0
CB A:LEU384 4.3 8.8 1.0
C4 A:63F601 4.3 11.7 1.0
C3 A:63F601 4.4 11.2 1.0
CD1 A:PHE415 4.5 10.7 1.0
CA A:SER368 4.6 7.3 1.0
N A:SER368 5.0 9.0 1.0
CB A:CYS366 5.0 13.8 1.0

Fluorine binding site 2 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 2 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:21.3
occ:1.00
 F42 A:63F601 0.0 21.3 1.0
C27 A:63F601 1.4 22.8 1.0
F41 A:63F601 2.2 24.7 1.0
F43 A:63F601 2.2 23.9 1.0
O39 A:63F601 2.2 19.6 1.0
C12 A:63F601 2.7 14.3 1.0
C4 A:63F601 3.2 11.7 1.0
C3 A:63F601 3.6 11.2 1.0
O A:HOH1055 3.7 34.9 1.0
CZ A:PHE415 3.7 9.9 1.0
CE A:MET414 3.7 4.8 1.0
CE2 A:PHE415 4.2 12.3 1.0
CE1 A:PHE415 4.3 11.0 1.0
C2 A:63F601 4.3 12.5 1.0
CE2 A:TYR448 4.3 13.7 1.0
OH A:TYR448 4.4 25.3 1.0
CB A:MET414 4.4 5.7 1.0
C1 A:63F601 4.6 10.3 1.0
O A:CYS366 4.6 13.8 1.0
CG A:MET414 4.8 8.0 1.0
CZ A:TYR448 4.9 22.4 1.0
OG A:SER368 4.9 17.5 1.0
C11 A:63F601 4.9 10.2 1.0

Fluorine binding site 3 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 3 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:23.9
occ:1.00
 F43 A:63F601 0.0 23.9 1.0
C27 A:63F601 1.4 22.8 1.0
F42 A:63F601 2.2 21.3 1.0
F41 A:63F601 2.2 24.7 1.0
O39 A:63F601 2.3 19.6 1.0
C12 A:63F601 3.0 14.3 1.0
C3 A:63F601 3.1 11.2 1.0
CB A:PRO197 3.5 8.8 1.0
CG A:PRO197 3.5 12.7 1.0
CD2 A:LEU384 3.7 15.0 1.0
CE1 A:PHE415 4.1 11.0 1.0
CA A:PRO197 4.1 7.5 1.0
CE A:MET414 4.1 4.8 1.0
CB A:LEU384 4.1 8.8 1.0
CZ A:PHE415 4.2 9.9 1.0
C4 A:63F601 4.2 11.7 1.0
CG A:LEU384 4.2 14.9 1.0
O A:MET414 4.3 9.3 1.0
C1 A:63F601 4.4 10.3 1.0
CB A:MET414 4.6 5.7 1.0
CD1 A:PHE415 4.8 10.7 1.0
OG A:SER368 4.8 17.5 1.0
O A:HOH729 4.8 11.9 1.0
CD A:PRO197 4.8 8.4 1.0
N A:PRO197 4.9 8.1 1.0
C A:MET414 4.9 10.5 1.0
CE2 A:PHE415 4.9 12.3 1.0

Fluorine binding site 4 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 4 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:17.3
occ:1.00
 F44 A:63F601 0.0 17.3 1.0
C28 A:63F601 1.3 16.9 1.0
F45 A:63F601 2.2 21.8 1.0
F46 A:63F601 2.2 15.6 1.0
O40 A:63F601 2.2 19.2 1.0
C13 A:63F601 2.9 13.4 1.0
C6 A:63F601 3.0 10.4 1.0
CG2 A:ILE462 3.2 11.7 1.0
CG2 A:ILE413 3.7 8.3 1.0
CD2 A:LEU547 3.9 26.4 1.0
C5 A:63F601 4.1 11.0 1.0
CD1 A:ILE413 4.2 10.7 1.0
C8 A:63F601 4.3 9.4 1.0
CD1 A:ILE454 4.3 19.3 1.0
CB A:ILE462 4.5 11.8 1.0
CG1 A:ILE413 4.6 10.0 1.0
CD1 A:ILE462 4.7 6.9 1.0
CG1 A:ILE462 4.7 11.6 1.0
CB A:ILE413 4.8 8.9 1.0
CD2 A:LEU466 4.8 15.9 1.0

Fluorine binding site 5 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 5 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:21.8
occ:1.00
 F45 A:63F601 0.0 21.8 1.0
C28 A:63F601 1.3 16.9 1.0
F44 A:63F601 2.2 17.3 1.0
F46 A:63F601 2.2 15.6 1.0
O40 A:63F601 2.2 19.2 1.0
C6 A:63F601 3.0 10.4 1.0
C13 A:63F601 3.0 13.4 1.0
CD1 A:ILE454 3.3 19.3 1.0
CG A:TYR452 3.4 7.2 1.0
CD1 A:TYR452 3.4 8.7 1.0
CD2 A:TYR452 3.6 7.2 1.0
CE1 A:TYR452 3.8 7.6 1.0
CD1 A:ILE413 3.9 10.7 1.0
CB A:TYR452 3.9 6.9 1.0
CE2 A:TYR452 4.0 8.1 1.0
CZ A:TYR452 4.0 12.4 1.0
CD1 A:ILE447 4.2 13.4 1.0
CG2 A:ILE413 4.3 8.3 1.0
C8 A:63F601 4.3 9.4 1.0
C5 A:63F601 4.3 11.0 1.0
CG1 A:ILE454 4.5 13.7 1.0
CG1 A:ILE413 4.9 10.0 1.0
OH A:TYR452 4.9 15.0 1.0
CG2 A:ILE462 5.0 11.7 1.0

Fluorine binding site 6 out of 6 in 3qgh

Go back to Fluorine Binding Sites List in 3qgh
Fluorine binding site 6 out of 6 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-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 Genotype 1A Complex with N-Cyclopropyl-6-[(3R)-3-{[4- (Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:15.6
occ:1.00
 F46 A:63F601 0.0 15.6 1.0
C28 A:63F601 1.3 16.9 1.0
O40 A:63F601 2.1 19.2 1.0
F44 A:63F601 2.2 17.3 1.0
F45 A:63F601 2.2 21.8 1.0
CD2 A:PHE551 3.4 11.8 1.0
C13 A:63F601 3.5 13.4 1.0
CB A:PHE551 3.6 9.5 1.0
CD1 A:ILE454 3.6 19.3 1.0
CG A:PHE551 3.7 11.2 1.0
CD1 A:TYR452 3.9 8.7 1.0
O A:LEU547 3.9 24.6 1.0
C6 A:63F601 4.2 10.4 1.0
CG1 A:ILE454 4.2 13.7 1.0
CD1 A:ILE462 4.3 6.9 1.0
CG2 A:ILE462 4.3 11.7 1.0
CD2 A:LEU547 4.3 26.4 1.0
CE1 A:TYR452 4.3 7.6 1.0
CE2 A:PHE551 4.4 13.6 1.0
O A:HOH1104 4.4 31.1 1.0
CG A:TYR452 4.4 7.2 1.0
C5 A:63F601 4.5 11.0 1.0
CG1 A:ILE462 4.6 11.6 1.0
CB A:TYR452 4.7 6.9 1.0
C A:LEU547 4.8 23.9 1.0
CD1 A:PHE551 4.8 13.8 1.0
CA A:LEU547 4.9 18.2 1.0
CA A:PHE551 5.0 8.2 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: Mon Jul 14 18:55:09 2025

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