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Fluorine in PDB 3qgi: Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase Genotype 1A Complex with N-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-6-[(3R)-3- {[4-(Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide, PDB code: 3qgi was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.35 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.400, 84.300, 132.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.9

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-[(2S)-Butan-2-Yl]-6-[(3R)-3- {[4-(Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide (pdb code 3qgi). 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-[(2S)-Butan-2-Yl]-6-[(3R)-3- {[4-(Trifluoromethoxy)Benzyl]Carbamoyl}-4-{[4-(Trifluoromethoxy) Phenyl]Sulfonyl}Piperazin-1-Yl]Pyridazine-3-Carboxamide, PDB code: 3qgi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qgi

Go back to Fluorine Binding Sites List in 3qgi
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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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
 F42 A:33F601 0.0 21.8 1.0
C28 A:33F601 1.3 22.2 1.0
F44 A:33F601 2.2 23.3 1.0
F43 A:33F601 2.2 23.4 1.0
O40 A:33F601 2.3 16.8 1.0
C12 A:33F601 2.8 13.4 1.0
O A:HOH1109 3.0 33.7 1.0
C3 A:33F601 3.3 13.8 1.0
C4 A:33F601 3.6 13.3 1.0
CE A:MET414 3.7 8.4 1.0
CZ A:PHE415 3.7 8.3 1.0
CE1 A:PHE415 4.3 10.2 1.0
CE2 A:PHE415 4.3 8.9 1.0
CB A:MET414 4.3 8.1 1.0
C1 A:33F601 4.5 13.9 1.0
O A:CYS366 4.6 17.8 1.0
CE2 A:TYR448 4.7 13.9 1.0
OH A:TYR448 4.7 20.0 1.0
C2 A:33F601 4.7 13.0 1.0
CG A:MET414 4.7 9.4 1.0
OG A:SER368 4.9 18.5 1.0
O A:HOH1090 4.9 34.5 1.0
CG A:PRO197 5.0 12.6 1.0

Fluorine binding site 2 out of 6 in 3qgi

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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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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:23.4
occ:1.00
 F43 A:33F601 0.0 23.4 1.0
C28 A:33F601 1.4 22.2 1.0
F42 A:33F601 2.2 21.8 1.0
F44 A:33F601 2.2 23.3 1.0
O40 A:33F601 2.3 16.8 1.0
C12 A:33F601 2.9 13.4 1.0
C4 A:33F601 3.0 13.3 1.0
CB A:PRO197 3.4 8.9 1.0
CG A:PRO197 3.4 12.6 1.0
CD2 A:LEU384 3.7 17.7 1.0
CA A:PRO197 3.9 7.2 1.0
CE A:MET414 4.1 8.4 1.0
CB A:LEU384 4.1 9.8 1.0
C3 A:33F601 4.2 13.8 1.0
O A:MET414 4.3 9.2 1.0
CG A:LEU384 4.3 17.9 1.0
CE1 A:PHE415 4.3 10.2 1.0
C2 A:33F601 4.3 13.0 1.0
CZ A:PHE415 4.5 8.3 1.0
CB A:MET414 4.7 8.1 1.0
CD A:PRO197 4.7 9.2 1.0
N A:PRO197 4.7 8.3 1.0
O A:HOH707 4.8 10.1 1.0
OG A:SER368 4.9 18.5 1.0
CD1 A:PHE415 4.9 9.5 1.0
C A:MET414 4.9 8.7 1.0

Fluorine binding site 3 out of 6 in 3qgi

Go back to Fluorine Binding Sites List in 3qgi
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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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:23.3
occ:1.00
 F44 A:33F601 0.0 23.3 1.0
C28 A:33F601 1.4 22.2 1.0
F42 A:33F601 2.2 21.8 1.0
F43 A:33F601 2.2 23.4 1.0
O40 A:33F601 2.2 16.8 1.0
OG A:SER368 3.0 18.5 1.0
CB A:SER368 3.1 11.7 1.0
CE1 A:PHE415 3.3 10.2 1.0
CZ A:PHE415 3.3 8.3 1.0
C12 A:33F601 3.5 13.4 1.0
O A:HOH1109 3.8 33.7 1.0
CB A:LEU384 4.0 9.8 1.0
CD2 A:LEU384 4.0 17.7 1.0
CG A:LEU384 4.0 17.9 1.0
O A:CYS366 4.1 17.8 1.0
C4 A:33F601 4.3 13.3 1.0
C3 A:33F601 4.4 13.8 1.0
CE2 A:PHE415 4.4 8.9 1.0
CD1 A:PHE415 4.4 9.5 1.0
CA A:SER368 4.6 8.0 1.0

Fluorine binding site 4 out of 6 in 3qgi

Go back to Fluorine Binding Sites List in 3qgi
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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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:18.9
occ:1.00
 F45 A:33F601 0.0 18.9 1.0
C29 A:33F601 1.3 21.1 1.0
F46 A:33F601 2.2 22.7 1.0
F47 A:33F601 2.2 21.6 1.0
O41 A:33F601 2.2 19.4 1.0
C13 A:33F601 2.8 15.7 1.0
C6 A:33F601 3.0 15.7 1.0
CG2 A:ILE462 3.2 11.7 1.0
CG2 A:ILE413 3.6 12.7 1.0
C5 A:33F601 4.0 15.3 1.0
CD2 A:LEU547 4.0 22.6 1.0
C8 A:33F601 4.2 15.3 1.0
CD1 A:ILE454 4.3 19.1 1.0
CD1 A:ILE413 4.4 15.2 1.0
CD2 A:LEU466 4.5 12.0 1.0
CB A:ILE462 4.6 11.4 1.0
CG1 A:ILE413 4.7 12.6 1.0
CG1 A:ILE462 4.8 11.1 1.0
CB A:ILE413 4.8 10.8 1.0
CD1 A:ILE462 4.8 12.5 1.0

Fluorine binding site 5 out of 6 in 3qgi

Go back to Fluorine Binding Sites List in 3qgi
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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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:22.7
occ:1.00
 F46 A:33F601 0.0 22.7 1.0
C29 A:33F601 1.3 21.1 1.0
F45 A:33F601 2.2 18.9 1.0
F47 A:33F601 2.2 21.6 1.0
O41 A:33F601 2.2 19.4 1.0
C6 A:33F601 3.0 15.7 1.0
C13 A:33F601 3.0 15.7 1.0
CD1 A:ILE454 3.2 19.1 1.0
CG A:TYR452 3.4 10.6 1.0
CD1 A:TYR452 3.5 12.4 1.0
CD2 A:TYR452 3.7 10.7 1.0
CB A:TYR452 3.9 9.7 1.0
CE1 A:TYR452 3.9 14.3 1.0
CD1 A:ILE413 3.9 15.2 1.0
CE2 A:TYR452 4.1 10.7 1.0
CG2 A:ILE413 4.2 12.7 1.0
CZ A:TYR452 4.2 15.0 1.0
CD1 A:ILE447 4.2 13.9 1.0
C8 A:33F601 4.3 15.3 1.0
C5 A:33F601 4.4 15.3 1.0
CG1 A:ILE454 4.4 11.8 1.0
CG1 A:ILE413 4.8 12.6 1.0
CG2 A:ILE462 5.0 11.7 1.0
CB A:ILE413 5.0 10.8 1.0

Fluorine binding site 6 out of 6 in 3qgi

Go back to Fluorine Binding Sites List in 3qgi
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-[(2S)-Butan-2-Yl]-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-[(2S)-Butan-2-Yl]-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:21.6
occ:1.00
 F47 A:33F601 0.0 21.6 1.0
C29 A:33F601 1.4 21.1 1.0
O41 A:33F601 2.2 19.4 1.0
F46 A:33F601 2.2 22.7 1.0
F45 A:33F601 2.2 18.9 1.0
CD1 A:ILE454 3.4 19.1 1.0
C13 A:33F601 3.5 15.7 1.0
CB A:PHE551 3.5 9.8 1.0
CD2 A:PHE551 3.5 12.9 1.0
CG A:PHE551 3.7 11.5 1.0
CD1 A:TYR452 3.9 12.4 1.0
CG1 A:ILE454 4.0 11.8 1.0
O A:LEU547 4.1 27.6 1.0
C6 A:33F601 4.2 15.7 1.0
CG2 A:ILE462 4.2 11.7 1.0
CD1 A:ILE462 4.3 12.5 1.0
CG A:TYR452 4.4 10.6 1.0
CE1 A:TYR452 4.4 14.3 1.0
CE2 A:PHE551 4.5 14.3 1.0
CD2 A:LEU547 4.5 22.6 1.0
C5 A:33F601 4.5 15.3 1.0
CG1 A:ILE462 4.6 11.1 1.0
CD1 A:PHE551 4.7 13.1 1.0
CB A:TYR452 4.7 9.7 1.0
CA A:PHE551 4.9 8.2 1.0
C A:LEU547 5.0 25.1 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 22:01:59 2024

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