Fluorine in PDB 3vqs: Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor

The structure of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor, PDB code: 3vqs was solved by T.Adachi, S.Doi, I.Ando, K.Sugimoto, T.Orita, A.Nomura, M.Kamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.97 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.120, 101.180, 250.060, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.4

The structure of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor (pdb code 3vqs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 28 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor, PDB code: 3vqs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:34.3 occ:1.00 F37 A:JT11000 0.0 34.3 1.0 C36 A:JT11000 1.3 31.5 1.0 F38 A:JT11000 2.1 31.7 1.0 F39 A:JT11000 2.2 34.0 1.0 O35 A:JT11000 2.2 26.9 1.0 OG A:SER368 2.8 27.5 1.0 OH A:TYR415 3.4 26.9 1.0 CB A:SER368 3.4 25.1 1.0 CE2 A:TYR415 3.4 24.6 1.0 C23 A:JT11000 3.5 23.7 1.0 CB A:LEU384 3.6 23.4 1.0 CZ A:TYR415 3.6 26.8 1.0 CD1 A:LEU384 3.7 23.0 1.0 F47 A:JT11000 4.0 26.6 1.0 C24 A:JT11000 4.2 23.5 1.0 CG A:LEU384 4.3 25.2 1.0 C22 A:JT11000 4.4 23.7 1.0 CD2 A:TYR415 4.4 23.5 1.0 O A:HOH3109 4.4 40.6 1.0 O A:CYS366 4.4 28.4 1.0 CE1 A:TYR415 4.7 25.1 1.0 CA A:SER368 4.9 26.9 1.0 CA A:LEU384 5.0 23.5 1.0 O A:MET414 5.0 23.2 1.0 CD2 A:LEU384 5.0 24.9 1.0

Fluorine binding site 2 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:31.7 occ:1.00 F38 A:JT11000 0.0 31.7 1.0 C36 A:JT11000 1.3 31.5 1.0 F39 A:JT11000 2.1 34.0 1.0 F37 A:JT11000 2.1 34.3 1.0 O35 A:JT11000 2.2 26.9 1.0 C23 A:JT11000 2.8 23.7 1.0 F47 A:JT11000 2.9 26.6 1.0 C24 A:JT11000 3.1 23.5 1.0 CE A:MET414 3.6 22.7 1.0 C22 A:JT11000 3.7 23.7 1.0 CG A:PRO197 3.8 20.8 1.0 CB A:PRO197 3.8 19.8 1.0 O A:MET414 3.9 23.2 1.0 CB A:MET414 4.2 23.6 1.0 CD1 A:LEU384 4.2 23.0 1.0 C25 A:JT11000 4.2 23.2 1.0 CA A:PRO197 4.4 20.3 1.0 CE2 A:TYR415 4.5 24.6 1.0 C A:MET414 4.6 23.6 1.0 CZ A:TYR415 4.6 26.8 1.0 OH A:TYR415 4.7 26.9 1.0 CA A:MET414 4.7 22.9 1.0 CB A:LEU384 4.7 23.4 1.0 SD A:MET414 4.7 23.1 1.0 C21 A:JT11000 4.8 21.9 1.0 CG A:MET414 4.8 21.4 1.0 OG A:SER368 4.9 27.5 1.0 O A:HOH3008 4.9 26.1 1.0 O A:HOH3109 4.9 40.6 1.0 CD A:PRO197 4.9 20.7 1.0 C20 A:JT11000 4.9 22.7 1.0

Fluorine binding site 3 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:34.0 occ:1.00 F39 A:JT11000 0.0 34.0 1.0 C36 A:JT11000 1.3 31.5 1.0 F38 A:JT11000 2.1 31.7 1.0 F37 A:JT11000 2.2 34.3 1.0 O35 A:JT11000 2.3 26.9 1.0 O A:HOH3109 2.9 40.6 1.0 C23 A:JT11000 2.9 23.7 1.0 C22 A:JT11000 3.2 23.7 1.0 OH A:TYR415 3.2 26.9 1.0 CZ A:TYR415 3.7 26.8 1.0 OG A:SER368 3.8 27.5 1.0 OH A:TYR448 3.9 30.0 1.0 C24 A:JT11000 4.0 23.5 1.0 CE1 A:TYR448 4.0 31.6 1.0 CE A:MET414 4.1 22.7 1.0 CE2 A:TYR415 4.2 24.6 1.0 O A:CYS366 4.2 28.4 1.0 CE1 A:TYR415 4.2 25.1 1.0 F47 A:JT11000 4.3 26.6 1.0 CZ A:TYR448 4.4 29.0 1.0 C21 A:JT11000 4.4 21.9 1.0 CB A:MET414 4.5 23.6 1.0 CB A:CYS366 4.8 26.0 1.0 CB A:SER368 4.8 25.1 1.0 C25 A:JT11000 5.0 23.2 1.0

Fluorine binding site 4 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:29.1 occ:1.00 F41 A:JT11000 0.0 29.1 1.0 C40 A:JT11000 1.3 29.7 1.0 F43 A:JT11000 2.1 29.6 1.0 F42 A:JT11000 2.2 30.5 1.0 C9 A:JT11000 2.4 24.6 1.0 C10 A:JT11000 2.9 23.6 1.0 CD1 A:ILE454 3.0 33.9 0.3 CG A:TYR452 3.1 32.6 1.0 CD1 A:TYR452 3.3 31.1 1.0 CD2 A:TYR452 3.4 33.0 1.0 C8 A:JT11000 3.6 25.7 1.0 CB A:TYR452 3.6 35.2 1.0 CD1 A:ILE454 3.6 31.0 0.7 CE1 A:TYR452 3.8 28.1 1.0 CE2 A:TYR452 3.9 30.3 1.0 CZ A:TYR452 4.0 31.6 1.0 CG1 A:ILE454 4.1 31.1 0.7 CG1 A:ILE454 4.1 35.9 0.3 CD1 A:ILE447 4.2 27.4 1.0 C11 A:JT11000 4.2 22.8 1.0 CD1 A:ILE413 4.3 25.4 1.0 CG2 A:ILE413 4.7 24.3 1.0 C7 A:JT11000 4.8 25.4 1.0 SG A:CYS445 4.9 47.9 1.0 OH A:TYR452 5.0 29.5 1.0

Fluorine binding site 5 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:30.5 occ:1.00 F42 A:JT11000 0.0 30.5 1.0 C40 A:JT11000 1.4 29.7 1.0 F43 A:JT11000 2.1 29.6 1.0 F41 A:JT11000 2.2 29.1 1.0 C9 A:JT11000 2.4 24.6 1.0 C10 A:JT11000 3.1 23.6 1.0 C8 A:JT11000 3.3 25.7 1.0 CG2 A:ILE462 3.5 26.8 1.0 CD1 A:ILE454 4.0 33.9 0.3 CD1 A:LEU466 4.0 23.3 1.0 CD1 A:ILE454 4.1 31.0 0.7 CD2 A:LEU547 4.2 58.9 1.0 CG2 A:ILE413 4.3 24.3 1.0 C11 A:JT11000 4.3 22.8 1.0 CG1 A:ILE462 4.4 28.0 1.0 CD1 A:ILE462 4.4 29.3 1.0 CD1 A:ILE413 4.5 25.4 1.0 CB A:ILE462 4.5 27.5 1.0 C7 A:JT11000 4.5 25.4 1.0 CG1 A:ILE454 4.7 35.9 0.3 CG A:LEU466 4.9 22.9 1.0 C4 A:JT11000 4.9 21.9 1.0 CD2 A:TYR452 4.9 33.0 1.0 CG1 A:ILE454 5.0 31.1 0.7

Fluorine binding site 6 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


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 Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:29.6 occ:1.00 F43 A:JT11000 0.0 29.6 1.0 C40 A:JT11000 1.3 29.7 1.0 F42 A:JT11000 2.1 30.5 1.0 F41 A:JT11000 2.1 29.1 1.0 C9 A:JT11000 2.5 24.6 1.0 C8 A:JT11000 2.9 25.7 1.0 CD2 A:TYR452 3.1 33.0 1.0 CE2 A:TYR452 3.4 30.3 1.0 C10 A:JT11000 3.7 23.6 1.0 CG A:TYR452 3.7 32.6 1.0 O A:LEU547 3.8 56.5 1.0 CA A:LEU547 3.9 67.2 1.0 CD1 A:ILE454 4.0 31.0 0.7 C A:LEU547 4.0 61.1 1.0 CZ A:TYR452 4.1 31.6 1.0 CB A:LEU547 4.2 60.9 1.0 CD1 A:ILE454 4.2 33.9 0.3 C7 A:JT11000 4.3 25.4 1.0 CB A:TYR452 4.3 35.2 1.0 CD1 A:TYR452 4.4 31.1 1.0 CD2 A:LEU547 4.4 58.9 1.0 CE1 A:TYR452 4.5 28.1 1.0 CG1 A:ILE454 4.8 35.9 0.3 O A:ASP546 4.8 64.2 1.0 C11 A:JT11000 4.8 22.8 1.0 OH A:TYR452 4.9 29.5 1.0 CG A:LEU547 4.9 65.0 1.0

Fluorine binding site 7 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:26.6 occ:1.00 F47 A:JT11000 0.0 26.6 1.0 C24 A:JT11000 1.3 23.5 1.0 C23 A:JT11000 2.3 23.7 1.0 C25 A:JT11000 2.4 23.2 1.0 O35 A:JT11000 2.6 26.9 1.0 F38 A:JT11000 2.9 31.7 1.0 CA A:PRO197 3.1 20.3 1.0 CD A:ARG200 3.2 22.5 1.0 C36 A:JT11000 3.3 31.5 1.0 CD1 A:LEU384 3.4 23.0 1.0 CB A:ARG200 3.5 19.9 1.0 C22 A:JT11000 3.6 23.7 1.0 C20 A:JT11000 3.6 22.7 1.0 CB A:PRO197 3.6 19.8 1.0 N A:PRO197 3.7 20.9 1.0 CG A:ARG200 3.9 21.0 1.0 CG A:PRO197 4.0 20.8 1.0 O A:SER196 4.0 20.4 1.0 F37 A:JT11000 4.0 34.3 1.0 C A:SER196 4.1 20.5 1.0 C21 A:JT11000 4.1 21.9 1.0 C A:PRO197 4.2 21.4 1.0 O A:PRO197 4.3 21.6 1.0 F39 A:JT11000 4.3 34.0 1.0 CD A:PRO197 4.4 20.7 1.0 NE A:ARG200 4.4 23.1 1.0 CE A:MET414 4.5 22.7 1.0 CG A:LEU384 4.8 25.2 1.0 C19 A:JT11000 4.9 22.1 1.0 CA A:ARG200 4.9 20.2 1.0 O A:HOH3009 4.9 25.8 1.0

Fluorine binding site 8 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:45.1 occ:0.97 F37 B:JT1601 0.0 45.1 1.0 C36 B:JT1601 1.4 43.5 1.0 F38 B:JT1601 2.1 52.1 1.0 F39 B:JT1601 2.2 45.4 1.0 O35 B:JT1601 2.2 37.2 1.0 OG B:SER368 2.8 32.1 1.0 OH B:TYR415 3.2 35.6 1.0 CB B:SER368 3.3 28.5 1.0 CE2 B:TYR415 3.3 34.6 1.0 C23 B:JT1601 3.5 28.8 1.0 CZ B:TYR415 3.5 37.9 1.0 CD1 B:LEU384 3.6 35.9 1.0 CB B:LEU384 3.7 32.7 1.0 F47 B:JT1601 4.1 34.0 1.0 CG B:LEU384 4.1 37.1 1.0 C24 B:JT1601 4.3 28.1 1.0 CD2 B:TYR415 4.3 31.1 1.0 C22 B:JT1601 4.4 28.7 1.0 O B:CYS366 4.5 33.3 1.0 CE1 B:TYR415 4.7 35.3 1.0 CD2 B:LEU384 4.7 34.3 1.0 CA B:SER368 4.8 29.9 1.0

Fluorine binding site 9 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:52.1 occ:0.97 F38 B:JT1601 0.0 52.1 1.0 C36 B:JT1601 1.4 43.5 1.0 F37 B:JT1601 2.1 45.1 1.0 F39 B:JT1601 2.1 45.4 1.0 O35 B:JT1601 2.3 37.2 1.0 F47 B:JT1601 2.9 34.0 1.0 C23 B:JT1601 2.9 28.8 1.0 C24 B:JT1601 3.1 28.1 1.0 CG B:PRO197 3.6 23.8 1.0 CE B:MET414 3.8 23.0 1.0 CB B:PRO197 3.8 24.8 1.0 O B:MET414 3.8 26.7 1.0 C22 B:JT1601 4.0 28.7 1.0 CD1 B:LEU384 4.0 35.9 1.0 CB B:MET414 4.2 24.8 1.0 CE2 B:TYR415 4.3 34.6 1.0 C25 B:JT1601 4.3 29.2 1.0 CA B:PRO197 4.4 24.3 1.0 CZ B:TYR415 4.4 37.9 1.0 CB B:LEU384 4.5 32.7 1.0 OH B:TYR415 4.5 35.6 1.0 C B:MET414 4.6 28.5 1.0 CA B:MET414 4.8 26.2 1.0 CD2 B:TYR415 4.8 31.1 1.0 CD B:PRO197 4.9 24.3 1.0 OG B:SER368 4.9 32.1 1.0 SD B:MET414 4.9 25.9 1.0 O B:HOH3021 4.9 28.9 1.0 CG B:LEU384 4.9 37.1 1.0 C21 B:JT1601 4.9 30.7 1.0 CG B:MET414 5.0 23.2 1.0

Fluorine binding site 10 out of 28 in the Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Hcv NS5B Rna Polymerase with A Novel Piperazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:45.4 occ:0.97 F39 B:JT1601 0.0 45.4 1.0 C36 B:JT1601 1.3 43.5 1.0 F38 B:JT1601 2.1 52.1 1.0 F37 B:JT1601 2.2 45.1 1.0 O35 B:JT1601 2.3 37.2 1.0 C23 B:JT1601 2.9 28.8 1.0 OH B:TYR415 3.2 35.6 1.0 C22 B:JT1601 3.2 28.7 1.0 CZ B:TYR415 3.6 37.9 1.0 OG B:SER368 3.8 32.1 1.0 C24 B:JT1601 3.9 28.1 1.0 OH B:TYR448 4.0 45.1 1.0 CE B:MET414 4.1 23.0 1.0 CE2 B:TYR415 4.1 34.6 1.0 CE1 B:TYR448 4.2 44.6 1.0 CE1 B:TYR415 4.2 35.3 1.0 F47 B:JT1601 4.2 34.0 1.0 C21 B:JT1601 4.4 30.7 1.0 O B:CYS366 4.4 33.3 1.0 CB B:MET414 4.5 24.8 1.0 CZ B:TYR448 4.6 44.7 1.0 CB B:SER368 4.8 28.5 1.0 C25 B:JT1601 4.9 29.2 1.0 CG B:MET414 5.0 23.2 1.0 CB B:CYS366 5.0 33.5 1.0

I.Ando, T.Adachi, N.Ogura, Y.Toyonaga, K.Sugimoto, H.Abe, M.Kamada, T.Noguchi. Preclinical Characterization of Jtk-853, A Novel Nonnucleoside Inhibitor of the Hepatitis C Virus Rna-Dependent Rna Polymerase. Antimicrob.Agents Chemother. V. 56 4250 2012.
ISSN: ISSN 0066-4804
PubMed: 22615294
DOI: 10.1128/AAC.00312-12