Fluorine in PDB 3phe: Hcv NS5B with A Bound Quinolone Inhibitor

The structure of Hcv NS5B with A Bound Quinolone Inhibitor, PDB code: 3phe was solved by J.R.Somoza, N.To, I.Lehoux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.751, 101.972, 251.087, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Hcv NS5B with A Bound Quinolone Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Hcv NS5B with A Bound Quinolone Inhibitor (pdb code 3phe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hcv NS5B with A Bound Quinolone Inhibitor, PDB code: 3phe:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:46.3 occ:1.00 F10 A:C9A999 0.0 46.3 1.0 C9 A:C9A999 1.3 46.1 1.0 C11 A:C9A999 2.3 43.9 1.0 C8 A:C9A999 2.4 47.3 1.0 N5 A:C9A999 2.9 50.8 1.0 CA A:PRO479 3.2 36.6 1.0 O A:TYR477 3.3 40.4 1.0 N A:PRO479 3.4 37.5 1.0 C4 A:C9A999 3.5 51.2 1.0 C12 A:C9A999 3.6 43.0 1.0 CB A:PRO479 3.7 37.7 1.0 C30 A:C9A999 3.7 45.0 1.0 C A:SER478 3.7 38.9 1.0 O A:SER478 3.8 38.5 1.0 CG1 A:ILE482 3.9 32.8 1.0 CD A:PRO479 4.1 38.6 1.0 C29 A:C9A999 4.2 43.7 1.0 CB A:ILE482 4.2 35.1 1.0 C6 A:C9A999 4.3 50.9 1.0 C A:TYR477 4.3 39.5 1.0 C A:PRO479 4.5 35.0 1.0 CG A:PRO479 4.5 38.1 1.0 C3 A:C9A999 4.5 52.8 1.0 CA A:SER478 4.7 39.8 1.0 O A:PRO479 4.8 33.9 1.0 C13 A:C9A999 4.9 42.8 1.0 CG2 A:ILE482 4.9 36.1 1.0 N A:SER478 4.9 39.0 1.0 O14 A:C9A999 5.0 42.9 1.0

Fluorine binding site 2 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F998 b:45.3 occ:1.00 F10 B:C9A998 0.0 45.3 1.0 C9 B:C9A998 1.3 43.7 1.0 C11 B:C9A998 2.3 41.9 1.0 C8 B:C9A998 2.4 42.5 1.0 N5 B:C9A998 2.9 45.5 1.0 CA B:PRO479 3.2 35.2 1.0 C4 B:C9A998 3.2 46.8 1.0 N B:PRO479 3.4 35.2 1.0 O B:TYR477 3.5 36.0 1.0 C12 B:C9A998 3.7 41.4 1.0 C30 B:C9A998 3.7 41.6 1.0 CB B:PRO479 3.7 36.4 1.0 C B:SER478 3.8 35.5 1.0 O B:SER478 3.9 34.6 1.0 CG1 B:ILE482 4.0 43.1 1.0 CG2 B:ILE482 4.0 37.1 1.0 CD B:PRO479 4.0 36.8 1.0 C29 B:C9A998 4.2 41.0 1.0 C3 B:C9A998 4.2 48.6 1.0 C6 B:C9A998 4.4 45.8 1.0 C B:TYR477 4.4 35.6 1.0 C B:PRO479 4.5 34.8 1.0 CG B:PRO479 4.5 36.7 1.0 CB B:ILE482 4.7 39.4 1.0 CA B:SER478 4.7 35.3 1.0 O B:PRO479 4.8 36.5 1.0 C13 B:C9A998 4.9 41.9 1.0 N B:SER478 5.0 35.6 1.0 O14 B:C9A998 5.0 42.3 1.0

Fluorine binding site 3 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F997 b:47.6 occ:1.00 F10 C:C9A997 0.0 47.6 1.0 C9 C:C9A997 1.3 45.5 1.0 C11 C:C9A997 2.3 44.7 1.0 C8 C:C9A997 2.4 47.2 1.0 N5 C:C9A997 2.9 50.6 1.0 CA C:PRO479 3.1 35.7 1.0 N C:PRO479 3.3 35.4 1.0 C4 C:C9A997 3.3 51.1 1.0 CB C:PRO479 3.5 35.1 1.0 O C:TYR477 3.5 35.6 1.0 C12 C:C9A997 3.6 42.5 1.0 C30 C:C9A997 3.7 43.2 1.0 C C:SER478 3.7 35.0 1.0 CD C:PRO479 3.8 34.4 1.0 O C:SER478 3.9 34.0 1.0 CG1 C:ILE482 4.2 40.5 1.0 CG C:PRO479 4.2 34.6 1.0 C29 C:C9A997 4.2 40.7 1.0 CB C:ILE482 4.2 40.1 1.0 C6 C:C9A997 4.3 51.7 1.0 CD1 C:ILE482 4.3 44.0 1.0 C3 C:C9A997 4.3 53.0 1.0 C C:PRO479 4.4 36.5 1.0 C C:TYR477 4.5 36.2 1.0 CA C:SER478 4.7 34.6 1.0 O C:PRO479 4.8 37.2 1.0 C13 C:C9A997 4.9 43.5 1.0 CG2 C:ILE482 4.9 39.7 1.0 N C:SER478 5.0 35.0 1.0

Fluorine binding site 4 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:F996 b:50.7 occ:1.00 F10 D:C9A996 0.0 50.7 1.0 C9 D:C9A996 1.3 48.8 1.0 C11 D:C9A996 2.3 47.1 1.0 C8 D:C9A996 2.4 48.5 1.0 N5 D:C9A996 2.9 50.6 1.0 CA D:PRO479 3.2 41.2 1.0 N D:PRO479 3.3 40.6 1.0 C4 D:C9A996 3.4 52.6 1.0 O D:TYR477 3.4 44.8 1.0 CB D:PRO479 3.5 42.1 1.0 C12 D:C9A996 3.6 45.4 1.0 C30 D:C9A996 3.7 46.4 1.0 C D:SER478 3.8 40.8 1.0 CD D:PRO479 3.8 41.5 1.0 CG2 D:ILE482 4.0 42.1 1.0 O D:SER478 4.1 41.1 1.0 C29 D:C9A996 4.2 45.4 1.0 CG D:PRO479 4.2 43.2 1.0 C6 D:C9A996 4.3 51.0 1.0 CG1 D:ILE482 4.3 41.7 1.0 C3 D:C9A996 4.4 55.0 1.0 C D:TYR477 4.4 43.1 1.0 C D:PRO479 4.5 40.9 1.0 CA D:SER478 4.7 40.8 1.0 CB D:ILE482 4.8 43.0 1.0 C13 D:C9A996 4.8 44.6 1.0 O D:PRO479 4.9 43.0 1.0 O14 D:C9A996 5.0 46.6 1.0 N D:SER478 5.0 42.1 1.0

D.V.Kumar, R.Rai, K.A.Brameld, J.R.Somoza, R.Rajagopalan, J.W.Janc, Y.M.Xia, T.L.Ton, M.B.Shaghafi, H.Hu, I.Lehoux, N.To, W.B.Young, M.J.Green. Quinolones As Hcv NS5B Polymerase Inhibitors. Bioorg.Med.Chem.Lett. V. 21 82 2011.
ISSN: ISSN 0960-894X
PubMed: 21145235
DOI: 10.1016/J.BMCL.2010.11.068