Fluorine in PDB 3udl: 3-Heterocyclyl Quinolone Bound to Hcv NS5B

The structure of 3-Heterocyclyl Quinolone Bound to Hcv NS5B, PDB code: 3udl was solved by J.R.Somoza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.91 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.746, 101.863, 250.867, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.3

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B (pdb code 3udl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 20 binding sites of Fluorine where determined in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B, PDB code: 3udl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ A:F571 b:44.6 occ:1.00 F39 A:KLI571 0.0 44.6 1.0 C24 A:KLI571 1.3 46.6 1.0 F41 A:KLI571 2.2 44.5 1.0 F40 A:KLI571 2.2 46.8 1.0 C21 A:KLI571 2.3 40.3 1.0 C22 A:KLI571 3.2 42.1 1.0 N A:ALA486 3.2 32.9 1.0 C20 A:KLI571 3.2 41.5 1.0 O A:ILE482 3.3 38.6 1.0 CG1 A:VAL485 3.5 28.9 1.0 CA A:ALA486 3.5 40.1 1.0 CB A:VAL485 3.5 32.4 1.0 CB A:ALA486 3.6 37.2 1.0 CG2 A:ILE482 3.7 32.5 1.0 C A:VAL485 3.8 32.5 1.0 C A:ILE482 4.2 30.8 1.0 CA A:VAL485 4.3 35.8 1.0 C23 A:KLI571 4.4 44.9 1.0 C19 A:KLI571 4.4 41.8 1.0 CA A:ILE482 4.5 36.6 1.0 O A:VAL485 4.5 32.3 1.0 CD2 A:LEU419 4.6 32.9 1.0 CB A:ILE482 4.7 31.5 1.0 CG2 A:VAL485 4.7 32.3 1.0 O A:HOH617 4.7 37.6 1.0 CD1 A:ILE482 4.8 40.7 1.0 CD1 A:LEU489 4.8 35.3 1.0 C18 A:KLI571 4.9 40.0 1.0 N A:VAL485 5.0 33.5 1.0 C A:ALA486 5.0 34.4 1.0

Fluorine binding site 2 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ A:F571 b:46.8 occ:1.00 F40 A:KLI571 0.0 46.8 1.0 C24 A:KLI571 1.3 46.6 1.0 F39 A:KLI571 2.2 44.6 1.0 F41 A:KLI571 2.2 44.5 1.0 C21 A:KLI571 2.4 40.3 1.0 C20 A:KLI571 2.8 41.5 1.0 O A:HOH617 3.1 37.6 1.0 CB A:ALA486 3.2 37.2 1.0 CA A:ALA486 3.4 40.1 1.0 C22 A:KLI571 3.6 42.1 1.0 N A:ALA486 3.9 32.9 1.0 C19 A:KLI571 4.2 41.8 1.0 CD1 A:LEU489 4.3 35.3 1.0 C A:ALA486 4.7 34.4 1.0 O A:ILE482 4.7 38.6 1.0 C A:VAL485 4.8 32.5 1.0 C23 A:KLI571 4.8 44.9 1.0 CG A:LEU489 4.9 38.2 1.0 CG2 A:ILE482 4.9 32.5 1.0 O A:ALA486 5.0 39.9 1.0 CG1 A:VAL485 5.0 28.9 1.0

Fluorine binding site 3 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ A:F571 b:44.5 occ:1.00 F41 A:KLI571 0.0 44.5 1.0 C24 A:KLI571 1.3 46.6 1.0 F39 A:KLI571 2.2 44.6 1.0 F40 A:KLI571 2.2 46.8 1.0 C21 A:KLI571 2.4 40.3 1.0 C22 A:KLI571 2.8 42.1 1.0 O A:HOH617 3.2 37.6 1.0 CD1 A:LEU489 3.6 35.3 1.0 C20 A:KLI571 3.6 41.5 1.0 CE A:MET423 3.7 22.2 1.0 CG1 A:VAL485 4.0 28.9 1.0 C23 A:KLI571 4.1 44.9 1.0 SD A:MET423 4.2 35.0 1.0 CD2 A:LEU419 4.4 32.9 1.0 CG A:LEU489 4.5 38.2 1.0 CA A:ALA486 4.7 40.1 1.0 N A:ALA486 4.7 32.9 1.0 C19 A:KLI571 4.8 41.8 1.0 N A:LEU497 4.8 34.9 1.0 CB A:VAL485 4.8 32.4 1.0 F42 A:KLI571 4.9 49.7 1.0 CB A:LEU497 5.0 35.3 1.0 CB A:ALA486 5.0 37.2 1.0 C18 A:KLI571 5.0 40.0 1.0

Fluorine binding site 4 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ A:F571 b:49.7 occ:1.00 F42 A:KLI571 0.0 49.7 1.0 C23 A:KLI571 1.4 44.9 1.0 C22 A:KLI571 2.4 42.1 1.0 C18 A:KLI571 2.4 40.0 1.0 C12 A:KLI571 2.7 41.9 1.0 C17 A:KLI571 2.9 38.6 1.0 N01 A:KLI571 2.9 46.0 1.0 CD2 A:LEU497 3.2 45.7 1.0 CD1 A:LEU419 3.6 26.1 1.0 C13 A:KLI571 3.6 43.2 1.0 C21 A:KLI571 3.7 40.3 1.0 C19 A:KLI571 3.7 41.8 1.0 N02 A:KLI571 3.7 45.5 1.0 C09 A:KLI571 4.0 43.7 1.0 C15 A:KLI571 4.1 40.1 1.0 C20 A:KLI571 4.2 41.5 1.0 CG A:LEU497 4.3 37.9 1.0 CB A:LEU497 4.5 35.3 1.0 CD1 A:LEU497 4.5 33.6 1.0 C14 A:KLI571 4.6 41.8 1.0 C10 A:KLI571 4.7 37.9 1.0 C32 A:KLI571 4.7 38.4 1.0 CG A:LEU419 4.7 29.9 1.0 CD2 A:LEU419 4.8 32.9 1.0 C08 A:KLI571 4.9 41.9 1.0 C24 A:KLI571 4.9 46.6 1.0 F41 A:KLI571 4.9 44.5 1.0 C16 A:KLI571 5.0 48.1 1.0 CD1 A:ILE482 5.0 40.7 1.0

Fluorine binding site 5 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ A:F571 b:51.5 occ:1.00 F43 A:KLI571 0.0 51.5 1.0 C06 A:KLI571 1.4 43.9 1.0 C11 A:KLI571 2.4 40.4 1.0 C07 A:KLI571 2.4 45.6 1.0 N04 A:KLI571 2.8 46.0 1.0 CA A:PRO479 3.1 33.5 1.0 C25 A:KLI571 3.2 44.5 1.0 N A:PRO479 3.4 32.9 1.0 O A:TYR477 3.4 32.8 1.0 CB A:PRO479 3.6 36.1 1.0 C10 A:KLI571 3.7 37.9 1.0 C08 A:KLI571 3.7 41.9 1.0 C A:SER478 3.7 36.8 1.0 O A:SER478 3.8 35.1 1.0 CD A:PRO479 4.0 41.4 1.0 CG1 A:ILE482 4.1 31.5 1.0 C28 A:KLI571 4.2 42.2 1.0 C09 A:KLI571 4.2 43.7 1.0 CB A:ILE482 4.4 31.5 1.0 CG A:PRO479 4.4 44.7 1.0 C26 A:KLI571 4.4 55.3 1.0 C A:TYR477 4.5 40.6 1.0 C A:PRO479 4.5 35.4 1.0 CA A:SER478 4.7 37.5 1.0 N05 A:KLI571 4.7 49.3 1.0 O A:PRO479 4.8 38.8 1.0 C14 A:KLI571 4.9 41.8 1.0 CG2 A:ILE482 5.0 32.5 1.0

Fluorine binding site 6 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ B:F571 b:51.7 occ:1.00 F39 B:KLI571 0.0 51.7 1.0 C24 B:KLI571 1.3 54.0 1.0 F41 B:KLI571 2.2 47.3 1.0 F40 B:KLI571 2.2 57.3 1.0 C21 B:KLI571 2.3 46.8 1.0 N B:ALA486 3.1 38.6 1.0 C20 B:KLI571 3.2 46.3 1.0 C22 B:KLI571 3.2 44.2 1.0 CA B:ALA486 3.3 42.6 1.0 O B:ILE482 3.3 36.8 1.0 CB B:ALA486 3.4 44.3 1.0 CG1 B:VAL485 3.6 37.2 1.0 CB B:VAL485 3.7 35.1 1.0 C B:VAL485 3.8 43.9 1.0 CG2 B:ILE482 3.9 41.2 1.0 CD1 B:LEU489 4.3 44.8 1.0 C B:ILE482 4.4 35.8 1.0 CA B:VAL485 4.4 40.7 1.0 C19 B:KLI571 4.4 47.3 1.0 C23 B:KLI571 4.4 48.6 1.0 O B:VAL485 4.4 29.3 1.0 CD2 B:LEU419 4.6 36.2 1.0 O B:HOH728 4.7 45.0 1.0 CA B:ILE482 4.7 39.7 1.0 C B:ALA486 4.7 38.3 1.0 CB B:ILE482 4.9 39.0 1.0 C18 B:KLI571 4.9 47.2 1.0 CG B:LEU489 4.9 43.6 1.0 CG2 B:VAL485 5.0 39.8 1.0

Fluorine binding site 7 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ B:F571 b:57.3 occ:1.00 F40 B:KLI571 0.0 57.3 1.0 C24 B:KLI571 1.3 54.0 1.0 F39 B:KLI571 2.2 51.7 1.0 F41 B:KLI571 2.2 47.3 1.0 C21 B:KLI571 2.4 46.8 1.0 C20 B:KLI571 2.8 46.3 1.0 O B:HOH728 2.9 45.0 1.0 C22 B:KLI571 3.6 44.2 1.0 CA B:ALA486 3.7 42.6 1.0 CB B:ALA486 3.7 44.3 1.0 CD1 B:LEU489 3.7 44.8 1.0 C19 B:KLI571 4.2 47.3 1.0 N B:ALA486 4.3 38.6 1.0 CG B:LEU489 4.7 43.6 1.0 C23 B:KLI571 4.7 48.6 1.0 C B:ALA486 4.9 38.3 1.0 C B:VAL485 5.0 43.9 1.0

Fluorine binding site 8 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ B:F571 b:47.3 occ:1.00 F41 B:KLI571 0.0 47.3 1.0 C24 B:KLI571 1.3 54.0 1.0 F39 B:KLI571 2.2 51.7 1.0 F40 B:KLI571 2.2 57.3 1.0 C21 B:KLI571 2.4 46.8 1.0 C22 B:KLI571 2.7 44.2 1.0 CD1 B:LEU489 3.3 44.8 1.0 O B:HOH728 3.4 45.0 1.0 CE B:MET423 3.4 27.3 1.0 C20 B:KLI571 3.6 46.3 1.0 CG1 B:VAL485 4.0 37.2 1.0 C23 B:KLI571 4.1 48.6 1.0 SD B:MET423 4.2 36.8 1.0 CD2 B:LEU419 4.2 36.2 1.0 CG B:LEU489 4.5 43.6 1.0 N B:LEU497 4.7 34.3 1.0 N B:ALA486 4.7 38.6 1.0 CA B:ALA486 4.8 42.6 1.0 C19 B:KLI571 4.8 47.3 1.0 CB B:LEU497 4.8 36.8 1.0 CB B:VAL485 4.8 35.1 1.0 F42 B:KLI571 4.9 52.3 1.0 C18 B:KLI571 5.0 47.2 1.0

Fluorine binding site 9 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ B:F571 b:52.3 occ:1.00 F42 B:KLI571 0.0 52.3 1.0 C23 B:KLI571 1.4 48.6 1.0 C22 B:KLI571 2.4 44.2 1.0 C18 B:KLI571 2.4 47.2 1.0 C12 B:KLI571 2.6 40.9 1.0 C17 B:KLI571 2.9 40.8 1.0 N01 B:KLI571 2.9 50.4 1.0 CD1 B:LEU419 3.4 36.8 1.0 CD2 B:LEU497 3.5 39.7 1.0 C13 B:KLI571 3.5 42.2 1.0 C21 B:KLI571 3.7 46.8 1.0 C19 B:KLI571 3.7 47.3 1.0 N02 B:KLI571 3.7 46.9 1.0 C09 B:KLI571 4.0 42.2 1.0 C15 B:KLI571 4.1 41.0 1.0 C20 B:KLI571 4.2 46.3 1.0 CG B:LEU497 4.4 38.7 1.0 CD1 B:LEU497 4.4 36.8 1.0 C14 B:KLI571 4.5 35.2 1.0 C32 B:KLI571 4.5 36.0 1.0 CG B:LEU419 4.6 38.6 1.0 CD1 B:ILE482 4.6 49.0 1.0 C10 B:KLI571 4.6 42.9 1.0 CB B:LEU497 4.7 36.8 1.0 CD2 B:LEU419 4.7 36.2 1.0 C33 B:KLI571 4.8 37.4 1.0 C08 B:KLI571 4.8 42.4 1.0 C24 B:KLI571 4.9 54.0 1.0 F41 B:KLI571 4.9 47.3 1.0 C16 B:KLI571 4.9 47.4 1.0

Fluorine binding site 10 out of 20 in the 3-Heterocyclyl Quinolone Bound to Hcv NS5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 3-Heterocyclyl Quinolone Bound to Hcv NS5B within 5.0Å range: probe atom residue distance (Å) B Occ B:F571 b:53.4 occ:1.00 F43 B:KLI571 0.0 53.4 1.0 C06 B:KLI571 1.4 49.4 1.0 C11 B:KLI571 2.4 44.1 1.0 C07 B:KLI571 2.4 55.5 1.0 C28 B:KLI571 2.8 55.6 1.0 N04 B:KLI571 2.9 49.2 1.0 CA B:PRO479 3.2 39.8 1.0 N B:PRO479 3.3 39.5 1.0 O B:TYR477 3.5 40.9 1.0 CB B:PRO479 3.6 42.0 1.0 C10 B:KLI571 3.7 42.9 1.0 C08 B:KLI571 3.7 42.4 1.0 CD B:PRO479 3.7 47.9 1.0 C27 B:KLI571 3.8 66.2 1.0 C B:SER478 3.8 37.9 1.0 O B:SER478 4.1 38.0 1.0 C09 B:KLI571 4.2 42.2 1.0 CG1 B:ILE482 4.2 40.9 1.0 CG B:PRO479 4.3 48.8 1.0 C25 B:KLI571 4.3 46.5 1.0 CB B:ILE482 4.5 39.0 1.0 C B:TYR477 4.5 46.1 1.0 C B:PRO479 4.6 37.7 1.0 CA B:SER478 4.7 38.4 1.0 C14 B:KLI571 4.9 35.2 1.0 C26 B:KLI571 4.9 54.5 1.0 N05 B:KLI571 5.0 56.9 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