Fluorine in PDB 3d5m: Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone Inhibitor

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone Inhibitor:
2.7.7.48;

The structure of Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone Inhibitor, PDB code: 3d5m was solved by Q.Zhao, R.E.Showalter, Q.Han, C.R.Kissinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.304, 106.765, 126.254, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.1

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

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone Inhibitor (pdb code 3d5m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone Inhibitor, PDB code: 3d5m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone 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 Polymerase with A Novel Pyridazinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F579 b:42.3 occ:1.00 F34 A:4MS579 0.0 42.3 1.0 C10 A:4MS579 1.4 44.6 1.0 C5 A:4MS579 2.4 44.4 1.0 C12 A:4MS579 2.4 43.3 1.0 CL37 A:4MS579 3.0 49.9 1.0 CA A:PRO197 3.3 41.4 1.0 CD A:ARG200 3.4 39.9 1.0 CD1 A:LEU384 3.5 45.0 1.0 C4 A:4MS579 3.6 44.4 1.0 C6 A:4MS579 3.7 44.8 1.0 CB A:PRO197 3.8 40.9 1.0 N A:PRO197 3.9 40.7 1.0 OH A:TYR448 4.0 35.9 1.0 CB A:ARG200 4.0 41.0 1.0 CG A:PRO197 4.0 41.3 1.0 CE A:MET414 4.1 37.1 1.0 C8 A:4MS579 4.2 43.8 1.0 CG A:ARG200 4.2 40.3 1.0 O A:SER196 4.4 42.0 1.0 O A:HOH630 4.4 41.4 1.0 NE A:ARG200 4.4 37.9 1.0 C A:PRO197 4.4 43.3 1.0 C A:SER196 4.5 41.2 1.0 O A:PRO197 4.5 41.9 1.0 CD A:PRO197 4.5 40.2 1.0 CG A:LEU384 4.9 45.0 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Hcv NS5B Polymerase with A Novel Pyridazinone 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 Polymerase with A Novel Pyridazinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F579 b:39.0 occ:1.00 F34 B:4MS579 0.0 39.0 1.0 C10 B:4MS579 1.3 41.3 1.0 C12 B:4MS579 2.3 42.2 1.0 C5 B:4MS579 2.4 41.5 1.0 CL37 B:4MS579 2.9 47.4 1.0 CA B:PRO197 3.4 39.6 1.0 CD B:ARG200 3.4 37.4 1.0 CD1 B:LEU384 3.5 40.7 1.0 C4 B:4MS579 3.6 43.5 1.0 C6 B:4MS579 3.6 43.5 1.0 CB B:PRO197 3.8 38.0 1.0 CE B:MET414 4.0 42.7 1.0 OH B:TYR448 4.0 39.6 1.0 CB B:ARG200 4.0 41.1 1.0 N B:PRO197 4.1 38.3 1.0 C8 B:4MS579 4.1 41.8 1.0 CG B:PRO197 4.2 39.0 1.0 CG B:ARG200 4.3 39.4 1.0 NE B:ARG200 4.5 34.9 1.0 C B:PRO197 4.5 40.9 1.0 O B:PRO197 4.5 40.4 1.0 O B:SER196 4.6 37.9 1.0 C B:SER196 4.6 37.6 1.0 O B:HOH621 4.7 41.3 1.0 CD B:PRO197 4.7 36.0 1.0 CG B:LEU384 4.8 40.5 1.0 CB B:LEU384 5.0 39.7 1.0

S.H.Kim, M.T.Tran, F.Ruebsam, A.X.Xiang, B.Ayida, H.Mcguire, D.Ellis, J.Blazel, C.V.Tran, D.E.Murphy, S.E.Webber, Y.Zhou, A.M.Shah, M.Tsan, R.E.Showalter, R.Patel, A.Gobbi, L.A.Lebrun, D.M.Bartkowski, T.G.Nolan, D.A.Norris, M.V.Sergeeva, L.Kirkovsky, Q.Zhao, Q.Han, C.R.Kissinger. Structure-Based Design, Synthesis, and Biological Evaluation of 1,1-Dioxoisothiazole and Benzo[B]Thiophene-1,1-Dioxide Derivatives As Novel Inhibitors of Hepatitis C Virus NS5B Polymerase. Bioorg.Med.Chem.Lett. V. 18 4181 2008.
ISSN: ISSN 0960-894X
PubMed: 18554907
DOI: 10.1016/J.BMCL.2008.05.083