Fluorine in PDB 4jjs: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2, PDB code: 4jjs was solved by R.Coulombe, 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 (°)	107.270, 105.740, 134.950, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2 (pdb code 4jjs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2, PDB code: 4jjs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2


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 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:48.5 occ:1.00 F31 A:1M9601 0.0 48.5 1.0 C27 A:1M9601 1.4 45.8 1.0 F32 A:1M9601 2.2 44.7 1.0 F33 A:1M9601 2.2 46.3 1.0 C26 A:1M9601 2.4 44.9 1.0 C25 A:1M9601 2.8 44.4 1.0 O A:HOH845 3.5 35.6 1.0 CA A:ALA486 3.5 36.0 1.0 CD1 A:LEU489 3.6 40.1 1.0 CB A:ALA486 3.6 34.4 1.0 N A:ALA486 3.7 34.1 1.0 C21 A:1M9601 3.8 41.2 1.0 CG1 A:VAL485 3.9 31.4 1.0 O20 A:1M9601 4.2 39.1 1.0 C24 A:1M9601 4.3 44.2 1.0 C A:VAL485 4.4 32.7 1.0 CG A:LEU489 4.4 40.5 1.0 CB A:VAL485 4.6 31.3 1.0 O A:ILE482 4.7 35.2 1.0 O A:VAL485 4.8 32.3 1.0 C A:ALA486 4.9 37.2 1.0 C22 A:1M9601 4.9 42.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2


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 in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:44.7 occ:1.00 F32 A:1M9601 0.0 44.7 1.0 C27 A:1M9601 1.3 45.8 1.0 F33 A:1M9601 2.1 46.3 1.0 F31 A:1M9601 2.2 48.5 1.0 C26 A:1M9601 2.4 44.9 1.0 O20 A:1M9601 3.0 39.1 1.0 C21 A:1M9601 3.1 41.2 1.0 O A:ILE482 3.4 35.2 1.0 CG1 A:VAL485 3.5 31.4 1.0 C25 A:1M9601 3.5 44.4 1.0 CB A:VAL485 3.6 31.3 1.0 CD2 A:LEU419 3.6 32.2 1.0 N A:ALA486 3.7 34.1 1.0 CG2 A:ILE482 4.0 35.1 1.0 CB A:ALA486 4.1 34.4 1.0 CA A:ALA486 4.2 36.0 1.0 CA A:ILE482 4.2 35.4 1.0 C14 A:1M9601 4.2 38.4 1.0 C A:ILE482 4.2 35.7 1.0 C A:VAL485 4.4 32.7 1.0 C22 A:1M9601 4.4 42.4 1.0 CB A:ILE482 4.5 34.9 1.0 CA A:VAL485 4.6 31.8 1.0 CG A:LEU419 4.7 34.1 1.0 CG2 A:VAL485 4.7 31.2 1.0 C24 A:1M9601 4.7 44.2 1.0 CG1 A:ILE482 4.7 35.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 2


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 Polymerase in Complex with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:46.3 occ:1.00 F33 A:1M9601 0.0 46.3 1.0 C27 A:1M9601 1.4 45.8 1.0 F32 A:1M9601 2.1 44.7 1.0 F31 A:1M9601 2.2 48.5 1.0 C26 A:1M9601 2.4 44.9 1.0 O20 A:1M9601 2.9 39.1 1.0 C21 A:1M9601 3.1 41.2 1.0 C25 A:1M9601 3.6 44.4 1.0 C14 A:1M9601 3.6 38.4 1.0 C15 A:1M9601 3.9 38.3 1.0 CD2 A:LEU419 3.9 32.2 1.0 O A:HOH845 3.9 35.6 1.0 CG1 A:VAL485 4.3 31.4 1.0 SD A:MET423 4.3 37.2 1.0 CG A:LEU419 4.4 34.1 1.0 C22 A:1M9601 4.4 42.4 1.0 CE A:MET423 4.5 37.6 1.0 CD1 A:LEU419 4.5 33.4 1.0 CD1 A:LEU489 4.7 40.1 1.0 C13 A:1M9601 4.7 37.9 1.0 C24 A:1M9601 4.8 44.2 1.0 CB A:LEU497 4.8 32.8 1.0

P.L.Beaulieu, R.Coulombe, J.Duan, G.Fazal, C.Godbout, O.Hucke, A.Jakalian, M.A.Joly, O.Lepage, M.Llinas-Brunet, J.Naud, M.Poirier, N.Rioux, B.Thavonekham, G.Kukolj, T.A.Stammers. Structure-Based Design of Novel Hcv NS5B Thumb Pocket 2 Allosteric Inhibitors with Submicromolar GT1 Replicon Potency: Discovery of A Quinazolinone Chemotype. Bioorg.Med.Chem.Lett. V. 23 4132 2013.
ISSN: ISSN 0960-894X
PubMed: 23768906
DOI: 10.1016/J.BMCL.2013.05.037