Fluorine in PDB 5w2e: Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876

All present enzymatic activity of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

The structure of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876, PDB code: 5w2e was solved by C.A.Lesburg, A.Ummat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.15 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.092, 106.418, 126.091, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.9

The binding sites of Fluorine atom in the Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876 (pdb code 5w2e). 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 Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876, PDB code: 5w2e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:51.4 occ:1.00 F1 A:9VY601 0.0 51.4 1.0 C27 A:9VY601 1.3 46.7 1.0 C28 A:9VY601 2.3 45.6 1.0 C26 A:9VY601 2.3 46.4 1.0 H17 A:9VY601 2.6 46.7 1.0 H18 A:9VY601 2.6 45.7 1.0 O A:HOH703 2.9 21.9 1.0 CG2 A:ILE363 3.1 24.8 1.0 CB A:ILE363 3.2 26.1 1.0 C29 A:9VY601 3.6 46.2 1.0 C25 A:9VY601 3.6 45.0 1.0 O A:ILE363 3.6 33.7 1.0 C A:ILE363 4.0 34.2 1.0 C24 A:9VY601 4.1 43.8 1.0 CD1 A:LEU360 4.1 39.2 1.0 CA A:ILE363 4.1 25.1 1.0 O A:LEU360 4.2 40.6 1.0 CD1 A:ILE363 4.3 27.4 1.0 CG1 A:ILE363 4.3 26.0 1.0 CD1 A:LEU204 4.3 34.8 1.0 H19 A:9VY601 4.4 46.7 1.0 H16 A:9VY601 4.4 44.8 1.0 CG2 A:VAL321 4.5 22.9 1.0 CG2 A:VAL370 4.6 43.0 1.0 CG1 A:VAL321 4.7 23.0 1.0 N A:ILE363 4.8 26.8 1.0 N A:THR364 4.8 33.9 1.0 CD2 A:LEU204 4.9 37.7 1.0 CG A:LEU360 5.0 39.4 1.0

Fluorine binding site 2 out of 4 in the Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:47.6 occ:1.00 F A:9VY601 0.0 47.6 1.0 C16 A:9VY601 1.4 50.5 1.0 C14 A:9VY601 2.4 53.3 1.0 C17 A:9VY601 2.4 50.5 1.0 H9 A:9VY601 2.6 50.5 1.0 H8 A:9VY601 3.0 54.8 1.0 C15 A:9VY601 3.0 54.1 1.0 CD2 A:LEU466 3.3 27.6 1.0 CG A:PRO197 3.4 37.7 1.0 CD A:PRO197 3.5 33.3 1.0 C13 A:9VY601 3.6 55.0 1.0 C18 A:9VY601 3.6 50.2 1.0 CG2 A:ILE413 3.6 32.4 1.0 CZ A:PHE551 3.8 76.8 1.0 O A:ILE413 3.8 31.3 1.0 CA A:MET414 3.9 25.7 1.0 CE1 A:PHE551 4.1 78.5 1.0 C A:ILE413 4.1 30.3 1.0 CG A:MET414 4.1 32.0 1.0 C19 A:9VY601 4.1 52.6 1.0 N A:MET414 4.2 26.3 1.0 CG A:LEU466 4.3 32.7 1.0 C12 A:9VY601 4.3 54.6 1.0 O1 A:9VY601 4.3 44.0 1.0 H10 A:9VY601 4.5 49.6 1.0 N2 A:9VY601 4.6 57.6 1.0 CB A:MET414 4.6 27.3 1.0 CB A:PRO197 4.8 34.4 1.0 CB A:ILE413 4.9 29.5 1.0 N A:PRO197 4.9 32.6 1.0

Fluorine binding site 3 out of 4 in the Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:68.9 occ:1.00 F1 B:9VY601 0.0 68.9 1.0 C27 B:9VY601 1.3 65.5 1.0 C26 B:9VY601 2.3 65.1 1.0 C28 B:9VY601 2.3 65.0 1.0 H17 B:9VY601 2.6 65.4 1.0 H18 B:9VY601 2.6 64.7 1.0 O B:HOH708 3.2 41.0 1.0 CG2 B:ILE363 3.2 41.5 1.0 CB B:ILE363 3.3 40.1 1.0 C25 B:9VY601 3.6 65.4 1.0 C29 B:9VY601 3.6 65.6 1.0 O B:ILE363 3.7 45.0 1.0 CD1 B:LEU360 3.9 44.8 1.0 C24 B:9VY601 4.1 65.0 1.0 C B:ILE363 4.1 45.5 1.0 O B:LEU360 4.1 45.8 1.0 CA B:ILE363 4.2 38.1 1.0 CD1 B:ILE363 4.2 44.4 1.0 CD1 B:LEU204 4.2 36.9 1.0 CG1 B:ILE363 4.3 39.5 1.0 H16 B:9VY601 4.4 65.6 1.0 H19 B:9VY601 4.4 65.6 1.0 CG2 B:VAL370 4.6 46.6 1.0 CG2 B:VAL321 4.6 36.1 1.0 CG1 B:VAL321 4.6 36.1 1.0 CD2 B:LEU204 4.7 38.2 1.0 N B:ILE363 4.8 39.1 1.0 CG B:LEU360 4.8 45.0 1.0 CG B:LEU204 5.0 36.9 1.0 N B:THR364 5.0 45.0 1.0

Fluorine binding site 4 out of 4 in the Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS5B Rna-Dependent Rna Polymerase in Complex with Non-Nucleoside Inhibitor Mk-8876 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:52.8 occ:1.00 F B:9VY601 0.0 52.8 1.0 C16 B:9VY601 1.4 57.5 1.0 C17 B:9VY601 2.4 57.7 1.0 C14 B:9VY601 2.4 60.7 1.0 H9 B:9VY601 2.6 57.6 1.0 H8 B:9VY601 3.0 61.5 1.0 C15 B:9VY601 3.1 61.3 1.0 CD2 B:LEU466 3.3 51.6 1.0 CG B:PRO197 3.4 35.7 1.0 CD B:PRO197 3.6 31.1 1.0 CG2 B:ILE413 3.6 39.0 1.0 C13 B:9VY601 3.6 62.5 1.0 C18 B:9VY601 3.6 57.8 1.0 CZ B:PHE551 3.8 79.5 1.0 O B:ILE413 3.8 43.6 1.0 CA B:MET414 3.9 38.0 1.0 CE1 B:PHE551 4.1 80.7 1.0 C B:ILE413 4.1 41.3 1.0 CG B:MET414 4.1 43.3 1.0 C19 B:9VY601 4.1 60.6 1.0 N B:MET414 4.1 37.7 1.0 C12 B:9VY601 4.3 63.5 1.0 CG B:LEU466 4.3 50.8 1.0 H10 B:9VY601 4.5 57.2 1.0 O2 B:9VY601 4.5 64.4 1.0 CB B:MET414 4.6 39.4 1.0 N2 B:9VY601 4.6 64.1 1.0 H2 B:9VY601 4.7 63.5 1.0 CB B:ILE413 4.8 38.5 1.0 CB B:PRO197 4.9 31.6 1.0 N B:PRO197 5.0 30.1 1.0

C.C.Mccomas, A.Palani, W.Chang, M.K.Holloway, C.A.Lesburg, P.Li, N.Liverton, P.T.Meinke, D.B.Olsen, X.Peng, R.M.Soll, A.Ummat, J.Wu, J.Wu, N.Zorn, S.W.Ludmerer. Development of A New Structural Class of Broadly Acting Hcv Non-Nucleoside Inhibitors Leading to the Discovery of Mk-8876. Chemmedchem V. 12 1436 2017.
ISSN: ESSN 1860-7187
PubMed: 28741898
DOI: 10.1002/CMDC.201700228