Fluorine in PDB 2yoj: Hcv NS5B Polymerase Complexed with Pyridonylindole Compound

All present enzymatic activity of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound:
2.7.7.48;

The structure of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound, PDB code: 2yoj was solved by K.X.Chen, S.Venkatraman, G.N.Anilkumar, Q.Zeng, C.A.Lesburg, B.Vibulbhan, W.Yang, F.Velazquez, T.-Y.Chan, F.Bennett, M.Sannigrahi, Y.Jiang, J.S.Duca, P.Pinto, S.Gavalas, Y.Huang, W.Wu, O.Selyutin, S.Agrawal, B.Feld, H.-C.Huang, C.Li, K.-C.Cheng, N.-Y.Shih, J.A.Kozlowski, S.B.Rosenblum, F.G.Njoroge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.271, 106.227, 134.553, 90.00, 90.00, 90.00
R / Rfree (%)	17.67 / 20.89

The binding sites of Fluorine atom in the Hcv NS5B Polymerase Complexed with Pyridonylindole Compound (pdb code 2yoj). 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 Polymerase Complexed with Pyridonylindole Compound, PDB code: 2yoj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hcv NS5B Polymerase Complexed with Pyridonylindole Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:F1569 b:22.3 occ:1.00 F1 A:8Y61569 0.0 22.3 1.0 C6 A:8Y61569 1.3 19.7 1.0 C1 A:8Y61569 2.3 17.7 1.0 C5 A:8Y61569 2.4 22.9 1.0 C15 A:8Y61569 2.8 17.1 1.0 CB A:ASN316 3.1 13.3 1.0 O A:HOH2613 3.3 35.4 1.0 O A:HOH2306 3.4 34.2 1.0 SG A:CYS366 3.5 21.1 1.0 O A:ASN316 3.6 18.4 1.0 C2 A:8Y61569 3.6 19.0 1.0 C4 A:8Y61569 3.6 24.5 1.0 CZ A:PHE193 3.8 18.5 1.0 CG A:ASN316 3.9 16.1 1.0 ND2 A:ASN316 4.0 17.5 1.0 CE1 A:PHE193 4.1 18.0 1.0 C A:ASN316 4.1 19.3 1.0 C3 A:8Y61569 4.1 20.8 1.0 CA A:ASN316 4.2 13.4 1.0 N1 A:8Y61569 4.2 16.0 1.0 O A:HOH2854 4.4 25.6 1.0 CB A:ASP319 4.4 19.9 1.0 CB A:CYS366 4.5 18.2 1.0 O3 A:8Y61569 4.6 18.9 1.0 CE2 A:PHE193 4.7 18.7 1.0 N4 A:8Y61569 4.8 23.8 1.0 OD1 A:ASN316 4.9 16.9 1.0

Fluorine binding site 2 out of 4 in the Hcv NS5B Polymerase Complexed with Pyridonylindole Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:F1569 b:17.2 occ:1.00 F2 A:8Y61569 0.0 17.2 1.0 C12 A:8Y61569 1.3 17.2 1.0 C13 A:8Y61569 2.4 15.3 1.0 C22 A:8Y61569 2.4 16.2 1.0 CD A:ARG200 3.1 15.0 1.0 C25 A:8Y61569 3.1 18.6 1.0 NE A:ARG200 3.2 17.0 1.0 C9 A:8Y61569 3.6 14.8 1.0 C23 A:8Y61569 3.6 17.1 1.0 O A:HOH2513 3.7 22.5 1.0 CD1 A:LEU384 3.8 17.1 1.0 CB A:CYS366 3.8 18.2 1.0 CZ A:ARG200 3.9 27.7 1.0 OG A:SER368 4.0 20.1 1.0 C8 A:8Y61569 4.1 14.6 1.0 CB A:SER368 4.2 17.8 1.0 C24 A:8Y61569 4.4 15.1 1.0 CG A:ARG200 4.5 17.0 1.0 NH1 A:ARG200 4.5 17.9 1.0 O A:SER365 4.5 20.0 1.0 O A:HOH2500 4.6 16.7 1.0 SG A:CYS366 4.6 21.1 1.0 O5 A:8Y61569 4.6 15.5 1.0 NH2 A:ARG200 4.7 17.4 1.0 O A:CYS366 4.7 19.6 1.0 CG A:LEU384 4.8 16.8 1.0 N1 A:8Y61569 4.8 16.0 1.0

Fluorine binding site 3 out of 4 in the Hcv NS5B Polymerase Complexed with Pyridonylindole Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:F1564 b:23.0 occ:1.00 F1 B:8Y61564 0.0 23.0 1.0 C6 B:8Y61564 1.3 24.9 1.0 C5 B:8Y61564 2.4 25.4 1.0 C1 B:8Y61564 2.4 19.7 1.0 C15 B:8Y61564 2.9 19.9 1.0 O B:HOH2513 3.1 35.0 1.0 CB B:ASN316 3.1 15.8 1.0 SG B:CYS366 3.4 23.3 1.0 O B:ASN316 3.5 17.6 1.0 O B:HOH2252 3.5 35.6 1.0 C4 B:8Y61564 3.6 24.9 1.0 C2 B:8Y61564 3.6 18.9 1.0 CZ B:PHE193 3.8 18.9 1.0 CG B:ASN316 4.0 24.1 1.0 C B:ASN316 4.0 17.9 1.0 C3 B:8Y61564 4.1 22.2 1.0 CE1 B:PHE193 4.1 19.8 1.0 ND2 B:ASN316 4.1 18.6 1.0 CA B:ASN316 4.2 15.0 1.0 N1 B:8Y61564 4.3 21.1 1.0 CB B:ASP319 4.3 19.4 1.0 CB B:CYS366 4.5 20.1 1.0 O B:HOH2690 4.5 29.8 1.0 O3 B:8Y61564 4.6 18.0 1.0 CE2 B:PHE193 4.8 20.1 1.0 N4 B:8Y61564 4.8 25.2 1.0 OD1 B:ASN316 4.9 21.3 1.0

Fluorine binding site 4 out of 4 in the Hcv NS5B Polymerase Complexed with Pyridonylindole Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS5B Polymerase Complexed with Pyridonylindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:F1564 b:22.3 occ:1.00 F2 B:8Y61564 0.0 22.3 1.0 C12 B:8Y61564 1.3 21.2 1.0 C13 B:8Y61564 2.3 19.2 1.0 C22 B:8Y61564 2.4 20.7 1.0 CD B:ARG200 3.1 18.3 1.0 C25 B:8Y61564 3.1 20.9 1.0 NE B:ARG200 3.2 19.2 1.0 CD1 B:LEU384 3.6 25.6 1.0 C9 B:8Y61564 3.6 20.5 1.0 C23 B:8Y61564 3.6 19.0 1.0 O B:HOH2399 3.7 26.1 1.0 CB B:CYS366 3.9 20.1 1.0 CZ B:ARG200 3.9 27.6 1.0 OG B:SER368 4.0 24.0 1.0 C8 B:8Y61564 4.1 17.6 1.0 CB B:SER368 4.1 21.0 1.0 C24 B:8Y61564 4.4 21.1 1.0 NH1 B:ARG200 4.5 20.5 1.0 CG B:ARG200 4.5 19.4 1.0 O B:SER365 4.5 22.3 1.0 O B:CYS366 4.6 22.1 1.0 O5 B:8Y61564 4.6 21.2 1.0 SG B:CYS366 4.6 23.3 1.0 NH2 B:ARG200 4.6 23.5 1.0 O B:HOH2383 4.7 20.8 1.0 CG B:LEU384 4.7 23.4 1.0 N1 B:8Y61564 4.9 21.1 1.0

K.X.Chen, S.Venkatraman, G.N.Anilkumar, Q.Zeng, C.A.Lesburg, B.Vibulbhan, F.Velazquez, T.-Y.Chan, F.Bennett, Y.Jiang, P.Pinto, Y.Huang, O.Selyutin, S.Agrawal, H.-C.Huang, C.Li, K.-C.Cheng, N.-Y.Shih, J.A.Kozlowski, S.B.Rosenblum, F.G.Njoroge. Discovery of Sch 900188: A Potent Hepatitis C Virus NS5B Polymerase Inhibitor Prodrug As A Development Candidate Acs Med.Chem.Lett. V. 5 244 2014.
ISSN: ISSN 1948-5875
PubMed: 24900812
DOI: 10.1021/ML400192W