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Fluorine in PDB 3g86: Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor

Enzymatic activity of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor

All present enzymatic activity of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor:
2.7.7.48;

Protein crystallography data

The structure of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor, PDB code: 3g86 was solved by S.F.Harris, M.Ghate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.915, 106.169, 126.940, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.8

Other elements in 3g86:

The structure of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor (pdb code 3g86). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor, PDB code: 3g86:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3g86

Go back to Fluorine Binding Sites List in 3g86
Fluorine binding site 1 out of 4 in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F571

b:16.3
occ:1.00
 F28 A:T18571 0.0 16.3 1.0
C18 A:T18571 1.3 16.3 1.0
C21 A:T18571 2.3 17.1 1.0
C19 A:T18571 2.4 16.6 1.0
C A:GLY410 2.9 12.4 1.0
O A:GLY410 3.1 12.7 1.0
CA A:GLY410 3.2 12.6 1.0
N A:ASN411 3.4 12.9 1.0
C22 A:T18571 3.6 15.7 1.0
C20 A:T18571 3.6 15.4 1.0
CG A:MET414 3.8 13.7 1.0
OD1 A:ASN411 3.9 13.5 1.0
O A:GLN446 4.0 19.6 1.0
O A:HOH653 4.0 20.5 1.0
CA A:ASN411 4.1 13.9 1.0
C23 A:T18571 4.1 16.2 1.0
CB A:MET414 4.4 13.2 1.0
N A:GLY410 4.4 12.4 1.0
CG A:ASN411 4.5 12.6 1.0
C27 A:T18571 4.8 16.1 1.0
O A:SER407 4.8 16.6 1.0
O29 A:T18571 4.9 14.4 1.0
CG1 A:ILE447 4.9 17.8 1.0
CB A:ASN411 4.9 13.6 1.0
O A:HOH645 4.9 15.8 1.0

Fluorine binding site 2 out of 4 in 3g86

Go back to Fluorine Binding Sites List in 3g86
Fluorine binding site 2 out of 4 in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F571

b:18.3
occ:1.00
 F38 A:T18571 0.0 18.3 1.0
C34 A:T18571 1.4 18.0 1.0
C36 A:T18571 2.4 16.1 1.0
C35 A:T18571 2.4 16.6 1.0
CA A:PRO197 3.0 14.6 1.0
CB A:PRO197 3.2 14.2 1.0
CG A:PRO197 3.6 13.9 1.0
CD2 A:LEU384 3.6 12.5 1.0
C33 A:T18571 3.6 17.3 1.0
C37 A:T18571 3.7 18.2 1.0
N A:PRO197 3.7 14.1 1.0
CD A:ARG200 3.8 12.9 1.0
CE A:MET414 4.0 14.5 1.0
CB A:ARG200 4.1 14.1 1.0
C32 A:T18571 4.1 16.4 1.0
OH A:TYR448 4.2 12.7 1.0
C A:PRO197 4.2 15.4 1.0
CD A:PRO197 4.2 14.2 1.0
O A:PRO197 4.3 16.4 1.0
C A:SER196 4.4 13.6 1.0
O A:SER196 4.4 14.1 1.0
CG A:ARG200 4.6 13.3 1.0
CG A:LEU384 4.6 16.4 1.0
NE A:ARG200 4.8 12.6 1.0
CB A:LEU384 4.9 15.2 1.0
O A:HOH578 4.9 9.3 1.0

Fluorine binding site 3 out of 4 in 3g86

Go back to Fluorine Binding Sites List in 3g86
Fluorine binding site 3 out of 4 in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F571

b:16.6
occ:1.00
 F28 B:T18571 0.0 16.6 1.0
C18 B:T18571 1.3 16.4 1.0
C21 B:T18571 2.3 16.6 1.0
C19 B:T18571 2.4 14.5 1.0
C B:GLY410 2.9 13.4 1.0
CA B:GLY410 3.1 13.5 1.0
O B:GLY410 3.2 14.1 1.0
N B:ASN411 3.4 13.5 1.0
C22 B:T18571 3.6 15.4 1.0
C20 B:T18571 3.6 14.4 1.0
O B:GLN446 3.7 18.7 1.0
CG B:MET414 3.9 12.6 1.0
OD1 B:ASN411 3.9 13.5 1.0
O B:HOH663 4.0 24.4 1.0
CA B:ASN411 4.1 14.4 1.0
C23 B:T18571 4.1 14.6 1.0
CB B:MET414 4.4 13.5 1.0
N B:GLY410 4.4 14.1 1.0
CG B:ASN411 4.5 14.0 1.0
O B:SER407 4.7 14.2 1.0
CG1 B:ILE447 4.7 17.2 1.0
C27 B:T18571 4.8 15.0 1.0
O29 B:T18571 4.9 11.6 1.0
CB B:ASN411 4.9 13.8 1.0
C B:GLN446 4.9 18.0 1.0

Fluorine binding site 4 out of 4 in 3g86

Go back to Fluorine Binding Sites List in 3g86
Fluorine binding site 4 out of 4 in the Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hepatitis C Virus Polymerase NS5B (Bk 1-570) with Thiazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F571

b:18.8
occ:1.00
 F38 B:T18571 0.0 18.8 1.0
C34 B:T18571 1.4 17.1 1.0
C36 B:T18571 2.4 14.7 1.0
C35 B:T18571 2.4 15.2 1.0
CA B:PRO197 3.0 15.1 1.0
CB B:PRO197 3.3 14.6 1.0
CG B:PRO197 3.6 14.0 1.0
C33 B:T18571 3.6 14.3 1.0
C37 B:T18571 3.6 18.1 1.0
CD2 B:LEU384 3.7 12.9 1.0
CD B:ARG200 3.7 14.1 1.0
N B:PRO197 3.7 14.6 1.0
CB B:ARG200 4.0 15.0 1.0
OH B:TYR448 4.0 10.7 1.0
CE B:MET414 4.1 8.9 1.0
C32 B:T18571 4.1 15.2 1.0
C B:PRO197 4.2 15.4 1.0
CD B:PRO197 4.2 14.7 1.0
O B:PRO197 4.3 16.2 1.0
C B:SER196 4.4 14.8 1.0
O B:SER196 4.4 14.9 1.0
CG B:ARG200 4.4 13.9 1.0
CG B:LEU384 4.6 15.8 1.0
O B:HOH614 4.8 17.0 1.0
NE B:ARG200 4.8 14.1 1.0
CB B:LEU384 4.9 16.1 1.0

Reference:

J.De Vicente, R.T.Hendricks, D.B.Smith, J.B.Fell, J.Fischer, S.R.Spencer, P.J.Stengel, P.Mohr, J.E.Robinson, J.F.Blake, R.K.Hilgenkamp, C.Yee, G.Adjabeng, T.R.Elworthy, J.Tracy, E.Chin, J.Li, B.Wang, J.T.Bamberg, R.Stephenson, C.Oshiro, S.F.Harris, M.Ghate, V.Leveque, I.Najera, S.Le Pogam, S.Rajyaguru, G.Ao-Ieong, L.Alexandrova, S.Larrabee, M.Brandl, A.Briggs, S.Sukhtankar, R.Farrell, B.Xu. Non-Nucleoside Inhibitors of Hcv Polymerase NS5B. Part 2: Synthesis and Structure-Activity Relationships of Benzothiazine-Substituted Quinolinediones Bioorg.Med.Chem.Lett. V. 19 3642 2009.
ISSN: ISSN 0960-894X
PubMed: 19457662
DOI: 10.1016/J.BMCL.2009.05.004
Page generated: Sun Dec 13 11:46:42 2020

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