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Fluorine in PDB 3tyv: Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase

Enzymatic activity of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase

All present enzymatic activity of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase:
2.7.7.48;

Protein crystallography data

The structure of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase, PDB code: 3tyv was solved by C.A.Lesburg, K.X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.650, 106.720, 133.940, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase (pdb code 3tyv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase, PDB code: 3tyv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 1 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:28.5
occ:1.00
 F1 A:HI3578 0.0 28.5 1.0
C11 A:HI3578 1.3 24.1 1.0
C4 A:HI3578 2.3 19.8 1.0
C1 A:HI3578 2.4 26.5 1.0
OG A:SER367 3.0 29.8 1.0
O A:HOH1044 3.2 34.4 1.0
CB A:SER367 3.2 23.2 1.0
O A:HOH620 3.2 43.1 1.0
O A:CYS366 3.3 20.2 1.0
O A:HOH772 3.3 26.7 1.0
C A:CYS366 3.4 20.8 1.0
C2 A:HI3578 3.6 27.1 1.0
C9 A:HI3578 3.7 18.6 1.0
O A:HOH911 3.8 55.7 1.0
N A:SER367 3.8 19.4 1.0
O A:HOH643 3.9 21.5 1.0
O A:HOH843 4.0 52.1 1.0
CA A:CYS366 4.1 18.1 1.0
C12 A:HI3578 4.1 24.6 1.0
CA A:SER367 4.2 20.1 1.0
NH1 A:ARG386 4.6 19.7 1.0
CB A:CYS366 4.7 18.4 1.0
C21 A:HI3578 4.8 28.5 1.0
C25 A:HI3578 4.9 18.5 1.0
N1 A:HI3578 4.9 17.6 1.0

Fluorine binding site 2 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 2 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:25.4
occ:1.00
 F2 A:HI3578 0.0 25.4 1.0
C12 A:HI3578 1.3 24.6 1.0
C9 A:HI3578 2.3 18.6 1.0
C2 A:HI3578 2.4 27.1 1.0
C25 A:HI3578 2.8 18.5 1.0
O A:HOH874 3.0 30.2 1.0
CB A:ASN316 3.1 17.5 1.0
CZ A:PHE193 3.5 18.1 1.0
C23 A:HI3578 3.6 28.0 1.0
O A:ASN316 3.6 18.9 1.0
SG A:CYS366 3.6 21.6 1.0
C4 A:HI3578 3.6 19.8 1.0
C1 A:HI3578 3.6 26.5 1.0
CE1 A:PHE193 3.8 19.2 1.0
CG A:ASN316 3.9 18.6 1.0
ND2 A:ASN316 4.0 18.1 1.0
C11 A:HI3578 4.1 24.1 1.0
C A:ASN316 4.1 19.0 1.0
N1 A:HI3578 4.2 17.6 1.0
CA A:ASN316 4.2 15.9 1.0
N3 A:HI3578 4.3 18.1 1.0
CB A:ASP319 4.5 20.2 1.0
S1 A:HI3578 4.5 23.4 1.0
O3 A:HI3578 4.5 27.8 1.0
C21 A:HI3578 4.5 28.5 1.0
CE2 A:PHE193 4.6 19.6 1.0
C22 A:HI3578 4.7 26.7 1.0
CB A:CYS366 4.7 18.4 1.0
C20 A:HI3578 4.9 18.2 1.0
OD1 A:ASN316 4.9 17.0 1.0
C14 A:HI3578 5.0 17.0 1.0
CD1 A:PHE193 5.0 17.0 1.0

Fluorine binding site 3 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 3 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:22.3
occ:1.00
 F3 A:HI3578 0.0 22.3 1.0
C13 A:HI3578 1.3 18.7 1.0
C5 A:HI3578 2.3 17.6 1.0
C8 A:HI3578 2.4 16.6 1.0
C24 A:HI3578 2.8 20.2 1.0
CD A:ARG200 3.1 16.8 1.0
NE A:ARG200 3.5 18.5 1.0
CD1 A:LEU384 3.5 19.8 1.0
C10 A:HI3578 3.6 17.3 1.0
C3 A:HI3578 3.6 16.9 1.0
O A:HOH649 4.1 22.0 1.0
C6 A:HI3578 4.1 16.5 1.0
OG A:SER368 4.1 22.8 1.0
CB A:CYS366 4.1 18.4 1.0
CZ A:ARG200 4.4 24.0 1.0
CB A:SER368 4.5 20.8 1.0
CG A:ARG200 4.5 18.1 1.0
O A:HOH631 4.6 20.6 1.0
CG A:LEU384 4.7 19.6 1.0
O A:CYS366 4.8 20.2 1.0
NH1 A:ARG200 4.8 20.0 1.0
N1 A:HI3578 4.8 17.6 1.0
CB A:ARG200 4.9 15.2 1.0
OH A:TYR448 4.9 18.9 1.0
CB A:LEU384 4.9 16.7 1.0
SG A:CYS366 5.0 21.6 1.0

Fluorine binding site 4 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 4 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:28.3
occ:1.00
 F1 B:HI3577 0.0 28.3 1.0
C11 B:HI3577 1.3 25.7 1.0
C4 B:HI3577 2.4 23.0 1.0
C1 B:HI3577 2.4 26.6 1.0
OG B:SER367 3.1 33.8 1.0
O B:HOH655 3.1 44.2 1.0
CB B:SER367 3.2 26.3 1.0
O B:CYS366 3.3 23.2 1.0
O B:HOH651 3.3 25.3 1.0
C B:CYS366 3.4 24.3 1.0
C2 B:HI3577 3.6 26.8 1.0
C9 B:HI3577 3.6 21.2 1.0
N B:SER367 3.8 23.5 1.0
CA B:CYS366 4.0 21.6 1.0
O B:HOH670 4.1 26.1 1.0
C12 B:HI3577 4.1 26.7 1.0
CA B:SER367 4.1 22.6 1.0
CB B:CYS366 4.6 21.5 1.0
C21 B:HI3577 4.6 33.8 1.0
NH1 B:ARG386 4.8 25.9 1.0
C25 B:HI3577 4.9 19.7 1.0
N1 B:HI3577 5.0 20.5 1.0

Fluorine binding site 5 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 5 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:25.5
occ:1.00
 F2 B:HI3577 0.0 25.5 1.0
C12 B:HI3577 1.3 26.7 1.0
C2 B:HI3577 2.3 26.8 1.0
C9 B:HI3577 2.4 21.2 1.0
C25 B:HI3577 2.8 19.7 1.0
O B:HOH750 3.0 31.5 1.0
CB B:ASN316 3.1 17.7 1.0
CZ B:PHE193 3.5 18.2 1.0
C23 B:HI3577 3.5 31.4 1.0
O B:ASN316 3.6 20.9 1.0
C1 B:HI3577 3.6 26.6 1.0
SG B:CYS366 3.6 24.7 1.0
C4 B:HI3577 3.6 23.0 1.0
CE1 B:PHE193 3.8 18.0 1.0
CG B:ASN316 3.9 20.1 1.0
ND2 B:ASN316 3.9 18.3 1.0
C11 B:HI3577 4.1 25.7 1.0
C B:ASN316 4.1 20.0 1.0
CA B:ASN316 4.2 17.2 1.0
N1 B:HI3577 4.2 20.5 1.0
N3 B:HI3577 4.3 19.7 1.0
C21 B:HI3577 4.4 33.8 1.0
CB B:ASP319 4.5 22.4 1.0
S1 B:HI3577 4.5 24.8 1.0
O3 B:HI3577 4.5 27.7 1.0
CE2 B:PHE193 4.6 19.5 1.0
CB B:CYS366 4.7 21.5 1.0
C22 B:HI3577 4.7 33.3 1.0
O B:HOH609 4.8 43.1 1.0
OD1 B:ASN316 4.9 20.0 1.0
C20 B:HI3577 4.9 20.9 1.0
CD1 B:PHE193 5.0 17.4 1.0

Fluorine binding site 6 out of 6 in 3tyv

Go back to Fluorine Binding Sites List in 3tyv
Fluorine binding site 6 out of 6 in the Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sar Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus NS5B Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:25.0
occ:1.00
 F3 B:HI3577 0.0 25.0 1.0
C13 B:HI3577 1.3 22.8 1.0
C5 B:HI3577 2.3 19.6 1.0
C8 B:HI3577 2.4 21.4 1.0
C24 B:HI3577 2.8 23.6 1.0
CD B:ARG200 3.1 17.4 1.0
CD1 B:LEU384 3.5 24.4 1.0
NE B:ARG200 3.6 20.9 1.0
C10 B:HI3577 3.6 19.7 1.0
C3 B:HI3577 3.6 20.0 1.0
C6 B:HI3577 4.1 18.8 1.0
OG B:SER368 4.1 26.0 1.0
O B:HOH662 4.2 25.9 1.0
CB B:CYS366 4.3 21.5 1.0
CZ B:ARG200 4.4 24.1 1.0
CB B:SER368 4.5 22.6 1.0
CG B:ARG200 4.5 19.9 1.0
CG B:LEU384 4.6 24.3 1.0
O B:HOH602 4.7 21.2 1.0
N1 B:HI3577 4.8 20.5 1.0
CB B:LEU384 4.8 20.3 1.0
NH1 B:ARG200 4.9 21.6 1.0
OH B:TYR448 4.9 22.5 1.0
CB B:ARG200 4.9 19.4 1.0
O B:CYS366 4.9 23.2 1.0

Reference:

K.X.Chen, B.Vibulbhan, W.Yang, M.Sannigrahi, F.Velazquez, T.Y.Chan, S.Venkatraman, G.N.Anilkumar, Q.Zeng, F.Bennet, Y.Jiang, C.A.Lesburg, J.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. Structure-Activity Relationship (Sar) Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus (Hcv) NS5B Polymerase. J.Med.Chem. V. 55 754 2012.
ISSN: ISSN 0022-2623
PubMed: 22148957
DOI: 10.1021/JM201258K
Page generated: Wed Jul 31 22:49:26 2024

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