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Fluorine in PDB 3ska: I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles

Enzymatic activity of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles

All present enzymatic activity of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles:
2.7.7.48;

Protein crystallography data

The structure of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles, PDB code: 3ska was solved by C.A.Lesburg, G.N.Anilkumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.670, 106.970, 133.740, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles (pdb code 3ska). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles, PDB code: 3ska:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 1 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:24.0
occ:1.00
F27 A:053578 0.0 24.0 1.0
C25 A:053578 1.3 23.9 1.0
F28 A:053578 2.1 22.0 1.0
F29 A:053578 2.2 22.8 1.0
C13 A:053578 2.3 20.1 1.0
C14 A:053578 2.9 19.5 1.0
CD1 A:LEU384 3.3 20.9 1.0
CB A:PRO197 3.4 19.9 1.0
C16 A:053578 3.5 17.7 1.0
CA A:PRO197 3.6 17.2 1.0
CG A:PRO197 3.9 24.3 1.0
CB A:LEU384 4.0 16.5 1.0
CD A:ARG200 4.0 16.8 1.0
C15 A:053578 4.2 17.3 1.0
CG A:LEU384 4.3 20.2 1.0
O A:PRO197 4.6 18.2 1.0
N A:PRO197 4.6 18.1 1.0
C17 A:053578 4.6 17.0 1.0
C A:PRO197 4.6 17.5 1.0
O A:MET414 4.7 16.4 1.0
CE A:MET414 4.7 18.0 1.0
O A:HOH600 4.8 19.5 1.0
CB A:ARG200 4.8 15.4 1.0
C18 A:053578 4.9 18.9 1.0
CD A:PRO197 4.9 20.9 1.0
NE A:ARG200 4.9 19.7 1.0
CG A:ARG200 4.9 16.8 1.0
CE1 A:TYR415 5.0 18.9 1.0

Fluorine binding site 2 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 2 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:22.0
occ:1.00
F28 A:053578 0.0 22.0 1.0
C25 A:053578 1.3 23.9 1.0
F29 A:053578 2.1 22.8 1.0
F27 A:053578 2.1 24.0 1.0
C13 A:053578 2.4 20.1 1.0
C14 A:053578 3.0 19.5 1.0
OG A:SER368 3.3 23.3 1.0
CB A:LEU384 3.4 16.5 1.0
CE1 A:TYR415 3.4 18.9 1.0
C16 A:053578 3.4 17.7 1.0
OH A:TYR415 3.5 19.4 1.0
CB A:SER368 3.6 21.1 1.0
CD1 A:LEU384 3.6 20.9 1.0
CZ A:TYR415 3.7 21.9 1.0
CG A:LEU384 4.0 20.2 1.0
C15 A:053578 4.3 17.3 1.0
CD1 A:TYR415 4.4 16.6 1.0
CD2 A:LEU384 4.5 21.5 1.0
C17 A:053578 4.6 17.0 1.0
CA A:LEU384 4.7 16.1 1.0
C A:LEU384 4.8 17.4 1.0
O A:HOH748 4.8 25.7 1.0
CD A:ARG200 4.8 16.8 1.0
CE2 A:TYR415 4.8 16.6 1.0
O A:LEU384 4.9 17.1 1.0
C18 A:053578 4.9 18.9 1.0
O A:HOH600 4.9 19.5 1.0

Fluorine binding site 3 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 3 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F578

b:22.8
occ:1.00
F29 A:053578 0.0 22.8 1.0
C25 A:053578 1.3 23.9 1.0
F28 A:053578 2.1 22.0 1.0
F27 A:053578 2.2 24.0 1.0
C13 A:053578 2.4 20.1 1.0
C16 A:053578 2.7 17.7 1.0
CE1 A:TYR415 3.3 18.9 1.0
O A:MET414 3.3 16.4 1.0
CZ A:TYR415 3.4 21.9 1.0
C14 A:053578 3.6 19.5 1.0
OH A:TYR415 3.7 19.4 1.0
CD1 A:TYR415 3.8 16.6 1.0
CB A:MET414 3.8 15.8 1.0
C A:MET414 4.0 16.9 1.0
CE2 A:TYR415 4.0 16.6 1.0
O A:HOH600 4.1 19.5 1.0
CB A:PRO197 4.1 19.9 1.0
C17 A:053578 4.1 17.0 1.0
CG A:PRO197 4.2 24.3 1.0
CG A:TYR415 4.3 15.3 1.0
CA A:MET414 4.4 14.8 1.0
CD2 A:TYR415 4.4 15.8 1.0
CE A:MET414 4.5 18.0 1.0
CB A:LEU384 4.5 16.5 1.0
C15 A:053578 4.8 17.3 1.0
N A:TYR415 4.8 15.2 1.0
OG A:SER368 4.8 23.3 1.0
CD1 A:LEU384 4.9 20.9 1.0
CG A:MET414 4.9 16.6 1.0
C18 A:053578 5.0 18.9 1.0
CA A:PRO197 5.0 17.2 1.0

Fluorine binding site 4 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 4 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:29.2
occ:1.00
F27 B:053577 0.0 29.2 1.0
C25 B:053577 1.4 27.3 1.0
F28 B:053577 2.2 28.2 1.0
F29 B:053577 2.2 28.1 1.0
C13 B:053577 2.3 23.5 1.0
C14 B:053577 2.9 24.1 1.0
CD1 B:LEU384 3.3 26.6 1.0
C16 B:053577 3.5 22.2 1.0
CB B:PRO197 3.6 23.8 1.0
CA B:PRO197 3.8 22.3 1.0
CB B:LEU384 4.0 21.4 1.0
CG B:PRO197 4.0 26.9 1.0
CD B:ARG200 4.1 18.9 1.0
C15 B:053577 4.2 24.4 1.0
CG B:LEU384 4.3 26.5 1.0
O B:MET414 4.5 20.5 1.0
C17 B:053577 4.6 20.3 1.0
O B:HOH659 4.6 25.8 1.0
O B:PRO197 4.7 23.1 1.0
N B:PRO197 4.7 22.0 1.0
C B:PRO197 4.7 23.6 1.0
O B:HOH621 4.8 22.8 1.0
CE B:MET414 4.8 21.4 1.0
C18 B:053577 4.8 23.7 1.0
CB B:ARG200 4.9 19.6 1.0
CE1 B:TYR415 5.0 24.5 1.0

Fluorine binding site 5 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 5 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:28.2
occ:1.00
F28 B:053577 0.0 28.2 1.0
C25 B:053577 1.3 27.3 1.0
F29 B:053577 2.1 28.1 1.0
F27 B:053577 2.2 29.2 1.0
C13 B:053577 2.3 23.5 1.0
C14 B:053577 2.9 24.1 1.0
OG B:SER368 3.1 30.8 1.0
CB B:LEU384 3.3 21.4 1.0
CE1 B:TYR415 3.3 24.5 1.0
C16 B:053577 3.4 22.2 1.0
OH B:TYR415 3.4 27.4 1.0
CB B:SER368 3.5 26.5 1.0
CZ B:TYR415 3.6 27.0 1.0
CD1 B:LEU384 3.7 26.6 1.0
CG B:LEU384 4.0 26.5 1.0
C15 B:053577 4.2 24.4 1.0
CD1 B:TYR415 4.3 21.3 1.0
CD2 B:LEU384 4.6 27.6 1.0
C17 B:053577 4.6 20.3 1.0
CA B:LEU384 4.6 21.8 1.0
C B:LEU384 4.7 23.4 1.0
CE2 B:TYR415 4.7 22.1 1.0
O B:HOH659 4.8 25.8 1.0
C18 B:053577 4.9 23.7 1.0
O B:LEU384 4.9 22.6 1.0
CD B:ARG200 4.9 18.9 1.0
CA B:SER368 5.0 25.3 1.0

Fluorine binding site 6 out of 6 in 3ska

Go back to Fluorine Binding Sites List in 3ska
Fluorine binding site 6 out of 6 in the I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids with C3-Heterocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F577

b:28.1
occ:1.00
F29 B:053577 0.0 28.1 1.0
C25 B:053577 1.4 27.3 1.0
F28 B:053577 2.1 28.2 1.0
F27 B:053577 2.2 29.2 1.0
C13 B:053577 2.4 23.5 1.0
C16 B:053577 2.7 22.2 1.0
O B:MET414 3.1 20.5 1.0
CE1 B:TYR415 3.3 24.5 1.0
CZ B:TYR415 3.4 27.0 1.0
C14 B:053577 3.7 24.1 1.0
CD1 B:TYR415 3.7 21.3 1.0
CB B:MET414 3.7 20.2 1.0
OH B:TYR415 3.8 27.4 1.0
C B:MET414 3.8 22.0 1.0
CE2 B:TYR415 3.9 22.1 1.0
O B:HOH659 4.0 25.8 1.0
C17 B:053577 4.1 20.3 1.0
CG B:TYR415 4.2 20.5 1.0
CD2 B:TYR415 4.3 20.9 1.0
CA B:MET414 4.3 18.8 1.0
CB B:PRO197 4.4 23.8 1.0
CG B:PRO197 4.4 26.9 1.0
CB B:LEU384 4.5 21.4 1.0
CE B:MET414 4.6 21.4 1.0
N B:TYR415 4.7 20.8 1.0
OG B:SER368 4.7 30.8 1.0
C15 B:053577 4.8 24.4 1.0
CG B:MET414 4.9 21.8 1.0
C18 B:053577 5.0 23.7 1.0
CD1 B:LEU384 5.0 26.6 1.0

Reference:

G.N.Anilkumar, C.A.Lesburg, O.Selyutin, S.B.Rosenblum, Q.Zeng, Y.Jiang, T.Y.Chan, H.Pu, H.Vaccaro, L.Wang, F.Bennett, K.X.Chen, J.Duca, S.Gavalas, Y.Huang, P.Pinto, M.Sannigrahi, F.Velazquez, S.Venkatraman, B.Vibulbhan, S.Agrawal, N.Butkiewicz, B.Feld, E.Ferrari, Z.He, C.K.Jiang, R.E.Palermo, P.Mcmonagle, H.C.Huang, N.Y.Shih, G.Njoroge, J.A.Kozlowski. I. Novel Hcv NS5B Polymerase Inhibitors: Discovery of Indole 2-Carboxylic Acids with C3-Heterocycles. Bioorg.Med.Chem.Lett. V. 21 5336 2011.
ISSN: ISSN 0960-894X
PubMed: 21840715
DOI: 10.1016/J.BMCL.2011.07.021
Page generated: Sun Dec 13 11:55:18 2020

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