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Fluorine in PDB 3ske: 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: 3ske 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 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.700, 107.260, 134.220, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20

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 3ske). 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: 3ske:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:32.3
occ:1.00
 F32 A:054578 0.0 32.3 1.0
C15 A:054578 1.4 29.2 1.0
F33 A:054578 2.2 29.0 1.0
F34 A:054578 2.2 29.8 1.0
C1 A:054578 2.4 25.9 1.0
C2 A:054578 2.9 24.3 1.0
CB A:PRO197 3.5 25.3 1.0
CD1 A:LEU384 3.5 25.1 1.0
C4 A:054578 3.5 25.6 1.0
CA A:PRO197 3.7 23.1 1.0
CG A:PRO197 4.0 29.0 1.0
CB A:LEU384 4.1 19.9 1.0
CD A:ARG200 4.2 22.6 1.0
C3 A:054578 4.2 23.4 1.0
CG A:LEU384 4.4 23.9 1.0
O A:MET414 4.4 22.2 1.0
CE A:MET414 4.5 21.9 1.0
C5 A:054578 4.6 25.1 1.0
O A:HOH635 4.7 25.9 1.0
N A:PRO197 4.7 22.9 1.0
O A:PRO197 4.8 21.6 1.0
C A:PRO197 4.8 24.5 1.0
C6 A:054578 4.9 25.0 1.0
CE1 A:TYR415 5.0 21.2 1.0
CB A:ARG200 5.0 20.0 1.0

Fluorine binding site 2 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:29.0
occ:1.00
 F33 A:054578 0.0 29.0 1.0
C15 A:054578 1.3 29.2 1.0
F34 A:054578 2.1 29.8 1.0
F32 A:054578 2.2 32.3 1.0
C1 A:054578 2.4 25.9 1.0
C2 A:054578 2.9 24.3 1.0
OG A:SER368 3.2 27.3 1.0
OH A:TYR415 3.4 27.6 1.0
CE1 A:TYR415 3.4 21.2 1.0
C4 A:054578 3.5 25.6 1.0
CB A:LEU384 3.6 19.9 1.0
CZ A:TYR415 3.6 28.0 1.0
CB A:SER368 3.6 23.3 1.0
CD1 A:LEU384 3.7 25.1 1.0
CG A:LEU384 4.2 23.9 1.0
C3 A:054578 4.2 23.4 1.0
CD1 A:TYR415 4.4 20.2 1.0
CE2 A:TYR415 4.6 21.1 1.0
C5 A:054578 4.6 25.1 1.0
CD2 A:LEU384 4.7 24.1 1.0
O A:HOH722 4.9 28.8 1.0
CA A:LEU384 4.9 19.8 1.0
CD A:ARG200 4.9 22.6 1.0
C6 A:054578 4.9 25.0 1.0
C A:LEU384 5.0 23.1 1.0
O A:HOH635 5.0 25.9 1.0
O A:CYS366 5.0 29.9 1.0

Fluorine binding site 3 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:29.8
occ:1.00
 F34 A:054578 0.0 29.8 1.0
C15 A:054578 1.3 29.2 1.0
F33 A:054578 2.1 29.0 1.0
F32 A:054578 2.2 32.3 1.0
C1 A:054578 2.4 25.9 1.0
C4 A:054578 2.8 25.6 1.0
O A:MET414 3.2 22.2 1.0
CZ A:TYR415 3.3 28.0 1.0
CE1 A:TYR415 3.3 21.2 1.0
OH A:TYR415 3.7 27.6 1.0
C2 A:054578 3.7 24.3 1.0
CE2 A:TYR415 3.7 21.1 1.0
CB A:MET414 3.7 19.9 1.0
CD1 A:TYR415 3.7 20.2 1.0
C A:MET414 3.8 21.9 1.0
CD2 A:TYR415 4.1 20.9 1.0
CG A:TYR415 4.1 19.7 1.0
O A:HOH635 4.1 25.9 1.0
C5 A:054578 4.2 25.1 1.0
CA A:MET414 4.3 18.0 1.0
CB A:PRO197 4.4 25.3 1.0
CE A:MET414 4.4 21.9 1.0
CG A:PRO197 4.5 29.0 1.0
N A:TYR415 4.7 19.0 1.0
CB A:LEU384 4.7 19.9 1.0
OG A:SER368 4.8 27.3 1.0
C3 A:054578 4.8 23.4 1.0
CG A:MET414 4.8 22.5 1.0

Fluorine binding site 4 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:37.0
occ:1.00
 F32 B:054577 0.0 37.0 1.0
C15 B:054577 1.4 34.6 1.0
F34 B:054577 2.2 34.5 1.0
F33 B:054577 2.2 33.5 1.0
C1 B:054577 2.3 32.1 1.0
C2 B:054577 2.9 30.2 1.0
CD1 B:LEU384 3.3 32.7 1.0
C4 B:054577 3.4 27.9 1.0
CB B:PRO197 3.5 25.4 1.0
CA B:PRO197 3.9 23.7 1.0
CG B:PRO197 3.9 28.6 1.0
CB B:LEU384 4.1 27.3 1.0
C3 B:054577 4.2 30.1 1.0
O B:MET414 4.3 24.3 1.0
CG B:LEU384 4.3 32.4 1.0
CD B:ARG200 4.4 22.7 1.0
O B:HOH655 4.6 31.0 1.0
C5 B:054577 4.6 25.7 1.0
CE B:MET414 4.7 25.5 1.0
O B:HOH621 4.8 28.3 1.0
N B:PRO197 4.8 23.9 1.0
C6 B:054577 4.8 28.8 1.0
O B:PRO197 4.9 26.0 1.0
C B:PRO197 4.9 27.6 1.0
CE1 B:TYR415 5.0 28.8 1.0

Fluorine binding site 5 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:33.5
occ:1.00
 F33 B:054577 0.0 33.5 1.0
C15 B:054577 1.4 34.6 1.0
F34 B:054577 2.2 34.5 1.0
F32 B:054577 2.2 37.0 1.0
C1 B:054577 2.3 32.1 1.0
C2 B:054577 2.9 30.2 1.0
OG B:SER368 3.2 34.6 1.0
CB B:LEU384 3.4 27.3 1.0
C4 B:054577 3.5 27.9 1.0
CE1 B:TYR415 3.5 28.8 1.0
OH B:TYR415 3.5 32.0 1.0
CD1 B:LEU384 3.6 32.7 1.0
CB B:SER368 3.6 32.6 1.0
CZ B:TYR415 3.7 31.5 1.0
CG B:LEU384 4.0 32.4 1.0
C3 B:054577 4.2 30.1 1.0
CD1 B:TYR415 4.4 25.2 1.0
C5 B:054577 4.6 25.7 1.0
CD2 B:LEU384 4.6 33.7 1.0
CA B:LEU384 4.7 26.8 1.0
CE2 B:TYR415 4.7 25.2 1.0
C B:LEU384 4.9 28.9 1.0
O B:HOH655 4.9 31.0 1.0
C6 B:054577 4.9 28.8 1.0
CD B:ARG200 5.0 22.7 1.0

Fluorine binding site 6 out of 6 in 3ske

Go back to Fluorine Binding Sites List in 3ske
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:34.5
occ:1.00
 F34 B:054577 0.0 34.5 1.0
C15 B:054577 1.4 34.6 1.0
F32 B:054577 2.2 37.0 1.0
F33 B:054577 2.2 33.5 1.0
C1 B:054577 2.4 32.1 1.0
C4 B:054577 2.8 27.9 1.0
O B:MET414 3.1 24.3 1.0
CE1 B:TYR415 3.2 28.8 1.0
CZ B:TYR415 3.3 31.5 1.0
CD1 B:TYR415 3.7 25.2 1.0
C2 B:054577 3.7 30.2 1.0
OH B:TYR415 3.7 32.0 1.0
CB B:MET414 3.7 25.3 1.0
CE2 B:TYR415 3.7 25.2 1.0
C B:MET414 3.8 26.2 1.0
O B:HOH655 4.0 31.0 1.0
CG B:TYR415 4.1 24.7 1.0
CD2 B:TYR415 4.1 25.6 1.0
C5 B:054577 4.2 25.7 1.0
CA B:MET414 4.2 23.8 1.0
CB B:PRO197 4.6 25.4 1.0
CB B:LEU384 4.6 27.3 1.0
N B:TYR415 4.6 25.2 1.0
CG B:PRO197 4.6 28.6 1.0
CE B:MET414 4.7 25.5 1.0
OG B:SER368 4.7 34.6 1.0
CG B:MET414 4.8 27.1 1.0
C3 B:054577 4.8 30.1 1.0
CD1 B:LEU384 4.9 32.7 1.0
CA B:TYR415 4.9 24.7 1.0
C6 B:054577 5.0 28.8 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: Wed Jul 31 22:33:21 2024

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