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Fluorine in PDB 3upi: Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors

Enzymatic activity of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors

All present enzymatic activity of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors:
2.7.7.48;

Protein crystallography data

The structure of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors, PDB code: 3upi was solved by F.Velazquez, S.Venkataraman, C.A.Lesburg, J.S.Duca, S.B.Rosenblum, J.A.Kozlowski, F.G.Njoroge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.816, 106.538, 134.274, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors (pdb code 3upi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors, PDB code: 3upi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3upi

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Fluorine binding site 1 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F587

b:44.3
occ:0.50
 F1 A:0C2587 0.0 44.3 0.5
F1 A:0C2587 0.1 44.9 0.5
C12 A:0C2587 1.3 42.8 0.5
C12 A:0C2587 1.4 43.7 0.5
C5 A:0C2587 2.3 41.8 0.5
C3 A:0C2587 2.4 41.8 0.5
C3 A:0C2587 2.4 42.7 0.5
C5 A:0C2587 2.4 42.9 0.5
OG A:SER367 3.1 45.2 1.0
O A:CYS366 3.1 34.0 1.0
C A:CYS366 3.2 36.0 1.0
CB A:SER367 3.4 36.7 1.0
C4 A:0C2587 3.6 41.7 0.5
N A:SER367 3.6 33.2 1.0
C9 A:0C2587 3.6 39.6 0.5
C4 A:0C2587 3.6 42.6 0.5
CA A:CYS366 3.7 32.6 1.0
C9 A:0C2587 3.7 41.0 0.5
O A:HOH630 3.7 52.4 1.0
O A:HOH964 4.1 42.3 1.0
C13 A:0C2587 4.1 40.4 0.5
C13 A:0C2587 4.1 41.4 0.5
CA A:SER367 4.2 33.2 1.0
O A:HOH780 4.2 35.9 1.0
CB A:CYS366 4.3 32.7 1.0
OD2 A:ASP319 4.8 39.7 1.0
C25 A:0C2587 4.9 34.8 0.5
N1 A:0C2587 5.0 32.6 0.5
N A:CYS366 5.0 33.7 1.0
C25 A:0C2587 5.0 36.7 0.5

Fluorine binding site 2 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 2 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F587

b:44.9
occ:0.50
 F1 A:0C2587 0.0 44.9 0.5
F1 A:0C2587 0.1 44.3 0.5
C12 A:0C2587 1.3 42.8 0.5
C12 A:0C2587 1.3 43.7 0.5
C5 A:0C2587 2.3 41.8 0.5
C5 A:0C2587 2.4 42.9 0.5
C3 A:0C2587 2.4 41.8 0.5
C3 A:0C2587 2.4 42.7 0.5
O A:CYS366 3.1 34.0 1.0
OG A:SER367 3.1 45.2 1.0
C A:CYS366 3.2 36.0 1.0
CB A:SER367 3.5 36.7 1.0
C9 A:0C2587 3.6 39.6 0.5
C4 A:0C2587 3.6 41.7 0.5
C4 A:0C2587 3.6 42.6 0.5
C9 A:0C2587 3.6 41.0 0.5
N A:SER367 3.6 33.2 1.0
CA A:CYS366 3.7 32.6 1.0
O A:HOH630 3.8 52.4 1.0
O A:HOH964 4.0 42.3 1.0
C13 A:0C2587 4.1 40.4 0.5
C13 A:0C2587 4.1 41.4 0.5
O A:HOH780 4.2 35.9 1.0
CA A:SER367 4.2 33.2 1.0
CB A:CYS366 4.2 32.7 1.0
OD2 A:ASP319 4.8 39.7 1.0
C25 A:0C2587 4.9 34.8 0.5
N1 A:0C2587 4.9 32.6 0.5
C25 A:0C2587 4.9 36.7 0.5
N1 A:0C2587 5.0 35.5 0.5
N A:CYS366 5.0 33.7 1.0

Fluorine binding site 3 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 3 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F587

b:39.2
occ:0.50
 F2 A:0C2587 0.0 39.2 0.5
F2 A:0C2587 0.1 40.0 0.5
C13 A:0C2587 1.3 41.4 0.5
C13 A:0C2587 1.3 40.4 0.5
C4 A:0C2587 2.3 42.6 0.5
C9 A:0C2587 2.3 41.0 0.5
C4 A:0C2587 2.4 41.7 0.5
C9 A:0C2587 2.4 39.6 0.5
C25 A:0C2587 2.8 34.8 0.5
C25 A:0C2587 2.8 36.7 0.5
CB A:ASN316 3.0 24.9 1.0
O A:HOH696 3.1 54.8 1.0
O A:ASN316 3.3 31.3 1.0
CZ A:PHE193 3.4 30.1 1.0
C3 A:0C2587 3.6 42.7 0.5
C5 A:0C2587 3.6 42.9 0.5
C3 A:0C2587 3.6 41.8 0.5
C5 A:0C2587 3.6 41.8 0.5
C24 A:0C2587 3.7 30.9 0.5
CE1 A:PHE193 3.7 32.2 1.0
C A:ASN316 3.8 31.7 1.0
SG A:CYS366 3.9 36.5 1.0
N3 A:0C2587 4.0 31.0 0.5
CG A:ASN316 4.0 31.2 1.0
CA A:ASN316 4.0 26.0 1.0
C12 A:0C2587 4.1 43.7 0.5
ND2 A:ASN316 4.1 27.5 1.0
C12 A:0C2587 4.1 42.8 0.5
N1 A:0C2587 4.2 32.6 0.5
N1 A:0C2587 4.2 35.5 0.5
O3 A:0C2587 4.3 23.5 0.5
CE2 A:PHE193 4.4 30.5 1.0
S1 A:0C2587 4.4 29.1 0.5
CB A:ASP319 4.5 33.3 1.0
O2 A:0C2587 4.7 36.9 0.5
N A:GLY317 4.8 28.6 1.0
O A:HOH915 4.8 40.6 1.0
CD1 A:PHE193 4.9 31.3 1.0
CB A:CYS366 5.0 32.7 1.0

Fluorine binding site 4 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 4 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F587

b:40.0
occ:0.50
 F2 A:0C2587 0.0 40.0 0.5
F2 A:0C2587 0.1 39.2 0.5
C13 A:0C2587 1.3 41.4 0.5
C13 A:0C2587 1.4 40.4 0.5
C4 A:0C2587 2.4 42.6 0.5
C9 A:0C2587 2.4 41.0 0.5
C9 A:0C2587 2.4 39.6 0.5
C4 A:0C2587 2.4 41.7 0.5
C25 A:0C2587 2.8 34.8 0.5
C25 A:0C2587 2.8 36.7 0.5
O A:HOH696 3.0 54.8 1.0
CB A:ASN316 3.1 24.9 1.0
CZ A:PHE193 3.3 30.1 1.0
O A:ASN316 3.4 31.3 1.0
C24 A:0C2587 3.6 30.9 0.5
C3 A:0C2587 3.6 42.7 0.5
C5 A:0C2587 3.6 42.9 0.5
CE1 A:PHE193 3.6 32.2 1.0
C5 A:0C2587 3.7 41.8 0.5
C3 A:0C2587 3.7 41.8 0.5
C A:ASN316 3.8 31.7 1.0
N3 A:0C2587 3.9 31.0 0.5
SG A:CYS366 3.9 36.5 1.0
CG A:ASN316 4.0 31.2 1.0
CA A:ASN316 4.0 26.0 1.0
ND2 A:ASN316 4.1 27.5 1.0
C12 A:0C2587 4.1 43.7 0.5
C12 A:0C2587 4.1 42.8 0.5
O3 A:0C2587 4.2 23.5 0.5
N1 A:0C2587 4.2 35.5 0.5
N1 A:0C2587 4.2 32.6 0.5
S1 A:0C2587 4.3 29.1 0.5
CE2 A:PHE193 4.3 30.5 1.0
CB A:ASP319 4.6 33.3 1.0
O2 A:0C2587 4.6 36.9 0.5
O A:HOH915 4.7 40.6 1.0
N A:GLY317 4.8 28.6 1.0
CD1 A:PHE193 4.9 31.3 1.0
C20 A:0C2587 5.0 31.4 0.5

Fluorine binding site 5 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 5 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F586

b:39.5
occ:0.50
 F1 B:0C2586 0.0 39.5 0.5
F1 B:0C2586 0.3 45.3 0.5
C12 B:0C2586 1.3 38.3 0.5
C12 B:0C2586 1.6 43.1 0.5
C5 B:0C2586 2.3 36.8 0.5
C3 B:0C2586 2.4 37.6 0.5
C5 B:0C2586 2.4 41.5 0.5
C3 B:0C2586 2.7 42.4 0.5
OG B:SER367 3.1 44.3 1.0
O B:CYS366 3.1 36.6 1.0
C B:CYS366 3.1 37.6 1.0
CB B:SER367 3.3 37.8 1.0
O B:HOH4004 3.5 42.2 1.0
N B:SER367 3.6 34.9 1.0
C9 B:0C2586 3.6 36.3 0.5
C4 B:0C2586 3.6 38.2 0.5
CA B:CYS366 3.7 34.7 1.0
C9 B:0C2586 3.8 40.8 0.5
C4 B:0C2586 3.9 42.5 0.5
CA B:SER367 4.1 35.4 1.0
C13 B:0C2586 4.1 37.4 0.5
O B:HOH670 4.1 38.7 1.0
CB B:CYS366 4.3 34.0 1.0
C13 B:0C2586 4.3 42.1 0.5
N1 B:0C2586 4.9 36.1 0.5
C25 B:0C2586 4.9 34.9 0.5
N1 B:0C2586 4.9 39.1 0.5
NH1 B:ARG386 5.0 41.3 1.0
C25 B:0C2586 5.0 38.8 0.5

Fluorine binding site 6 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 6 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F586

b:45.3
occ:0.50
 F1 B:0C2586 0.0 45.3 0.5
F1 B:0C2586 0.3 39.5 0.5
C12 B:0C2586 1.1 38.3 0.5
C12 B:0C2586 1.3 43.1 0.5
C3 B:0C2586 2.1 37.6 0.5
C5 B:0C2586 2.3 36.8 0.5
C5 B:0C2586 2.3 41.5 0.5
C3 B:0C2586 2.4 42.4 0.5
OG B:SER367 3.1 44.3 1.0
C B:CYS366 3.2 37.6 1.0
O B:CYS366 3.2 36.6 1.0
C4 B:0C2586 3.4 38.2 0.5
CB B:SER367 3.5 37.8 1.0
C9 B:0C2586 3.5 36.3 0.5
N B:SER367 3.6 34.9 1.0
CA B:CYS366 3.6 34.7 1.0
C4 B:0C2586 3.6 42.5 0.5
C9 B:0C2586 3.6 40.8 0.5
O B:HOH4004 3.7 42.2 1.0
C13 B:0C2586 3.9 37.4 0.5
C13 B:0C2586 4.1 42.1 0.5
CA B:SER367 4.2 35.4 1.0
CB B:CYS366 4.2 34.0 1.0
O B:HOH670 4.5 38.7 1.0
C25 B:0C2586 4.8 34.9 0.5
OD2 B:ASP319 4.8 46.0 1.0
N1 B:0C2586 4.9 36.1 0.5
N B:CYS366 4.9 35.2 1.0
C25 B:0C2586 4.9 38.8 0.5
N1 B:0C2586 4.9 39.1 0.5
O B:HOH618 5.0 51.6 1.0

Fluorine binding site 7 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 7 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F586

b:38.2
occ:0.50
 F2 B:0C2586 0.0 38.2 0.5
F2 B:0C2586 0.2 44.5 0.5
C13 B:0C2586 1.1 42.1 0.5
C13 B:0C2586 1.3 37.4 0.5
C9 B:0C2586 2.2 40.8 0.5
C4 B:0C2586 2.2 42.5 0.5
C4 B:0C2586 2.4 38.2 0.5
C9 B:0C2586 2.4 36.3 0.5
C25 B:0C2586 2.7 38.8 0.5
C25 B:0C2586 2.8 34.9 0.5
O B:ASN316 3.3 29.2 1.0
CB B:ASN316 3.3 26.1 1.0
C5 B:0C2586 3.4 41.5 0.5
C3 B:0C2586 3.4 42.4 0.5
C24 B:0C2586 3.5 36.4 0.5
CZ B:PHE193 3.6 29.0 1.0
C5 B:0C2586 3.6 36.8 0.5
C3 B:0C2586 3.6 37.6 0.5
CE1 B:PHE193 3.8 31.8 1.0
C B:ASN316 3.9 30.7 1.0
C12 B:0C2586 3.9 43.1 0.5
N3 B:0C2586 3.9 35.3 0.5
SG B:CYS366 4.0 37.1 1.0
C12 B:0C2586 4.1 38.3 0.5
N1 B:0C2586 4.1 39.1 0.5
CA B:ASN316 4.2 26.7 1.0
N1 B:0C2586 4.2 36.1 0.5
CG B:ASN316 4.2 31.1 1.0
ND2 B:ASN316 4.3 29.7 1.0
S1 B:0C2586 4.3 35.8 0.5
O3 B:0C2586 4.4 35.5 0.5
CB B:ASP319 4.5 32.0 1.0
O2 B:0C2586 4.6 38.8 0.5
CE2 B:PHE193 4.7 30.7 1.0
O B:HOH839 4.8 44.2 1.0
N B:GLY317 4.8 28.2 1.0
C20 B:0C2586 4.9 39.7 0.5
C14 B:0C2586 5.0 39.6 0.5
CB B:CYS366 5.0 34.0 1.0
C20 B:0C2586 5.0 36.7 0.5

Fluorine binding site 8 out of 8 in 3upi

Go back to Fluorine Binding Sites List in 3upi
Fluorine binding site 8 out of 8 in the Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Synthesis of Novel 4,5-Dihydrofurano Indoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F586

b:44.5
occ:0.50
 F2 B:0C2586 0.0 44.5 0.5
F2 B:0C2586 0.2 38.2 0.5
C13 B:0C2586 1.3 42.1 0.5
C13 B:0C2586 1.6 37.4 0.5
C4 B:0C2586 2.4 42.5 0.5
C9 B:0C2586 2.4 40.8 0.5
C4 B:0C2586 2.5 38.2 0.5
C9 B:0C2586 2.6 36.3 0.5
C25 B:0C2586 2.8 38.8 0.5
C25 B:0C2586 2.9 34.9 0.5
O B:ASN316 3.2 29.2 1.0
CB B:ASN316 3.2 26.1 1.0
CZ B:PHE193 3.4 29.0 1.0
C24 B:0C2586 3.5 36.4 0.5
C5 B:0C2586 3.6 41.5 0.5
C3 B:0C2586 3.6 42.4 0.5
CE1 B:PHE193 3.6 31.8 1.0
C B:ASN316 3.7 30.7 1.0
C5 B:0C2586 3.8 36.8 0.5
C3 B:0C2586 3.8 37.6 0.5
N3 B:0C2586 4.0 35.3 0.5
CA B:ASN316 4.1 26.7 1.0
C12 B:0C2586 4.1 43.1 0.5
SG B:CYS366 4.1 37.1 1.0
CG B:ASN316 4.2 31.1 1.0
N1 B:0C2586 4.2 39.1 0.5
ND2 B:ASN316 4.3 29.7 1.0
C12 B:0C2586 4.3 38.3 0.5
O3 B:0C2586 4.3 35.5 0.5
S1 B:0C2586 4.3 35.8 0.5
N1 B:0C2586 4.4 36.1 0.5
CE2 B:PHE193 4.5 30.7 1.0
O B:HOH839 4.6 44.2 1.0
CB B:ASP319 4.6 32.0 1.0
O2 B:0C2586 4.6 38.8 0.5
N B:GLY317 4.6 28.2 1.0
CD1 B:PHE193 4.9 31.4 1.0

Reference:

F.Velazquez, S.Venkatraman, C.A.Lesburg, J.Duca, S.B.Rosenblum, J.A.Kozlowski, F.G.Njoroge. Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation As Hcv NS5B Polymerase Inhibitors. Org.Lett. V. 14 556 2012.
ISSN: ISSN 1523-7060
PubMed: 22220815
DOI: 10.1021/OL203177G
Page generated: Mon Jul 14 19:45:58 2025

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