Fluorine in PDB 6p6v: Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir

Enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir

All present enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir:
3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir, PDB code: 6p6v was solved by J.Timm, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.81 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.551, 60.147, 83.788, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.3

Other elements in 6p6v:

The structure of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir (pdb code 6p6v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir, PDB code: 6p6v:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6p6v

Go back to Fluorine Binding Sites List in 6p6v
Fluorine binding site 1 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1204

b:15.3
occ:1.00
F15 A:O311204 0.0 15.3 1.0
C14 A:O311204 1.4 15.5 1.0
H141 A:O311204 1.9 18.7 1.0
F16 A:O311204 2.3 13.8 1.0
C13 A:O311204 2.4 13.0 1.0
HE2 A:LYS1136 2.6 29.3 1.0
HA A:LYS1136 2.7 19.6 1.0
H131 A:O311204 2.8 15.6 1.0
HD3 A:LYS1136 2.8 24.9 1.0
HG2 A:LYS1136 2.9 26.6 1.0
HD11 A:ILE1132 2.9 28.0 1.0
O10 A:O311204 3.1 13.0 1.0
C11 A:O311204 3.2 13.7 1.0
C09 A:O311204 3.2 12.1 1.0
CE A:LYS1136 3.3 24.4 1.0
CD A:LYS1136 3.3 20.8 1.0
HD12 A:ILE1132 3.5 28.0 1.0
CG A:LYS1136 3.5 22.1 1.0
CA A:LYS1136 3.5 16.3 1.0
CD1 A:ILE1132 3.6 23.3 1.0
O19 A:O311204 3.6 14.8 1.0
HG13 A:ILE1132 3.6 26.6 1.0
HZ1 A:LYS1136 3.6 33.3 1.0
C12 A:O311204 3.7 12.4 1.0
N A:LYS1136 3.7 16.1 1.0
H561 A:O311204 3.8 21.1 1.0
H122 A:O311204 3.8 15.0 1.0
HB2 A:LEU1135 3.9 17.4 1.0
NZ A:LYS1136 4.0 27.7 1.0
C A:LEU1135 4.0 15.7 1.0
O A:LEU1135 4.0 12.1 1.0
CG1 A:ILE1132 4.1 22.1 1.0
H A:LYS1136 4.1 19.4 1.0
CB A:LYS1136 4.1 18.6 1.0
HE3 A:LYS1136 4.1 29.3 1.0
N17 A:O311204 4.2 11.9 1.0
HD2 A:LYS1136 4.2 24.9 1.0
N08 A:O311204 4.3 11.4 1.0
HG12 A:ILE1132 4.3 26.6 1.0
C18 A:O311204 4.3 14.8 1.0
H583 A:O311204 4.3 18.1 1.0
HG3 A:LYS1136 4.3 26.6 1.0
HZ2 A:LYS1136 4.3 33.3 1.0
H A:GLY1137 4.4 14.7 1.0
HB3 A:LEU1135 4.4 17.4 1.0
HD13 A:ILE1132 4.4 28.0 1.0
HB3 A:ALA1157 4.4 24.9 1.0
HB2 A:ALA1157 4.4 24.9 1.0
O A:ILE1132 4.5 16.0 1.0
H121 A:O311204 4.5 15.0 1.0
H562 A:O311204 4.5 21.1 1.0
CB A:LEU1135 4.6 14.5 1.0
C56 A:O311204 4.6 17.6 1.0
O26 A:O311204 4.6 12.0 1.0
O07 A:O311204 4.6 11.1 1.0
H081 A:O311204 4.7 13.7 1.0
HB3 A:LYS1136 4.7 22.4 1.0
C A:LYS1136 4.7 14.1 1.0
HB2 A:LYS1136 4.7 22.4 1.0
HZ3 A:LYS1136 4.7 33.3 1.0
N A:GLY1137 4.8 12.2 1.0
HZ A:PHE1154 4.9 16.1 1.0
HE2 A:PHE1154 4.9 13.8 1.0
CA A:LEU1135 4.9 15.0 1.0
CB A:ALA1157 4.9 20.7 1.0
H171 A:O311204 4.9 14.3 1.0
H A:ALA1157 5.0 17.2 1.0

Fluorine binding site 2 out of 4 in 6p6v

Go back to Fluorine Binding Sites List in 6p6v
Fluorine binding site 2 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1204

b:13.8
occ:1.00
F16 A:O311204 0.0 13.8 1.0
C14 A:O311204 1.4 15.5 1.0
H141 A:O311204 2.0 18.7 1.0
F15 A:O311204 2.3 15.3 1.0
C13 A:O311204 2.4 13.0 1.0
HB2 A:ALA1157 2.5 24.9 1.0
H131 A:O311204 2.6 15.6 1.0
HB2 A:LEU1135 2.6 17.4 1.0
HZ A:PHE1154 2.8 16.1 1.0
HB3 A:LEU1135 2.8 17.4 1.0
HD11 A:ILE1132 2.9 28.0 1.0
HD12 A:ILE1132 3.0 28.0 1.0
CB A:LEU1135 3.2 14.5 1.0
HB3 A:ALA1157 3.2 24.9 1.0
CB A:ALA1157 3.3 20.7 1.0
C12 A:O311204 3.4 12.4 1.0
CD1 A:ILE1132 3.4 23.3 1.0
H122 A:O311204 3.4 15.0 1.0
HE2 A:PHE1154 3.5 13.8 1.0
CZ A:PHE1154 3.5 13.4 1.0
HD12 A:LEU1135 3.7 25.4 1.0
C11 A:O311204 3.8 13.7 1.0
HD13 A:LEU1135 3.8 25.4 1.0
O A:LEU1135 3.8 12.1 1.0
C A:LEU1135 3.8 15.7 1.0
HB1 A:ALA1157 3.9 24.9 1.0
CE2 A:PHE1154 3.9 11.5 1.0
H121 A:O311204 3.9 15.0 1.0
HD13 A:ILE1132 3.9 28.0 1.0
H561 A:O311204 4.0 21.1 1.0
CD1 A:LEU1135 4.1 21.1 1.0
HA A:LYS1136 4.1 19.6 1.0
H A:ALA1157 4.1 17.2 1.0
CA A:LEU1135 4.1 15.0 1.0
O10 A:O311204 4.2 13.0 1.0
N A:LYS1136 4.2 16.1 1.0
CG A:LEU1135 4.2 16.9 1.0
N A:ALA1157 4.3 14.3 1.0
CA A:ALA1157 4.3 15.0 1.0
C09 A:O311204 4.4 12.1 1.0
HG13 A:ILE1132 4.4 26.6 1.0
HG2 A:LYS1136 4.5 26.6 1.0
CG1 A:ILE1132 4.6 22.1 1.0
H A:LYS1136 4.6 19.4 1.0
HE2 A:LYS1136 4.6 29.3 1.0
CE1 A:PHE1154 4.6 12.4 1.0
CA A:LYS1136 4.7 16.3 1.0
HA A:ALA1157 4.7 18.0 1.0
O A:ILE1132 4.7 16.0 1.0
HG A:LEU1135 4.8 20.3 1.0
HA A:LEU1135 4.8 18.1 1.0
HA A:ALA1156 4.8 15.5 1.0
C56 A:O311204 4.8 17.6 1.0
O26 A:O311204 4.8 12.0 1.0
HE1 A:PHE1154 4.8 14.9 1.0
H562 A:O311204 4.8 21.1 1.0
H A:LEU1135 4.8 18.0 1.0
N17 A:O311204 4.9 11.9 1.0
C A:ALA1156 4.9 13.7 1.0
HA A:ILE1132 5.0 20.9 1.0
HB2 A:ALA1164 5.0 22.7 1.0
HD11 A:LEU1135 5.0 25.4 1.0

Fluorine binding site 3 out of 4 in 6p6v

Go back to Fluorine Binding Sites List in 6p6v
Fluorine binding site 3 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1204

b:15.9
occ:1.00
F53 A:O311204 0.0 15.9 1.0
C41 A:O311204 1.4 15.4 1.0
F54 A:O311204 2.2 19.6 1.0
HB2 A:ALA1156 2.3 19.3 1.0
C42 A:O311204 2.4 16.2 1.0
C40 A:O311204 2.4 16.1 1.0
HG2 A:ARG1155 2.7 17.8 1.0
H401 A:O311204 2.8 19.3 1.0
O52 A:O311204 2.9 12.0 1.0
C51 A:O311204 3.0 13.2 1.0
H201 A:O311204 3.0 15.0 1.0
CB A:ALA1156 3.3 16.1 1.0
C39 A:O311204 3.3 20.5 1.0
CG A:ARG1155 3.4 14.8 1.0
HG3 A:ARG1155 3.4 17.8 1.0
OD2 A:ASP1081 3.5 12.9 1.0
N43 A:O311204 3.5 17.3 1.0
H391 A:O311204 3.5 24.6 1.0
HB3 A:ALA1156 3.6 19.3 1.0
O A:ARG1155 3.6 10.9 1.0
HD2 A:ARG1155 3.6 18.1 1.0
HB1 A:ALA1156 3.7 19.3 1.0
C20 A:O311204 3.8 12.5 1.0
H361 A:O311204 4.0 21.3 1.0
CD A:ARG1155 4.1 15.1 1.0
C22 A:O311204 4.1 12.6 1.0
HD1 A:HIS1057 4.1 14.0 1.0
C A:ARG1155 4.1 12.2 1.0
N24 A:O311204 4.2 15.0 1.0
HE1 A:HIS1057 4.2 16.6 1.0
H211 A:O311204 4.3 14.7 1.0
CA A:ALA1156 4.3 12.9 1.0
N50 A:O311204 4.3 14.4 1.0
HA A:ALA1156 4.3 15.5 1.0
C21 A:O311204 4.3 12.2 1.0
H171 A:O311204 4.4 14.3 1.0
N A:ALA1156 4.4 13.6 1.0
CG A:ASP1081 4.5 12.7 1.0
ND1 A:HIS1057 4.5 11.6 1.0
HB2 A:ASP1081 4.5 15.5 1.0
CE1 A:HIS1057 4.6 13.8 1.0
HB3 A:ASP1081 4.6 15.5 1.0
CB A:ARG1155 4.6 12.3 1.0
C38 A:O311204 4.7 19.7 1.0
C23 A:O311204 4.7 13.3 1.0
C44 A:O311204 4.7 17.6 1.0
H221 A:O311204 4.7 15.1 1.0
C25 A:O311204 4.7 14.6 1.0
H382 A:O311204 4.8 23.7 1.0
H231 A:O311204 4.8 15.9 1.0
HE A:ARG1155 4.8 17.6 1.0
CB A:ASP1081 4.8 12.9 1.0
HD3 A:ARG1155 4.8 18.1 1.0
HB3 A:ARG1155 4.9 14.7 1.0
O26 A:O311204 4.9 12.0 1.0
O A:HOH1368 4.9 20.7 1.0
O30 A:O311204 4.9 16.7 1.0
NE A:ARG1155 4.9 14.6 1.0
C18 A:O311204 4.9 14.8 1.0
CA A:ARG1155 4.9 12.9 1.0
C36 A:O311204 4.9 17.8 1.0
N17 A:O311204 5.0 11.9 1.0

Fluorine binding site 4 out of 4 in 6p6v

Go back to Fluorine Binding Sites List in 6p6v
Fluorine binding site 4 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS3/4A Protease Domain of Genotype 5A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1204

b:19.6
occ:1.00
F54 A:O311204 0.0 19.6 1.0
C41 A:O311204 1.4 15.4 1.0
F53 A:O311204 2.2 15.9 1.0
C42 A:O311204 2.3 16.2 1.0
H391 A:O311204 2.3 24.6 1.0
C40 A:O311204 2.4 16.1 1.0
HD2 A:ARG1155 2.5 18.1 1.0
N43 A:O311204 2.6 17.3 1.0
C39 A:O311204 2.7 20.5 1.0
O A:HOH1368 2.8 20.7 1.0
HG2 A:ARG1155 3.2 17.8 1.0
HB2 A:ASP1081 3.2 15.5 1.0
H401 A:O311204 3.2 19.3 1.0
CD A:ARG1155 3.4 15.1 1.0
O A:HOH1373 3.4 32.1 1.0
CG A:ARG1155 3.6 14.8 1.0
HB3 A:ASP1081 3.7 15.5 1.0
OD2 A:ASP1081 3.7 12.9 1.0
C51 A:O311204 3.7 13.2 1.0
HG3 A:ARG1155 3.8 17.8 1.0
CB A:ASP1081 3.8 12.9 1.0
HD3 A:ARG1155 4.0 18.1 1.0
HB2 A:ALA1156 4.1 19.3 1.0
NE A:ARG1155 4.1 14.6 1.0
C44 A:O311204 4.2 17.6 1.0
CG A:ASP1081 4.2 12.7 1.0
C38 A:O311204 4.3 19.7 1.0
O52 A:O311204 4.3 12.0 1.0
HE A:ARG1155 4.3 17.6 1.0
O A:HOH1448 4.4 32.7 1.0
O A:HOH1518 4.5 40.8 1.0
H361 A:O311204 4.6 21.3 1.0
H381 A:O311204 4.6 23.7 1.0
H382 A:O311204 4.7 23.7 1.0
HB3 A:ALA1156 4.8 19.3 1.0
H451 A:O311204 4.8 20.8 1.0
HH11 A:ARG1155 4.8 20.6 1.0
N50 A:O311204 4.9 14.4 1.0
CB A:ALA1156 4.9 16.1 1.0
O37 A:O311204 4.9 19.7 1.0
CZ A:ARG1155 5.0 18.9 1.0

Reference:

J.Timm, K.Kosovrasti, M.Henes, F.Leidner, S.Hou, N.Kurt-Yilmaz, C.A.Schiffer. Molecular Mechanism of Pan-Genotypic Hcv NS3/4A Protease Inhibition By Glecaprevir and Characterization of Genotype-Specific Structural Differences To Be Published.
Page generated: Sun Dec 13 13:05:09 2020

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