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Fluorine in PDB 6p6s: Hcv NS3/4A Protease Domain of Genotype 3A in Complex with Glecaprevir

Enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 3A in Complex with Glecaprevir

All present enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 3A 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 3A in Complex with Glecaprevir, PDB code: 6p6s 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) 36.15 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 36.487, 36.487, 267.772, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.5

Other elements in 6p6s:

The structure of Hcv NS3/4A Protease Domain of Genotype 3A in Complex with Glecaprevir also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS3/4A Protease Domain of Genotype 3A in Complex with Glecaprevir (pdb code 6p6s). 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 3A in Complex with Glecaprevir, PDB code: 6p6s:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6p6s

Go back to Fluorine Binding Sites List in 6p6s
Fluorine binding site 1 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 3A 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 3A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:28.3
occ:1.00
F15 A:O311201 0.0 28.3 1.0
C14 A:O311201 1.4 25.3 1.0
H141 A:O311201 1.9 30.4 1.0
F16 A:O311201 2.2 25.5 1.0
HD3 A:LYS1136 2.3 53.9 0.3
C13 A:O311201 2.4 24.8 1.0
HD3 A:LYS1136 2.5 56.1 0.7
HD11 A:LEU1132 2.6 29.5 1.0
HE3 A:LYS1136 2.7 48.3 0.7
H131 A:O311201 2.8 29.8 1.0
HA A:LYS1136 3.0 36.6 0.7
HA A:LYS1136 3.0 37.5 0.3
HZ3 A:LYS1136 3.1 45.5 0.3
C11 A:O311201 3.1 24.9 1.0
O10 A:O311201 3.1 30.3 1.0
HG2 A:LYS1136 3.2 41.5 0.7
C09 A:O311201 3.2 30.4 1.0
CD A:LYS1136 3.2 46.7 0.7
CD A:LYS1136 3.2 44.8 0.3
CE A:LYS1136 3.3 40.2 0.7
CD1 A:LEU1132 3.4 24.5 1.0
HD12 A:LEU1132 3.5 29.5 1.0
HE2 A:LYS1136 3.5 47.3 0.3
HG2 A:LYS1136 3.5 40.7 0.3
H583 A:O311201 3.6 27.9 1.0
HE2 A:LYS1136 3.6 48.3 0.7
C12 A:O311201 3.6 27.6 1.0
NZ A:LYS1136 3.7 37.8 0.3
CG A:LYS1136 3.7 34.5 0.7
O19 A:O311201 3.7 25.0 1.0
CE A:LYS1136 3.7 39.4 0.3
CA A:LYS1136 3.7 30.5 0.7
HB2 A:LEU1135 3.8 33.0 1.0
CA A:LYS1136 3.8 31.1 0.3
H122 A:O311201 3.8 33.2 1.0
HZ2 A:LYS1136 3.8 45.5 0.3
HG A:LEU1132 3.8 35.3 1.0
N A:LYS1136 3.9 29.9 0.7
N A:LYS1136 3.9 29.2 0.3
CG A:LYS1136 3.9 33.9 0.3
HD2 A:LYS1136 3.9 53.9 0.3
HD2 A:LYS1136 4.1 56.1 0.7
C A:LEU1135 4.1 28.9 1.0
N17 A:O311201 4.1 26.6 1.0
H A:LYS1136 4.1 36.0 0.7
HD13 A:LEU1132 4.2 29.5 1.0
H A:LYS1136 4.2 35.2 0.3
O A:LEU1135 4.2 25.0 1.0
CG A:LEU1132 4.2 29.3 1.0
H572 A:O311201 4.2 37.7 1.0
N08 A:O311201 4.2 25.9 1.0
CB A:LYS1136 4.3 34.3 0.7
C18 A:O311201 4.3 28.3 1.0
HD21 A:LEU1132 4.3 34.4 1.0
HB3 A:LEU1135 4.3 33.0 1.0
HB3 A:ALA1157 4.3 30.9 1.0
CB A:LYS1136 4.4 32.1 0.3
O A:LEU1132 4.4 23.0 1.0
H121 A:O311201 4.4 33.2 1.0
HZ1 A:LYS1136 4.4 45.5 0.3
C58 A:O311201 4.5 23.1 1.0
CB A:LEU1135 4.5 27.4 1.0
H581 A:O311201 4.5 27.9 1.0
HG3 A:LYS1136 4.5 41.5 0.7
HB2 A:ALA1157 4.5 30.9 1.0
NZ A:LYS1136 4.6 40.3 0.7
HE3 A:LYS1136 4.6 47.3 0.3
H081 A:O311201 4.6 31.2 1.0
O26 A:O311201 4.7 23.3 1.0
H A:GLY1137 4.7 33.7 1.0
HZ2 A:LYS1136 4.7 48.5 0.7
HG3 A:LYS1136 4.7 40.7 0.3
HZ A:PHE1154 4.8 28.4 1.0
HB3 A:LYS1136 4.8 41.3 0.7
O07 A:O311201 4.8 26.8 1.0
CD2 A:LEU1132 4.8 28.6 1.0
H171 A:O311201 4.9 32.1 1.0
CB A:ALA1157 4.9 25.7 1.0
CA A:LEU1135 4.9 22.2 1.0
HB3 A:LYS1136 4.9 38.6 0.3
H582 A:O311201 5.0 27.9 1.0
C A:LYS1136 5.0 29.7 0.7
C A:LYS1136 5.0 29.8 0.3
HB2 A:LYS1136 5.0 41.3 0.7

Fluorine binding site 2 out of 4 in 6p6s

Go back to Fluorine Binding Sites List in 6p6s
Fluorine binding site 2 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 3A 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 3A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:25.5
occ:1.00
F16 A:O311201 0.0 25.5 1.0
C14 A:O311201 1.4 25.3 1.0
H141 A:O311201 1.9 30.4 1.0
F15 A:O311201 2.2 28.3 1.0
C13 A:O311201 2.4 24.8 1.0
HB2 A:LEU1135 2.6 33.0 1.0
HB2 A:ALA1157 2.6 30.9 1.0
H131 A:O311201 2.6 29.8 1.0
HD11 A:LEU1132 2.8 29.5 1.0
HZ A:PHE1154 2.8 28.4 1.0
HB3 A:LEU1135 2.8 33.0 1.0
HD12 A:LEU1132 2.9 29.5 1.0
HB3 A:ALA1157 3.1 30.9 1.0
CB A:LEU1135 3.2 27.4 1.0
CD1 A:LEU1132 3.2 24.5 1.0
CB A:ALA1157 3.3 25.7 1.0
C12 A:O311201 3.3 27.6 1.0
H122 A:O311201 3.4 33.2 1.0
HD12 A:LEU1135 3.4 28.9 1.0
HD13 A:LEU1135 3.5 28.9 1.0
CZ A:PHE1154 3.5 23.6 1.0
HD13 A:LEU1132 3.7 29.5 1.0
HE2 A:PHE1154 3.7 27.4 1.0
C11 A:O311201 3.8 24.9 1.0
HB1 A:ALA1157 3.8 30.9 1.0
CD1 A:LEU1135 3.8 24.0 1.0
H121 A:O311201 3.9 33.2 1.0
C A:LEU1135 4.0 28.9 1.0
CE2 A:PHE1154 4.0 22.8 1.0
H583 A:O311201 4.0 27.9 1.0
O A:LEU1135 4.0 25.0 1.0
CG A:LEU1135 4.1 27.9 1.0
O10 A:O311201 4.2 30.3 1.0
CA A:LEU1135 4.2 22.2 1.0
HA A:LYS1136 4.3 36.6 0.7
C09 A:O311201 4.3 30.4 1.0
HA A:LYS1136 4.4 37.5 0.3
N A:LYS1136 4.4 29.9 0.7
H A:ALA1157 4.4 26.7 1.0
N A:LYS1136 4.4 29.2 0.3
N A:ALA1157 4.4 22.2 1.0
HD3 A:LYS1136 4.4 53.9 0.3
CA A:ALA1157 4.4 22.8 1.0
HG A:LEU1132 4.5 35.3 1.0
O A:LEU1132 4.5 23.0 1.0
CG A:LEU1132 4.6 29.3 1.0
CE1 A:PHE1154 4.6 22.6 1.0
HE3 A:LYS1136 4.6 48.3 0.7
HG2 A:LYS1136 4.7 41.5 0.7
HG A:LEU1135 4.7 33.6 1.0
HE1 A:PHE1154 4.7 27.3 1.0
HD3 A:LYS1136 4.7 56.1 0.7
H A:LYS1136 4.7 36.0 0.7
H A:LYS1136 4.7 35.2 0.3
HD11 A:LEU1135 4.7 28.9 1.0
C58 A:O311201 4.8 23.1 1.0
N17 A:O311201 4.8 26.6 1.0
HA A:LEU1132 4.8 26.9 1.0
H582 A:O311201 4.8 27.9 1.0
H581 A:O311201 4.9 27.9 1.0
H A:LEU1135 4.9 33.2 1.0
HA A:LEU1135 4.9 26.8 1.0
HA A:ALA1157 4.9 27.5 1.0
O26 A:O311201 4.9 23.3 1.0
CA A:LYS1136 4.9 30.5 0.7
CA A:LYS1136 4.9 31.1 0.3
C A:ALA1156 5.0 22.3 1.0
HA A:ALA1156 5.0 28.6 1.0
HD22 A:LEU1135 5.0 35.9 1.0
HG2 A:LYS1136 5.0 40.7 0.3

Fluorine binding site 3 out of 4 in 6p6s

Go back to Fluorine Binding Sites List in 6p6s
Fluorine binding site 3 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 3A 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 3A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:33.7
occ:1.00
F53 A:O311201 0.0 33.7 1.0
C41 A:O311201 1.4 40.2 1.0
F54 A:O311201 2.2 32.3 1.0
C42 A:O311201 2.4 33.2 1.0
C40 A:O311201 2.4 29.9 1.0
H391 A:O311201 2.4 38.2 1.0
HD2 A:ARG1155 2.6 43.1 1.0
C39 A:O311201 2.7 31.8 1.0
N43 A:O311201 2.8 33.1 1.0
HB2 A:ASP1081 3.1 42.6 1.0
HG2 A:ARG1155 3.2 44.2 1.0
H401 A:O311201 3.2 36.0 1.0
O A:HOH1352 3.2 35.4 1.0
O A:HOH1348 3.2 40.1 1.0
CD A:ARG1155 3.4 35.8 1.0
HG3 A:ARG1155 3.5 44.2 1.0
CG A:ARG1155 3.6 36.8 1.0
OD2 A:ASP1081 3.7 35.8 1.0
C51 A:O311201 3.7 31.4 1.0
CB A:ASP1081 3.8 35.5 1.0
HB3 A:ASP1081 3.8 42.6 1.0
HB2 A:ALA1156 3.9 31.1 1.0
CG A:ASP1081 4.0 33.5 1.0
HD3 A:ARG1155 4.1 43.1 1.0
O52 A:O311201 4.2 27.5 1.0
C38 A:O311201 4.2 29.3 1.0
NE A:ARG1155 4.3 36.5 1.0
C44 A:O311201 4.3 36.5 1.0
HE A:ARG1155 4.5 43.9 1.0
HE22 A:GLN1168 4.5 51.7 1.0
H381 A:O311201 4.6 35.3 1.0
H382 A:O311201 4.6 35.3 1.0
H361 A:O311201 4.7 36.8 1.0
HD1 A:HIS1057 4.8 36.1 1.0
CB A:ALA1156 4.8 25.9 1.0
HB3 A:ALA1156 4.8 31.1 1.0
N50 A:O311201 4.9 31.8 1.0
HH11 A:ARG1155 4.9 49.8 1.0
O37 A:O311201 5.0 29.2 1.0
H451 A:O311201 5.0 45.9 1.0

Fluorine binding site 4 out of 4 in 6p6s

Go back to Fluorine Binding Sites List in 6p6s
Fluorine binding site 4 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 3A 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 3A in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:32.3
occ:1.00
F54 A:O311201 0.0 32.3 1.0
C41 A:O311201 1.4 40.2 1.0
F53 A:O311201 2.2 33.7 1.0
C42 A:O311201 2.3 33.2 1.0
C40 A:O311201 2.4 29.9 1.0
HB2 A:ALA1156 2.4 31.1 1.0
O52 A:O311201 2.7 27.5 1.0
H201 A:O311201 2.8 29.3 1.0
C51 A:O311201 2.8 31.4 1.0
H401 A:O311201 2.9 36.0 1.0
HG2 A:ARG1155 3.0 44.2 1.0
C39 A:O311201 3.3 31.8 1.0
H391 A:O311201 3.4 38.2 1.0
CB A:ALA1156 3.4 25.9 1.0
HG3 A:ARG1155 3.5 44.2 1.0
N43 A:O311201 3.5 33.1 1.0
OD2 A:ASP1081 3.6 35.8 1.0
C20 A:O311201 3.6 24.3 1.0
CG A:ARG1155 3.7 36.8 1.0
O A:ARG1155 3.7 25.5 1.0
HB1 A:ALA1156 3.7 31.1 1.0
H211 A:O311201 3.8 33.6 1.0
C22 A:O311201 3.8 28.5 1.0
HB3 A:ALA1156 3.8 31.1 1.0
HD1 A:HIS1057 3.9 36.1 1.0
HD2 A:ARG1155 3.9 43.1 1.0
C21 A:O311201 4.0 27.9 1.0
N24 A:O311201 4.0 21.9 1.0
H361 A:O311201 4.1 36.8 1.0
N50 A:O311201 4.2 31.8 1.0
C A:ARG1155 4.2 21.6 1.0
HA A:ALA1156 4.3 28.6 1.0
ND1 A:HIS1057 4.3 30.0 1.0
HE1 A:HIS1057 4.3 44.1 1.0
CA A:ALA1156 4.3 23.8 1.0
CD A:ARG1155 4.4 35.8 1.0
H171 A:O311201 4.4 32.1 1.0
C23 A:O311201 4.5 26.5 1.0
CG A:ASP1081 4.5 33.5 1.0
CE1 A:HIS1057 4.5 36.7 1.0
H221 A:O311201 4.5 34.2 1.0
HB2 A:ASP1081 4.5 42.6 1.0
H232 A:O311201 4.6 31.9 1.0
C38 A:O311201 4.6 29.3 1.0
N A:ALA1156 4.6 21.2 1.0
H382 A:O311201 4.6 35.3 1.0
C25 A:O311201 4.7 22.8 1.0
O30 A:O311201 4.7 24.9 1.0
C44 A:O311201 4.7 36.5 1.0
O26 A:O311201 4.8 23.3 1.0
C18 A:O311201 4.8 28.3 1.0
CB A:ARG1155 4.9 30.5 1.0
HB3 A:ASP1081 4.9 42.6 1.0
CB A:ASP1081 4.9 35.5 1.0
H212 A:O311201 5.0 33.6 1.0
N17 A:O311201 5.0 26.6 1.0
C49 A:O311201 5.0 34.3 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: Tue Jul 15 14:30:32 2025

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