Fluorine in PDB 6p6r: Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera in Complex with Glecaprevir
Enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera in Complex with Glecaprevir
All present enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera 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 1A3A Chimera in Complex with Glecaprevir, PDB code: 6p6r
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)
|
26.34 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.571,
58.623,
60.053,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
13.9 /
17.9
|
Other elements in 6p6r:
The structure of Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera in Complex with Glecaprevir also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera in Complex with Glecaprevir
(pdb code 6p6r). 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 1A3A Chimera in Complex with Glecaprevir, PDB code: 6p6r:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6p6r
Go back to
Fluorine Binding Sites List in 6p6r
Fluorine binding site 1 out
of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera 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 1A3A Chimera in Complex with Glecaprevir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1206
b:12.6
occ:1.00
|
F15
|
A:O311206
|
0.0
|
12.6
|
1.0
|
|
C14
|
A:O311206
|
1.4
|
13.3
|
1.0
|
|
H141
|
A:O311206
|
1.9
|
16.0
|
1.0
|
|
F16
|
A:O311206
|
2.2
|
13.2
|
1.0
|
|
C13
|
A:O311206
|
2.4
|
10.7
|
1.0
|
|
HA
|
A:LYS1136
|
2.7
|
10.7
|
1.0
|
|
H131
|
A:O311206
|
2.8
|
12.8
|
1.0
|
|
HD11
|
A:LEU1132
|
3.0
|
24.3
|
1.0
|
|
O
|
A:HOH1446
|
3.1
|
16.8
|
1.0
|
|
C11
|
A:O311206
|
3.2
|
8.6
|
1.0
|
|
O10
|
A:O311206
|
3.3
|
10.9
|
1.0
|
|
C09
|
A:O311206
|
3.3
|
8.6
|
1.0
|
|
CA
|
A:LYS1136
|
3.5
|
8.9
|
1.0
|
|
HD12
|
A:LEU1132
|
3.6
|
24.3
|
1.0
|
|
O19
|
A:O311206
|
3.7
|
12.6
|
1.0
|
|
HG
|
A:LEU1132
|
3.7
|
27.8
|
1.0
|
|
CD1
|
A:LEU1132
|
3.7
|
20.2
|
1.0
|
|
C12
|
A:O311206
|
3.7
|
11.6
|
1.0
|
|
HB2
|
A:LYS1136
|
3.7
|
15.6
|
1.0
|
|
N
|
A:LYS1136
|
3.8
|
11.4
|
1.0
|
|
H571
|
A:O311206
|
3.8
|
15.5
|
1.0
|
|
H121
|
A:O311206
|
3.9
|
13.9
|
1.0
|
|
HG3
|
A:LYS1136
|
4.0
|
17.5
|
1.0
|
|
O
|
A:LEU1135
|
4.0
|
9.2
|
1.0
|
|
C
|
A:LEU1135
|
4.1
|
10.4
|
1.0
|
|
CB
|
A:LYS1136
|
4.1
|
13.0
|
1.0
|
|
HB2
|
A:LEU1135
|
4.1
|
14.9
|
1.0
|
|
HD21
|
A:LEU1132
|
4.2
|
31.4
|
1.0
|
|
CG
|
A:LEU1132
|
4.2
|
23.1
|
1.0
|
|
H
|
A:LYS1136
|
4.2
|
13.7
|
1.0
|
|
H
|
A:GLY1137
|
4.2
|
12.1
|
1.0
|
|
N17
|
A:O311206
|
4.2
|
11.8
|
1.0
|
|
N08
|
A:O311206
|
4.3
|
9.9
|
1.0
|
|
HB2
|
A:ALA1157
|
4.3
|
13.5
|
1.0
|
|
C18
|
A:O311206
|
4.3
|
10.8
|
1.0
|
|
H561
|
A:O311206
|
4.3
|
17.0
|
1.0
|
|
HB3
|
A:ALA1157
|
4.4
|
13.5
|
1.0
|
|
H122
|
A:O311206
|
4.5
|
13.9
|
1.0
|
|
O06
|
A:O311206
|
4.5
|
10.4
|
1.0
|
|
HB3
|
A:LEU1135
|
4.5
|
14.9
|
1.0
|
|
HD13
|
A:LEU1132
|
4.5
|
24.3
|
1.0
|
|
O
|
A:LEU1132
|
4.6
|
14.4
|
1.0
|
|
CG
|
A:LYS1136
|
4.6
|
14.6
|
1.0
|
|
H081
|
A:O311206
|
4.6
|
11.9
|
1.0
|
|
C
|
A:LYS1136
|
4.7
|
10.1
|
1.0
|
|
C57
|
A:O311206
|
4.7
|
12.9
|
1.0
|
|
CB
|
A:LEU1135
|
4.7
|
12.4
|
1.0
|
|
CD2
|
A:LEU1132
|
4.7
|
26.1
|
1.0
|
|
O26
|
A:O311206
|
4.7
|
11.1
|
1.0
|
|
N
|
A:GLY1137
|
4.7
|
10.1
|
1.0
|
|
H573
|
A:O311206
|
4.8
|
15.5
|
1.0
|
|
CB
|
A:ALA1157
|
4.8
|
11.3
|
1.0
|
|
H
|
A:ALA1157
|
4.9
|
15.2
|
1.0
|
|
HZ
|
A:PHE1154
|
5.0
|
15.4
|
1.0
|
|
HB3
|
A:LYS1136
|
5.0
|
15.6
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6p6r
Go back to
Fluorine Binding Sites List in 6p6r
Fluorine binding site 2 out
of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera 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 1A3A Chimera in Complex with Glecaprevir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1206
b:13.2
occ:1.00
|
F16
|
A:O311206
|
0.0
|
13.2
|
1.0
|
|
C14
|
A:O311206
|
1.4
|
13.3
|
1.0
|
|
H141
|
A:O311206
|
2.0
|
16.0
|
1.0
|
|
F15
|
A:O311206
|
2.2
|
12.6
|
1.0
|
|
C13
|
A:O311206
|
2.3
|
10.7
|
1.0
|
|
HB2
|
A:ALA1157
|
2.5
|
13.5
|
1.0
|
|
H131
|
A:O311206
|
2.6
|
12.8
|
1.0
|
|
HB2
|
A:LEU1135
|
2.8
|
14.9
|
1.0
|
|
HB3
|
A:LEU1135
|
2.9
|
14.9
|
1.0
|
|
HZ
|
A:PHE1154
|
2.9
|
15.4
|
1.0
|
|
HD12
|
A:LEU1132
|
3.0
|
24.3
|
1.0
|
|
HD11
|
A:LEU1132
|
3.0
|
24.3
|
1.0
|
|
C12
|
A:O311206
|
3.2
|
11.6
|
1.0
|
|
CB
|
A:ALA1157
|
3.3
|
11.3
|
1.0
|
|
HB3
|
A:ALA1157
|
3.3
|
13.5
|
1.0
|
|
H121
|
A:O311206
|
3.3
|
13.9
|
1.0
|
|
CB
|
A:LEU1135
|
3.3
|
12.4
|
1.0
|
|
CD1
|
A:LEU1132
|
3.5
|
20.2
|
1.0
|
|
CZ
|
A:PHE1154
|
3.6
|
12.8
|
1.0
|
|
C11
|
A:O311206
|
3.7
|
8.6
|
1.0
|
|
O
|
A:LEU1135
|
3.7
|
9.2
|
1.0
|
|
H122
|
A:O311206
|
3.8
|
13.9
|
1.0
|
|
C
|
A:LEU1135
|
3.8
|
10.4
|
1.0
|
|
HD12
|
A:LEU1135
|
3.9
|
20.6
|
1.0
|
|
HB1
|
A:ALA1157
|
3.9
|
13.5
|
1.0
|
|
HD13
|
A:LEU1135
|
3.9
|
20.6
|
1.0
|
|
HE2
|
A:PHE1154
|
3.9
|
15.4
|
1.0
|
|
HA
|
A:LYS1136
|
4.0
|
10.7
|
1.0
|
|
H
|
A:ALA1157
|
4.0
|
15.2
|
1.0
|
|
HD13
|
A:LEU1132
|
4.1
|
24.3
|
1.0
|
|
O10
|
A:O311206
|
4.1
|
10.9
|
1.0
|
|
CE2
|
A:PHE1154
|
4.1
|
12.8
|
1.0
|
|
N
|
A:LYS1136
|
4.2
|
11.4
|
1.0
|
|
CA
|
A:LEU1135
|
4.2
|
11.6
|
1.0
|
|
CD1
|
A:LEU1135
|
4.2
|
17.1
|
1.0
|
|
N
|
A:ALA1157
|
4.2
|
12.6
|
1.0
|
|
H571
|
A:O311206
|
4.2
|
15.5
|
1.0
|
|
CA
|
A:ALA1157
|
4.3
|
12.7
|
1.0
|
|
C09
|
A:O311206
|
4.3
|
8.6
|
1.0
|
|
HG
|
A:LEU1132
|
4.3
|
27.8
|
1.0
|
|
CG
|
A:LEU1135
|
4.4
|
13.7
|
1.0
|
|
HA
|
A:ALA1157
|
4.5
|
15.2
|
1.0
|
|
CE1
|
A:PHE1154
|
4.5
|
10.9
|
1.0
|
|
CG
|
A:LEU1132
|
4.6
|
23.1
|
1.0
|
|
H
|
A:LYS1136
|
4.6
|
13.7
|
1.0
|
|
O
|
A:LEU1132
|
4.6
|
14.4
|
1.0
|
|
HE1
|
A:PHE1154
|
4.6
|
13.1
|
1.0
|
|
CA
|
A:LYS1136
|
4.6
|
8.9
|
1.0
|
|
H573
|
A:O311206
|
4.6
|
15.5
|
1.0
|
|
N17
|
A:O311206
|
4.8
|
11.8
|
1.0
|
|
O26
|
A:O311206
|
4.8
|
11.1
|
1.0
|
|
HA
|
A:LEU1132
|
4.8
|
24.7
|
1.0
|
|
HA
|
A:LEU1135
|
4.8
|
14.0
|
1.0
|
|
H
|
A:LEU1135
|
4.9
|
14.1
|
1.0
|
|
C57
|
A:O311206
|
4.9
|
12.9
|
1.0
|
|
HG
|
A:LEU1135
|
5.0
|
16.5
|
1.0
|
|
C
|
A:ALA1156
|
5.0
|
11.9
|
1.0
|
|
HA
|
A:ALA1156
|
5.0
|
14.4
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6p6r
Go back to
Fluorine Binding Sites List in 6p6r
Fluorine binding site 3 out
of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera 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 1A3A Chimera in Complex with Glecaprevir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1206
b:15.3
occ:1.00
|
F53
|
A:O311206
|
0.0
|
15.3
|
1.0
|
|
C41
|
A:O311206
|
1.4
|
14.6
|
1.0
|
|
F54
|
A:O311206
|
2.2
|
17.6
|
1.0
|
|
C42
|
A:O311206
|
2.3
|
14.8
|
1.0
|
|
C40
|
A:O311206
|
2.4
|
15.7
|
1.0
|
|
HB2
|
A:ALA1156
|
2.4
|
14.9
|
1.0
|
|
H401
|
A:O311206
|
2.7
|
18.9
|
1.0
|
|
O52
|
A:O311206
|
2.8
|
14.1
|
1.0
|
|
HG2
|
A:ARG1155
|
2.8
|
14.6
|
1.0
|
|
H201
|
A:O311206
|
2.9
|
11.2
|
1.0
|
|
C51
|
A:O311206
|
2.9
|
12.9
|
1.0
|
|
HG3
|
A:ARG1155
|
3.1
|
14.6
|
1.0
|
|
CB
|
A:ALA1156
|
3.4
|
12.4
|
1.0
|
|
C39
|
A:O311206
|
3.4
|
20.2
|
1.0
|
|
CG
|
A:ARG1155
|
3.4
|
12.2
|
1.0
|
|
N43
|
A:O311206
|
3.4
|
13.2
|
1.0
|
|
OD2
|
A:ASP1081
|
3.5
|
9.7
|
1.0
|
|
O
|
A:ARG1155
|
3.5
|
11.1
|
1.0
|
|
H391
|
A:O311206
|
3.6
|
24.3
|
1.0
|
|
C20
|
A:O311206
|
3.7
|
9.3
|
1.0
|
|
HB1
|
A:ALA1156
|
3.7
|
14.9
|
1.0
|
|
HB3
|
A:ALA1156
|
3.8
|
14.9
|
1.0
|
|
H211
|
A:O311206
|
3.8
|
15.2
|
1.0
|
|
HD2
|
A:ARG1155
|
3.9
|
13.3
|
1.0
|
|
HD1
|
A:HIS1057
|
3.9
|
10.9
|
1.0
|
|
C
|
A:ARG1155
|
4.0
|
9.7
|
1.0
|
|
C22
|
A:O311206
|
4.0
|
11.6
|
1.0
|
|
C21
|
A:O311206
|
4.1
|
12.6
|
1.0
|
|
H361
|
A:O311206
|
4.1
|
16.7
|
1.0
|
|
HA
|
A:ALA1156
|
4.1
|
14.4
|
1.0
|
|
N24
|
A:O311206
|
4.2
|
11.2
|
1.0
|
|
CA
|
A:ALA1156
|
4.2
|
12.0
|
1.0
|
|
CD
|
A:ARG1155
|
4.2
|
11.1
|
1.0
|
|
HE1
|
A:HIS1057
|
4.2
|
14.3
|
1.0
|
|
N50
|
A:O311206
|
4.2
|
12.9
|
1.0
|
|
ND1
|
A:HIS1057
|
4.3
|
9.1
|
1.0
|
|
N
|
A:ALA1156
|
4.3
|
10.3
|
1.0
|
|
H171
|
A:O311206
|
4.4
|
14.2
|
1.0
|
|
CG
|
A:ASP1081
|
4.5
|
9.8
|
1.0
|
|
CE1
|
A:HIS1057
|
4.5
|
11.9
|
1.0
|
|
CB
|
A:ARG1155
|
4.6
|
10.1
|
1.0
|
|
HB2
|
A:ASP1081
|
4.6
|
15.2
|
1.0
|
|
C23
|
A:O311206
|
4.6
|
12.7
|
1.0
|
|
C44
|
A:O311206
|
4.6
|
16.3
|
1.0
|
|
H221
|
A:O311206
|
4.7
|
14.0
|
1.0
|
|
H232
|
A:O311206
|
4.7
|
15.3
|
1.0
|
|
C38
|
A:O311206
|
4.7
|
20.8
|
1.0
|
|
H381
|
A:O311206
|
4.7
|
25.0
|
1.0
|
|
CA
|
A:ARG1155
|
4.8
|
8.9
|
1.0
|
|
C25
|
A:O311206
|
4.8
|
11.2
|
1.0
|
|
HB3
|
A:ASP1081
|
4.8
|
15.2
|
1.0
|
|
HD3
|
A:ARG1155
|
4.9
|
13.3
|
1.0
|
|
CB
|
A:ASP1081
|
4.9
|
12.7
|
1.0
|
|
HA
|
A:ARG1155
|
4.9
|
10.7
|
1.0
|
|
HB3
|
A:ARG1155
|
4.9
|
12.1
|
1.0
|
|
O26
|
A:O311206
|
4.9
|
11.1
|
1.0
|
|
C18
|
A:O311206
|
4.9
|
10.8
|
1.0
|
|
H
|
A:ALA1156
|
4.9
|
12.4
|
1.0
|
|
O30
|
A:O311206
|
4.9
|
15.3
|
1.0
|
|
C49
|
A:O311206
|
5.0
|
15.6
|
1.0
|
|
N17
|
A:O311206
|
5.0
|
11.8
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6p6r
Go back to
Fluorine Binding Sites List in 6p6r
Fluorine binding site 4 out
of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A3A Chimera 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 1A3A Chimera in Complex with Glecaprevir within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1206
b:17.6
occ:1.00
|
F54
|
A:O311206
|
0.0
|
17.6
|
1.0
|
|
C41
|
A:O311206
|
1.4
|
14.6
|
1.0
|
|
F53
|
A:O311206
|
2.2
|
15.3
|
1.0
|
|
C42
|
A:O311206
|
2.3
|
14.8
|
1.0
|
|
H391
|
A:O311206
|
2.4
|
24.3
|
1.0
|
|
C40
|
A:O311206
|
2.4
|
15.7
|
1.0
|
|
HD2
|
A:ARG1155
|
2.6
|
13.3
|
1.0
|
|
N43
|
A:O311206
|
2.7
|
13.2
|
1.0
|
|
C39
|
A:O311206
|
2.7
|
20.2
|
1.0
|
|
HG2
|
A:ARG1155
|
3.0
|
14.6
|
1.0
|
|
O
|
A:HOH1409
|
3.2
|
21.3
|
1.0
|
|
HB2
|
A:ASP1081
|
3.2
|
15.2
|
1.0
|
|
H401
|
A:O311206
|
3.2
|
18.9
|
1.0
|
|
HG3
|
A:ARG1155
|
3.4
|
14.6
|
1.0
|
|
CD
|
A:ARG1155
|
3.4
|
11.1
|
1.0
|
|
CG
|
A:ARG1155
|
3.5
|
12.2
|
1.0
|
|
O
|
A:HOH1417
|
3.5
|
17.5
|
1.0
|
|
OD2
|
A:ASP1081
|
3.7
|
9.7
|
1.0
|
|
C51
|
A:O311206
|
3.7
|
12.9
|
1.0
|
|
HB3
|
A:ASP1081
|
3.8
|
15.2
|
1.0
|
|
CB
|
A:ASP1081
|
3.9
|
12.7
|
1.0
|
|
HB2
|
A:ALA1156
|
3.9
|
14.9
|
1.0
|
|
O
|
A:HOH1464
|
4.0
|
17.7
|
1.0
|
|
HD3
|
A:ARG1155
|
4.1
|
13.3
|
1.0
|
|
CG
|
A:ASP1081
|
4.1
|
9.8
|
1.0
|
|
C44
|
A:O311206
|
4.1
|
16.3
|
1.0
|
|
O52
|
A:O311206
|
4.2
|
14.1
|
1.0
|
|
C38
|
A:O311206
|
4.3
|
20.8
|
1.0
|
|
NE
|
A:ARG1155
|
4.3
|
17.0
|
1.0
|
|
O
|
A:HOH1577
|
4.3
|
26.4
|
1.0
|
|
HE
|
A:ARG1155
|
4.5
|
20.4
|
1.0
|
|
H361
|
A:O311206
|
4.6
|
16.7
|
1.0
|
|
HE22
|
A:GLN1168
|
4.6
|
23.2
|
1.0
|
|
H382
|
A:O311206
|
4.7
|
25.0
|
1.0
|
|
H381
|
A:O311206
|
4.7
|
25.0
|
1.0
|
|
CB
|
A:ALA1156
|
4.8
|
12.4
|
1.0
|
|
H451
|
A:O311206
|
4.8
|
18.1
|
1.0
|
|
HH11
|
A:ARG1155
|
4.8
|
19.5
|
1.0
|
|
O
|
A:HOH1516
|
4.9
|
22.2
|
0.6
|
|
HD1
|
A:HIS1057
|
4.9
|
10.9
|
1.0
|
|
HB3
|
A:ALA1156
|
4.9
|
14.9
|
1.0
|
|
N50
|
A:O311206
|
4.9
|
12.9
|
1.0
|
|
O37
|
A:O311206
|
4.9
|
17.7
|
1.0
|
|
CB
|
A:ARG1155
|
4.9
|
10.1
|
1.0
|
|
O
|
A:HOH1549
|
4.9
|
34.1
|
1.0
|
|
C45
|
A:O311206
|
5.0
|
15.1
|
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 14:29:13 2025
|
