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:
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: Fri Aug 2 00:06:36 2024
|