Fluorine in PDB 6vdm: Hcv NS3/4A Protease A156T, D168E Double Mutant in Complex with Glecaprevir
Enzymatic activity of Hcv NS3/4A Protease A156T, D168E Double Mutant in Complex with Glecaprevir
Protein crystallography data
The structure of Hcv NS3/4A Protease A156T, D168E Double Mutant in Complex with Glecaprevir, PDB code: 6vdm
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)
|
23.71 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.337,
58.643,
60.056,
90,
90,
90
|
R / Rfree (%)
|
16.2 /
19.6
|
Other elements in 6vdm:
The structure of Hcv NS3/4A Protease A156T, D168E Double Mutant 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 A156T, D168E Double Mutant in Complex with Glecaprevir
(pdb code 6vdm). 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 A156T, D168E Double Mutant in Complex with Glecaprevir, PDB code: 6vdm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6vdm
Go back to
Fluorine Binding Sites List in 6vdm
Fluorine binding site 1 out
of 4 in the Hcv NS3/4A Protease A156T, D168E Double Mutant 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 A156T, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:12.4
occ:1.00
|
F15
|
A:O311202
|
0.0
|
12.4
|
1.0
|
C14
|
A:O311202
|
1.4
|
11.2
|
1.0
|
F16
|
A:O311202
|
2.2
|
13.4
|
1.0
|
C13
|
A:O311202
|
2.4
|
12.1
|
1.0
|
HA
|
A:LYS1136
|
2.6
|
10.8
|
1.0
|
HD11
|
A:ILE1132
|
3.0
|
30.5
|
1.0
|
O
|
A:HOH1406
|
3.3
|
12.2
|
1.0
|
C11
|
A:O311202
|
3.3
|
11.2
|
1.0
|
O10
|
A:O311202
|
3.3
|
8.9
|
1.0
|
C09
|
A:O311202
|
3.4
|
9.7
|
1.0
|
HG13
|
A:ILE1132
|
3.4
|
26.6
|
1.0
|
CA
|
A:LYS1136
|
3.4
|
9.0
|
1.0
|
HD12
|
A:ILE1132
|
3.4
|
30.5
|
1.0
|
CD1
|
A:ILE1132
|
3.5
|
25.4
|
1.0
|
HB2
|
A:LYS1136
|
3.5
|
12.9
|
1.0
|
N
|
A:LYS1136
|
3.7
|
10.4
|
1.0
|
O19
|
A:O311202
|
3.7
|
11.6
|
1.0
|
C12
|
A:O311202
|
3.7
|
11.6
|
1.0
|
CG1
|
A:ILE1132
|
3.9
|
22.2
|
1.0
|
CB
|
A:LYS1136
|
4.0
|
10.8
|
1.0
|
C
|
A:LEU1135
|
4.0
|
11.6
|
1.0
|
H
|
A:LYS1136
|
4.0
|
12.4
|
1.0
|
HB2
|
A:LEU1135
|
4.0
|
12.8
|
1.0
|
HG12
|
A:ILE1132
|
4.0
|
26.6
|
1.0
|
O
|
A:LEU1135
|
4.1
|
10.9
|
1.0
|
HG3
|
A:LYS1136
|
4.1
|
15.6
|
1.0
|
N17
|
A:O311202
|
4.2
|
11.4
|
1.0
|
H
|
A:GLY1137
|
4.2
|
10.1
|
1.0
|
N08
|
A:O311202
|
4.3
|
10.4
|
1.0
|
HB3
|
A:ALA1157
|
4.4
|
14.4
|
1.0
|
C18
|
A:O311202
|
4.4
|
12.1
|
1.0
|
HB2
|
A:ALA1157
|
4.4
|
14.4
|
1.0
|
HD13
|
A:ILE1132
|
4.4
|
30.5
|
1.0
|
O
|
A:ILE1132
|
4.4
|
13.5
|
1.0
|
HB3
|
A:LEU1135
|
4.5
|
12.8
|
1.0
|
O07
|
A:O311202
|
4.5
|
9.8
|
1.0
|
CG
|
A:LYS1136
|
4.6
|
13.0
|
1.0
|
C
|
A:LYS1136
|
4.6
|
7.8
|
1.0
|
CB
|
A:LEU1135
|
4.6
|
10.7
|
1.0
|
C56
|
A:O311202
|
4.7
|
13.3
|
1.0
|
N
|
A:GLY1137
|
4.7
|
8.4
|
1.0
|
HB3
|
A:LYS1136
|
4.8
|
12.9
|
1.0
|
O26
|
A:O311202
|
4.8
|
14.6
|
1.0
|
CB
|
A:ALA1157
|
4.9
|
12.0
|
1.0
|
CA
|
A:LEU1135
|
4.9
|
11.2
|
1.0
|
HZ
|
A:PHE1154
|
5.0
|
13.2
|
1.0
|
C58
|
A:O311202
|
5.0
|
12.4
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6vdm
Go back to
Fluorine Binding Sites List in 6vdm
Fluorine binding site 2 out
of 4 in the Hcv NS3/4A Protease A156T, D168E Double Mutant 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 A156T, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:13.4
occ:1.00
|
F16
|
A:O311202
|
0.0
|
13.4
|
1.0
|
C14
|
A:O311202
|
1.4
|
11.2
|
1.0
|
F15
|
A:O311202
|
2.2
|
12.4
|
1.0
|
C13
|
A:O311202
|
2.3
|
12.1
|
1.0
|
HD11
|
A:ILE1132
|
2.5
|
30.5
|
1.0
|
HD12
|
A:ILE1132
|
2.5
|
30.5
|
1.0
|
HB2
|
A:ALA1157
|
2.6
|
14.4
|
1.0
|
HB2
|
A:LEU1135
|
2.7
|
12.8
|
1.0
|
CD1
|
A:ILE1132
|
2.9
|
25.4
|
1.0
|
HB3
|
A:LEU1135
|
2.9
|
12.8
|
1.0
|
HZ
|
A:PHE1154
|
3.0
|
13.2
|
1.0
|
HB3
|
A:ALA1157
|
3.2
|
14.4
|
1.0
|
CB
|
A:LEU1135
|
3.2
|
10.7
|
1.0
|
CB
|
A:ALA1157
|
3.3
|
12.0
|
1.0
|
C12
|
A:O311202
|
3.3
|
11.6
|
1.0
|
HD13
|
A:ILE1132
|
3.6
|
30.5
|
1.0
|
HD12
|
A:LEU1135
|
3.7
|
15.2
|
1.0
|
CZ
|
A:PHE1154
|
3.7
|
11.0
|
1.0
|
C11
|
A:O311202
|
3.8
|
11.2
|
1.0
|
C
|
A:LEU1135
|
3.8
|
11.6
|
1.0
|
HB1
|
A:ALA1157
|
3.8
|
14.4
|
1.0
|
O
|
A:LEU1135
|
3.9
|
10.9
|
1.0
|
HG13
|
A:ILE1132
|
3.9
|
26.6
|
1.0
|
HA
|
A:LYS1136
|
3.9
|
10.8
|
1.0
|
CG1
|
A:ILE1132
|
4.0
|
22.2
|
1.0
|
HE2
|
A:PHE1154
|
4.1
|
13.0
|
1.0
|
N
|
A:LYS1136
|
4.1
|
10.4
|
1.0
|
HD13
|
A:LEU1135
|
4.1
|
15.2
|
1.0
|
CA
|
A:LEU1135
|
4.1
|
11.2
|
1.0
|
O10
|
A:O311202
|
4.2
|
8.9
|
1.0
|
CD1
|
A:LEU1135
|
4.2
|
12.7
|
1.0
|
H
|
A:ALA1157
|
4.3
|
15.2
|
1.0
|
CE2
|
A:PHE1154
|
4.3
|
10.8
|
1.0
|
CG
|
A:LEU1135
|
4.3
|
11.7
|
1.0
|
C09
|
A:O311202
|
4.3
|
9.7
|
1.0
|
H
|
A:LYS1136
|
4.4
|
12.4
|
1.0
|
HG12
|
A:ILE1132
|
4.4
|
26.6
|
1.0
|
N
|
A:ALA1157
|
4.4
|
12.7
|
1.0
|
CA
|
A:ALA1157
|
4.4
|
13.7
|
1.0
|
CA
|
A:LYS1136
|
4.5
|
9.0
|
1.0
|
O
|
A:ILE1132
|
4.5
|
13.5
|
1.0
|
CE1
|
A:PHE1154
|
4.7
|
11.2
|
1.0
|
HE1
|
A:PHE1154
|
4.7
|
13.4
|
1.0
|
HG
|
A:LEU1135
|
4.7
|
14.1
|
1.0
|
HA
|
A:ILE1132
|
4.7
|
18.6
|
1.0
|
N17
|
A:O311202
|
4.8
|
11.4
|
1.0
|
H
|
A:LEU1135
|
4.8
|
14.1
|
1.0
|
HA
|
A:ALA1157
|
4.8
|
16.4
|
1.0
|
C56
|
A:O311202
|
4.8
|
13.3
|
1.0
|
HA
|
A:LEU1135
|
4.8
|
13.4
|
1.0
|
O26
|
A:O311202
|
4.9
|
14.6
|
1.0
|
HB2
|
A:LYS1136
|
5.0
|
12.9
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6vdm
Go back to
Fluorine Binding Sites List in 6vdm
Fluorine binding site 3 out
of 4 in the Hcv NS3/4A Protease A156T, D168E Double Mutant 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 A156T, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:38.0
occ:1.00
|
F53
|
A:O311202
|
0.0
|
38.0
|
1.0
|
C41
|
A:O311202
|
1.4
|
32.2
|
1.0
|
F54
|
A:O311202
|
2.2
|
35.2
|
1.0
|
C42
|
A:O311202
|
2.4
|
24.1
|
1.0
|
C40
|
A:O311202
|
2.4
|
31.8
|
1.0
|
N43
|
A:O311202
|
2.8
|
22.0
|
1.0
|
C39
|
A:O311202
|
2.8
|
34.4
|
1.0
|
O
|
A:HOH1459
|
3.3
|
33.6
|
1.0
|
HB2
|
A:ASP1081
|
3.4
|
12.5
|
1.0
|
OG1
|
A:THR1156
|
3.5
|
18.4
|
1.0
|
O
|
A:HOH1453
|
3.6
|
39.7
|
1.0
|
CD
|
A:ARG1155
|
3.6
|
17.0
|
0.6
|
O
|
A:HOH1301
|
3.7
|
24.6
|
1.0
|
C51
|
A:O311202
|
3.7
|
21.0
|
1.0
|
O
|
A:HOH1423
|
3.7
|
49.8
|
1.0
|
OD2
|
A:ASP1081
|
3.9
|
11.8
|
1.0
|
CB
|
A:ASP1081
|
4.1
|
10.4
|
1.0
|
CD
|
A:ARG1155
|
4.2
|
17.2
|
0.4
|
O52
|
A:O311202
|
4.2
|
20.1
|
1.0
|
NH2
|
A:ARG1155
|
4.2
|
20.3
|
0.6
|
HB3
|
A:ASP1081
|
4.2
|
12.5
|
1.0
|
CG
|
A:ASP1081
|
4.3
|
12.1
|
1.0
|
C44
|
A:O311202
|
4.3
|
22.6
|
1.0
|
C38
|
A:O311202
|
4.4
|
35.5
|
1.0
|
NE
|
A:ARG1155
|
4.4
|
19.5
|
0.4
|
NE
|
A:ARG1155
|
4.4
|
18.5
|
0.6
|
CG
|
A:ARG1155
|
4.6
|
15.8
|
0.4
|
CG
|
A:ARG1155
|
4.6
|
15.7
|
0.6
|
CZ
|
A:ARG1155
|
4.7
|
20.6
|
0.6
|
CB
|
A:THR1156
|
4.7
|
15.2
|
1.0
|
CG2
|
A:THR1156
|
4.8
|
19.3
|
1.0
|
N50
|
A:O311202
|
4.9
|
20.6
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6vdm
Go back to
Fluorine Binding Sites List in 6vdm
Fluorine binding site 4 out
of 4 in the Hcv NS3/4A Protease A156T, D168E Double Mutant 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 A156T, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:35.2
occ:1.00
|
F54
|
A:O311202
|
0.0
|
35.2
|
1.0
|
C41
|
A:O311202
|
1.4
|
32.2
|
1.0
|
F53
|
A:O311202
|
2.2
|
38.0
|
1.0
|
C42
|
A:O311202
|
2.4
|
24.1
|
1.0
|
C40
|
A:O311202
|
2.4
|
31.8
|
1.0
|
O52
|
A:O311202
|
2.7
|
20.1
|
1.0
|
OG1
|
A:THR1156
|
2.7
|
18.4
|
1.0
|
C51
|
A:O311202
|
2.9
|
21.0
|
1.0
|
C39
|
A:O311202
|
3.3
|
34.4
|
1.0
|
C20
|
A:O311202
|
3.5
|
13.0
|
1.0
|
N43
|
A:O311202
|
3.5
|
22.0
|
1.0
|
O
|
A:ARG1155
|
3.6
|
9.7
|
1.0
|
CG2
|
A:THR1156
|
3.6
|
19.3
|
1.0
|
CB
|
A:THR1156
|
3.7
|
15.2
|
1.0
|
OD2
|
A:ASP1081
|
3.7
|
11.8
|
1.0
|
C22
|
A:O311202
|
3.9
|
16.8
|
1.0
|
C21
|
A:O311202
|
3.9
|
13.7
|
1.0
|
N24
|
A:O311202
|
4.0
|
14.0
|
1.0
|
C
|
A:ARG1155
|
4.2
|
10.7
|
1.0
|
CA
|
A:THR1156
|
4.2
|
12.6
|
1.0
|
N50
|
A:O311202
|
4.2
|
20.6
|
1.0
|
CD
|
A:ARG1155
|
4.3
|
17.0
|
0.6
|
O
|
A:HOH1301
|
4.4
|
24.6
|
1.0
|
ND1
|
A:HIS1057
|
4.5
|
9.8
|
1.0
|
C23
|
A:O311202
|
4.5
|
15.8
|
1.0
|
N
|
A:THR1156
|
4.5
|
11.7
|
1.0
|
CG
|
A:ARG1155
|
4.6
|
15.8
|
0.4
|
C25
|
A:O311202
|
4.6
|
14.8
|
1.0
|
CG
|
A:ARG1155
|
4.6
|
15.7
|
0.6
|
CE1
|
A:HIS1057
|
4.6
|
10.7
|
1.0
|
CG
|
A:ASP1081
|
4.6
|
12.1
|
1.0
|
C38
|
A:O311202
|
4.6
|
35.5
|
1.0
|
O26
|
A:O311202
|
4.7
|
14.6
|
1.0
|
CB
|
A:ARG1155
|
4.7
|
13.8
|
0.6
|
HB2
|
A:ASP1081
|
4.7
|
12.5
|
1.0
|
CB
|
A:ARG1155
|
4.7
|
13.8
|
0.4
|
C44
|
A:O311202
|
4.8
|
22.6
|
1.0
|
C18
|
A:O311202
|
4.8
|
12.1
|
1.0
|
CD
|
A:ARG1155
|
4.9
|
17.2
|
0.4
|
N17
|
A:O311202
|
5.0
|
11.4
|
1.0
|
|
Reference:
J.Timm,
J.Zephyr,
S.Hou,
N.Kurt Yilmaz,
C.A.Schiffer.
Ras at Position 156 of Hcv NS3/4A Protease Abolish Inhibition By Current Hcv Drugs To Be Published.
Page generated: Fri Aug 2 03:00:04 2024
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