Fluorine in PDB 7mm6: Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
Enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
All present enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49:
3.4.21.98;
Protein crystallography data
The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49, PDB code: 7mm6
was solved by
J.Zephyr,
C.A.Schiffer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
26.18 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.613,
58.646,
59.648,
90,
90,
90
|
R / Rfree (%)
|
17.4 /
19.6
|
Other elements in 7mm6:
The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
(pdb code 7mm6). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49, PDB code: 7mm6:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7mm6
Go back to
Fluorine Binding Sites List in 7mm6
Fluorine binding site 1 out
of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:27.8
occ:1.00
|
F55
|
A:ZJY1202
|
0.0
|
27.8
|
1.0
|
C54
|
A:ZJY1202
|
1.4
|
23.6
|
1.0
|
F57
|
A:ZJY1202
|
2.2
|
28.2
|
1.0
|
F56
|
A:ZJY1202
|
2.2
|
22.0
|
1.0
|
C51
|
A:ZJY1202
|
2.4
|
28.3
|
1.0
|
H521
|
A:ZJY1202
|
2.4
|
37.4
|
1.0
|
HH21
|
A:ARG1123
|
2.5
|
41.6
|
1.0
|
H532
|
A:ZJY1202
|
2.6
|
32.0
|
1.0
|
HB2
|
A:ASP1168
|
2.7
|
17.9
|
1.0
|
HE
|
A:ARG1123
|
2.7
|
36.7
|
1.0
|
NH2
|
A:ARG1123
|
2.7
|
34.6
|
1.0
|
C52
|
A:ZJY1202
|
2.8
|
31.0
|
1.0
|
C53
|
A:ZJY1202
|
2.9
|
26.5
|
1.0
|
NE
|
A:ARG1123
|
3.0
|
30.4
|
1.0
|
CZ
|
A:ARG1123
|
3.0
|
36.5
|
1.0
|
HH22
|
A:ARG1123
|
3.3
|
41.6
|
1.0
|
HG22
|
A:VAL1158
|
3.3
|
30.0
|
1.0
|
CB
|
A:ASP1168
|
3.4
|
14.7
|
1.0
|
HB3
|
A:ASP1168
|
3.6
|
17.9
|
1.0
|
HG21
|
A:VAL1158
|
3.7
|
30.0
|
1.0
|
O
|
A:HOH1429
|
3.7
|
33.6
|
1.0
|
H522
|
A:ZJY1202
|
3.7
|
37.4
|
1.0
|
O
|
A:HOH1313
|
3.8
|
25.1
|
1.0
|
C17
|
A:ZJY1202
|
3.8
|
23.1
|
1.0
|
H531
|
A:ZJY1202
|
3.8
|
32.0
|
1.0
|
CG2
|
A:VAL1158
|
3.9
|
24.8
|
1.0
|
CG
|
A:ASP1168
|
3.9
|
19.4
|
1.0
|
HG23
|
A:VAL1158
|
4.0
|
30.0
|
1.0
|
H171
|
A:ZJY1202
|
4.0
|
27.9
|
1.0
|
NH1
|
A:ARG1123
|
4.0
|
44.9
|
1.0
|
HD3
|
A:ARG1123
|
4.0
|
38.7
|
1.0
|
CD
|
A:ARG1123
|
4.1
|
32.1
|
1.0
|
OD1
|
A:ASP1168
|
4.3
|
15.4
|
1.0
|
HD2
|
A:ARG1123
|
4.3
|
38.7
|
1.0
|
OD2
|
A:ASP1168
|
4.3
|
21.3
|
1.0
|
HH12
|
A:ARG1123
|
4.4
|
54.0
|
1.0
|
O15
|
A:ZJY1202
|
4.4
|
19.7
|
1.0
|
H172
|
A:ZJY1202
|
4.4
|
27.9
|
1.0
|
HH11
|
A:ARG1123
|
4.5
|
54.0
|
1.0
|
O
|
A:HOH1345
|
4.6
|
24.1
|
1.0
|
HB3
|
A:ALA1156
|
4.7
|
16.8
|
1.0
|
CA
|
A:ASP1168
|
4.7
|
14.8
|
1.0
|
HB1
|
A:ALA1156
|
4.7
|
16.8
|
1.0
|
HA
|
A:ASP1168
|
4.8
|
18.0
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7mm6
Go back to
Fluorine Binding Sites List in 7mm6
Fluorine binding site 2 out
of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:22.0
occ:1.00
|
F56
|
A:ZJY1202
|
0.0
|
22.0
|
1.0
|
C54
|
A:ZJY1202
|
1.4
|
23.6
|
1.0
|
F57
|
A:ZJY1202
|
2.2
|
28.2
|
1.0
|
F55
|
A:ZJY1202
|
2.2
|
27.8
|
1.0
|
C51
|
A:ZJY1202
|
2.4
|
28.3
|
1.0
|
HG22
|
A:VAL1158
|
2.6
|
30.0
|
1.0
|
HB1
|
A:ALA1156
|
2.7
|
16.8
|
1.0
|
HB3
|
A:ASP1168
|
2.8
|
17.9
|
1.0
|
HB2
|
A:ASP1168
|
3.0
|
17.9
|
1.0
|
H532
|
A:ZJY1202
|
3.0
|
32.0
|
1.0
|
O15
|
A:ZJY1202
|
3.1
|
19.7
|
1.0
|
C17
|
A:ZJY1202
|
3.1
|
23.1
|
1.0
|
C53
|
A:ZJY1202
|
3.1
|
26.5
|
1.0
|
H171
|
A:ZJY1202
|
3.2
|
27.9
|
1.0
|
HB3
|
A:ALA1156
|
3.2
|
16.8
|
1.0
|
CB
|
A:ASP1168
|
3.3
|
14.7
|
1.0
|
CB
|
A:ALA1156
|
3.4
|
13.9
|
1.0
|
CG2
|
A:VAL1158
|
3.4
|
24.8
|
1.0
|
HG23
|
A:VAL1158
|
3.4
|
30.0
|
1.0
|
C52
|
A:ZJY1202
|
3.7
|
31.0
|
1.0
|
H531
|
A:ZJY1202
|
3.7
|
32.0
|
1.0
|
HG21
|
A:VAL1158
|
3.8
|
30.0
|
1.0
|
C14
|
A:ZJY1202
|
3.8
|
17.9
|
1.0
|
H521
|
A:ZJY1202
|
3.9
|
37.4
|
1.0
|
O
|
A:ALA1157
|
4.0
|
18.6
|
1.0
|
H172
|
A:ZJY1202
|
4.0
|
27.9
|
1.0
|
C
|
A:ALA1156
|
4.0
|
14.5
|
1.0
|
C
|
A:ALA1157
|
4.0
|
19.4
|
1.0
|
HB2
|
A:ALA1156
|
4.1
|
16.8
|
1.0
|
H131
|
A:ZJY1202
|
4.1
|
20.2
|
1.0
|
CG
|
A:ASP1168
|
4.1
|
19.4
|
1.0
|
O
|
A:ALA1156
|
4.2
|
15.9
|
1.0
|
N
|
A:ALA1157
|
4.2
|
16.0
|
1.0
|
H
|
A:ASP1168
|
4.2
|
18.6
|
1.0
|
OD2
|
A:ASP1168
|
4.2
|
21.3
|
1.0
|
N
|
A:VAL1158
|
4.3
|
19.0
|
1.0
|
HA
|
A:VAL1158
|
4.3
|
26.2
|
1.0
|
CA
|
A:ALA1156
|
4.3
|
15.3
|
1.0
|
N13
|
A:ZJY1202
|
4.3
|
16.7
|
1.0
|
H
|
A:ALA1157
|
4.4
|
19.4
|
1.0
|
H522
|
A:ZJY1202
|
4.5
|
37.4
|
1.0
|
N
|
A:ASP1168
|
4.5
|
15.3
|
1.0
|
CA
|
A:ASP1168
|
4.6
|
14.8
|
1.0
|
O16
|
A:ZJY1202
|
4.6
|
18.0
|
1.0
|
H
|
A:VAL1158
|
4.6
|
23.0
|
1.0
|
CA
|
A:VAL1158
|
4.6
|
21.7
|
1.0
|
CA
|
A:ALA1157
|
4.6
|
16.3
|
1.0
|
CB
|
A:VAL1158
|
4.6
|
23.8
|
1.0
|
HE
|
A:ARG1123
|
4.6
|
36.7
|
1.0
|
HH21
|
A:ARG1123
|
4.7
|
41.6
|
1.0
|
HA
|
A:ALA1157
|
4.7
|
19.7
|
1.0
|
NE
|
A:ARG1123
|
4.8
|
30.4
|
1.0
|
NH2
|
A:ARG1123
|
4.8
|
34.6
|
1.0
|
CZ
|
A:ARG1123
|
4.9
|
36.5
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7mm6
Go back to
Fluorine Binding Sites List in 7mm6
Fluorine binding site 3 out
of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:28.2
occ:1.00
|
F57
|
A:ZJY1202
|
0.0
|
28.2
|
1.0
|
C54
|
A:ZJY1202
|
1.4
|
23.6
|
1.0
|
F55
|
A:ZJY1202
|
2.2
|
27.8
|
1.0
|
F56
|
A:ZJY1202
|
2.2
|
22.0
|
1.0
|
C51
|
A:ZJY1202
|
2.4
|
28.3
|
1.0
|
H171
|
A:ZJY1202
|
2.6
|
27.9
|
1.0
|
C17
|
A:ZJY1202
|
3.0
|
23.1
|
1.0
|
O
|
A:HOH1345
|
3.0
|
24.1
|
1.0
|
HB3
|
A:ALA1156
|
3.1
|
16.8
|
1.0
|
OD2
|
A:ASP1168
|
3.1
|
21.3
|
1.0
|
HB3
|
A:ASP1168
|
3.2
|
17.9
|
1.0
|
HB2
|
A:ASP1168
|
3.2
|
17.9
|
1.0
|
C52
|
A:ZJY1202
|
3.3
|
31.0
|
1.0
|
CG
|
A:ASP1168
|
3.4
|
19.4
|
1.0
|
H521
|
A:ZJY1202
|
3.4
|
37.4
|
1.0
|
HB1
|
A:ALA1156
|
3.4
|
16.8
|
1.0
|
CB
|
A:ASP1168
|
3.5
|
14.7
|
1.0
|
CB
|
A:ALA1156
|
3.7
|
13.9
|
1.0
|
H172
|
A:ZJY1202
|
3.7
|
27.9
|
1.0
|
C53
|
A:ZJY1202
|
3.7
|
26.5
|
1.0
|
H332
|
A:ZJY1202
|
3.8
|
21.0
|
1.0
|
O15
|
A:ZJY1202
|
3.8
|
19.7
|
1.0
|
H333
|
A:ZJY1202
|
3.9
|
21.0
|
1.0
|
H532
|
A:ZJY1202
|
4.0
|
32.0
|
1.0
|
H522
|
A:ZJY1202
|
4.0
|
37.4
|
1.0
|
O
|
A:HOH1429
|
4.0
|
33.6
|
1.0
|
HB2
|
A:ALA1156
|
4.1
|
16.8
|
1.0
|
H331
|
A:ZJY1202
|
4.1
|
21.0
|
1.0
|
OD1
|
A:ASP1168
|
4.1
|
15.4
|
1.0
|
C33
|
A:ZJY1202
|
4.1
|
17.4
|
1.0
|
HH21
|
A:ARG1123
|
4.2
|
41.6
|
1.0
|
HE
|
A:ARG1123
|
4.4
|
36.7
|
1.0
|
C14
|
A:ZJY1202
|
4.4
|
17.9
|
1.0
|
H531
|
A:ZJY1202
|
4.5
|
32.0
|
1.0
|
O16
|
A:ZJY1202
|
4.6
|
18.0
|
1.0
|
HG22
|
A:VAL1158
|
4.7
|
30.0
|
1.0
|
HE
|
A:ARG1155
|
4.7
|
19.7
|
1.0
|
NH2
|
A:ARG1123
|
4.7
|
34.6
|
1.0
|
O
|
A:HOH1313
|
4.8
|
25.1
|
1.0
|
NE
|
A:ARG1123
|
5.0
|
30.4
|
1.0
|
CA
|
A:ALA1156
|
5.0
|
15.3
|
1.0
|
HG2
|
A:ARG1155
|
5.0
|
17.7
|
1.0
|
|
Reference:
J.Zephyr,
D.Nageswara Rao,
S.V.Vo,
M.Henes,
K.Kosovrasti,
A.N.Matthew,
A.K.Hedger,
J.Timm,
E.T.Chan,
A.Ali,
N.Kurt Yilmaz,
C.A.Schiffer.
Deciphering the Molecular Mechanism of Hcv Protease Inhibitor Fluorination As A General Approach to Avoid Drug Resistance. J.Mol.Biol. V. 434 67503 2022.
ISSN: ESSN 1089-8638
PubMed: 35183560
DOI: 10.1016/J.JMB.2022.167503
Page generated: Fri Aug 2 09:32:18 2024
|