Fluorine in PDB 7l7p: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24
Protein crystallography data
The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24, PDB code: 7l7p
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)
|
24.93 /
1.58
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.062,
60.042,
58.808,
90,
90,
90
|
R / Rfree (%)
|
16.3 /
18.5
|
Other elements in 7l7p:
The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24
(pdb code 7l7p). 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 D168A Protease in Complex with Ch-24, PDB code: 7l7p:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7l7p
Go back to
Fluorine Binding Sites List in 7l7p
Fluorine binding site 1 out
of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24
![](/pictures/F/pdb/l7/7l7p-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/l7/7l7p-F-sphere_01_stereo.jpg) 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 D168A Protease in Complex with Ch-24 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:24.6
occ:1.00
|
F52
|
A:XT41202
|
0.0
|
24.6
|
1.0
|
C32
|
A:XT41202
|
1.3
|
17.5
|
1.0
|
F54
|
A:XT41202
|
2.2
|
23.1
|
1.0
|
F53
|
A:XT41202
|
2.2
|
22.8
|
1.0
|
C25
|
A:XT41202
|
2.3
|
22.3
|
1.0
|
N30
|
A:XT41202
|
2.6
|
23.8
|
1.0
|
HD2
|
A:ARG1155
|
2.6
|
18.5
|
1.0
|
O
|
A:HOH1474
|
3.1
|
38.9
|
1.0
|
HG2
|
A:ARG1155
|
3.1
|
19.7
|
1.0
|
O
|
A:HOH1350
|
3.2
|
34.5
|
1.0
|
HB2
|
A:ASP1081
|
3.3
|
12.0
|
1.0
|
HG3
|
A:ARG1155
|
3.3
|
19.7
|
1.0
|
CD
|
A:ARG1155
|
3.4
|
15.3
|
1.0
|
CG
|
A:ARG1155
|
3.4
|
16.3
|
1.0
|
OD1
|
A:ASP1081
|
3.5
|
11.1
|
1.0
|
O
|
A:HOH1445
|
3.6
|
33.0
|
1.0
|
C24
|
A:XT41202
|
3.7
|
16.6
|
1.0
|
O
|
A:HOH1405
|
3.9
|
26.2
|
1.0
|
CB
|
A:ASP1081
|
3.9
|
9.9
|
1.0
|
CG
|
A:ASP1081
|
3.9
|
13.7
|
1.0
|
HB3
|
A:ASP1081
|
3.9
|
12.0
|
1.0
|
C28
|
A:XT41202
|
4.1
|
18.6
|
1.0
|
HB2
|
A:ALA1156
|
4.1
|
14.3
|
1.0
|
HD3
|
A:ARG1155
|
4.1
|
18.5
|
1.0
|
NE
|
A:ARG1155
|
4.1
|
20.4
|
1.0
|
O07
|
A:XT41202
|
4.2
|
13.8
|
1.0
|
HE
|
A:ARG1155
|
4.3
|
24.6
|
1.0
|
HD1
|
A:HIS1057
|
4.5
|
14.2
|
1.0
|
H511
|
A:XT41202
|
4.6
|
23.6
|
1.0
|
H311
|
A:XT41202
|
4.8
|
26.4
|
1.0
|
H513
|
A:XT41202
|
4.8
|
23.6
|
1.0
|
N26
|
A:XT41202
|
4.9
|
20.5
|
1.0
|
OD2
|
A:ASP1081
|
4.9
|
11.5
|
1.0
|
HH11
|
A:ARG1155
|
4.9
|
33.8
|
1.0
|
CB
|
A:ARG1155
|
4.9
|
13.6
|
1.0
|
H011
|
A:XT41202
|
4.9
|
16.6
|
1.0
|
CZ
|
A:ARG1155
|
5.0
|
25.8
|
1.0
|
CB
|
A:ALA1156
|
5.0
|
11.8
|
1.0
|
C31
|
A:XT41202
|
5.0
|
21.9
|
1.0
|
C27
|
A:XT41202
|
5.0
|
15.8
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7l7p
Go back to
Fluorine Binding Sites List in 7l7p
Fluorine binding site 2 out
of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24
![](/pictures/F/pdb/l7/7l7p-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/l7/7l7p-F-sphere_02_stereo.jpg) 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 D168A Protease in Complex with Ch-24 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:22.8
occ:1.00
|
F53
|
A:XT41202
|
0.0
|
22.8
|
1.0
|
C32
|
A:XT41202
|
1.3
|
17.5
|
1.0
|
F54
|
A:XT41202
|
2.2
|
23.1
|
1.0
|
F52
|
A:XT41202
|
2.2
|
24.6
|
1.0
|
C25
|
A:XT41202
|
2.3
|
22.3
|
1.0
|
O07
|
A:XT41202
|
2.8
|
13.8
|
1.0
|
C24
|
A:XT41202
|
3.0
|
16.6
|
1.0
|
H513
|
A:XT41202
|
3.0
|
23.6
|
1.0
|
H511
|
A:XT41202
|
3.0
|
23.6
|
1.0
|
HB2
|
A:ALA1156
|
3.3
|
14.3
|
1.0
|
C51
|
A:XT41202
|
3.4
|
19.6
|
1.0
|
N30
|
A:XT41202
|
3.5
|
23.8
|
1.0
|
O
|
A:HOH1474
|
3.6
|
38.9
|
1.0
|
O
|
A:HOH1463
|
3.7
|
40.1
|
1.0
|
O21
|
A:XT41202
|
3.8
|
16.6
|
1.0
|
H512
|
A:XT41202
|
3.9
|
23.6
|
1.0
|
HG2
|
A:ARG1155
|
3.9
|
19.7
|
1.0
|
HB1
|
A:ALA1156
|
4.0
|
14.3
|
1.0
|
CB
|
A:ALA1156
|
4.0
|
11.8
|
1.0
|
O
|
A:HOH1405
|
4.0
|
26.2
|
1.0
|
C05
|
A:XT41202
|
4.1
|
12.4
|
1.0
|
H011
|
A:XT41202
|
4.1
|
16.6
|
1.0
|
H061
|
A:XT41202
|
4.3
|
16.8
|
1.0
|
HB3
|
A:ALA1156
|
4.3
|
14.3
|
1.0
|
N26
|
A:XT41202
|
4.3
|
20.5
|
1.0
|
C19
|
A:XT41202
|
4.5
|
15.5
|
1.0
|
HD2
|
A:ARG1155
|
4.5
|
18.5
|
1.0
|
N03
|
A:XT41202
|
4.6
|
12.6
|
1.0
|
C06
|
A:XT41202
|
4.6
|
13.9
|
1.0
|
HG3
|
A:ARG1155
|
4.6
|
19.7
|
1.0
|
H051
|
A:XT41202
|
4.7
|
15.0
|
1.0
|
CG
|
A:ARG1155
|
4.7
|
16.3
|
1.0
|
C28
|
A:XT41202
|
4.7
|
18.6
|
1.0
|
O
|
A:HOH1350
|
4.7
|
34.5
|
1.0
|
C01
|
A:XT41202
|
4.7
|
13.7
|
1.0
|
C48
|
A:XT41202
|
4.8
|
18.2
|
1.0
|
H503
|
A:XT41202
|
4.8
|
24.3
|
1.0
|
C02
|
A:XT41202
|
5.0
|
10.7
|
1.0
|
O20
|
A:XT41202
|
5.0
|
15.7
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7l7p
Go back to
Fluorine Binding Sites List in 7l7p
Fluorine binding site 3 out
of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with Ch-24
![](/pictures/F/pdb/l7/7l7p-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/l7/7l7p-F-sphere_03_stereo.jpg) 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 D168A Protease in Complex with Ch-24 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1202
b:23.1
occ:1.00
|
F54
|
A:XT41202
|
0.0
|
23.1
|
1.0
|
C32
|
A:XT41202
|
1.4
|
17.5
|
1.0
|
F53
|
A:XT41202
|
2.2
|
22.8
|
1.0
|
F52
|
A:XT41202
|
2.2
|
24.6
|
1.0
|
C25
|
A:XT41202
|
2.3
|
22.3
|
1.0
|
HB2
|
A:ALA1156
|
2.6
|
14.3
|
1.0
|
HG2
|
A:ARG1155
|
2.7
|
19.7
|
1.0
|
H011
|
A:XT41202
|
2.8
|
16.6
|
1.0
|
HG3
|
A:ARG1155
|
2.9
|
19.7
|
1.0
|
O07
|
A:XT41202
|
2.9
|
13.8
|
1.0
|
C24
|
A:XT41202
|
3.0
|
16.6
|
1.0
|
CG
|
A:ARG1155
|
3.2
|
16.3
|
1.0
|
O
|
A:ARG1155
|
3.4
|
10.5
|
1.0
|
OD1
|
A:ASP1081
|
3.4
|
11.1
|
1.0
|
N30
|
A:XT41202
|
3.4
|
23.8
|
1.0
|
CB
|
A:ALA1156
|
3.5
|
11.8
|
1.0
|
HD1
|
A:HIS1057
|
3.6
|
14.2
|
1.0
|
C01
|
A:XT41202
|
3.7
|
13.7
|
1.0
|
HD2
|
A:ARG1155
|
3.7
|
18.5
|
1.0
|
HE1
|
A:HIS1057
|
3.8
|
13.3
|
1.0
|
HB1
|
A:ALA1156
|
3.9
|
14.3
|
1.0
|
C
|
A:ARG1155
|
3.9
|
10.5
|
1.0
|
ND1
|
A:HIS1057
|
3.9
|
11.8
|
1.0
|
H021
|
A:XT41202
|
3.9
|
12.9
|
1.0
|
C05
|
A:XT41202
|
4.0
|
12.4
|
1.0
|
HB3
|
A:ALA1156
|
4.0
|
14.3
|
1.0
|
CE1
|
A:HIS1057
|
4.0
|
11.0
|
1.0
|
CD
|
A:ARG1155
|
4.1
|
15.3
|
1.0
|
C02
|
A:XT41202
|
4.1
|
10.7
|
1.0
|
HA
|
A:ALA1156
|
4.2
|
13.8
|
1.0
|
H511
|
A:XT41202
|
4.2
|
23.6
|
1.0
|
N03
|
A:XT41202
|
4.3
|
12.6
|
1.0
|
H101
|
A:XT41202
|
4.3
|
11.2
|
1.0
|
CA
|
A:ALA1156
|
4.3
|
11.4
|
1.0
|
N26
|
A:XT41202
|
4.3
|
20.5
|
1.0
|
N
|
A:ALA1156
|
4.4
|
10.5
|
1.0
|
CG
|
A:ASP1081
|
4.4
|
13.7
|
1.0
|
CB
|
A:ARG1155
|
4.4
|
13.6
|
1.0
|
O
|
A:HOH1405
|
4.5
|
26.2
|
1.0
|
C28
|
A:XT41202
|
4.6
|
18.6
|
1.0
|
CA
|
A:ARG1155
|
4.7
|
11.5
|
1.0
|
O
|
A:HOH1474
|
4.7
|
38.9
|
1.0
|
H051
|
A:XT41202
|
4.7
|
15.0
|
1.0
|
HB2
|
A:ASP1081
|
4.7
|
12.0
|
1.0
|
C06
|
A:XT41202
|
4.7
|
13.9
|
1.0
|
HA
|
A:ARG1155
|
4.7
|
13.9
|
1.0
|
HB3
|
A:ARG1155
|
4.8
|
16.4
|
1.0
|
HD3
|
A:ARG1155
|
4.8
|
18.5
|
1.0
|
H061
|
A:XT41202
|
4.8
|
16.8
|
1.0
|
H513
|
A:XT41202
|
4.8
|
23.6
|
1.0
|
HE
|
A:ARG1155
|
4.8
|
24.6
|
1.0
|
CG
|
A:HIS1057
|
4.9
|
10.6
|
1.0
|
C04
|
A:XT41202
|
4.9
|
10.4
|
1.0
|
N10
|
A:XT41202
|
4.9
|
9.2
|
1.0
|
HB3
|
A:ASP1081
|
4.9
|
12.0
|
1.0
|
NE
|
A:ARG1155
|
4.9
|
20.4
|
1.0
|
C08
|
A:XT41202
|
4.9
|
12.2
|
1.0
|
CB
|
A:ASP1081
|
5.0
|
9.9
|
1.0
|
C27
|
A:XT41202
|
5.0
|
15.8
|
1.0
|
O16
|
A:XT41202
|
5.0
|
11.4
|
1.0
|
C51
|
A:XT41202
|
5.0
|
19.6
|
1.0
|
HB3
|
A:HIS1057
|
5.0
|
11.4
|
1.0
|
|
Reference:
D.Nageswara Rao,
J.Zephyr,
M.Henes,
E.T.Chan,
A.N.Matthew,
A.K.Hedger,
H.L.Conway,
M.Saeed,
A.Newton,
C.J.Petropoulos,
W.Huang,
N.Kurt Yilmaz,
C.A.Schiffer,
A.Ali.
Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity Against Drug-Resistant Hepatitis C Virus Variants. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34405680
DOI: 10.1021/ACS.JMEDCHEM.1C00554
Page generated: Fri Aug 2 08:46:43 2024
|