Fluorine in PDB 7i18: Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group
Enzymatic activity of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group
All present enzymatic activity of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group:
3.4.22.69;
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i18
was solved by
T.Barthel,
L.S.Benz,
J.Wollenhaupt,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.89 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.05,
99.28,
103.5,
90,
90,
90
|
R / Rfree (%)
|
21 /
25.5
|
Other elements in 7i18:
The structure of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group
(pdb code 7i18). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the
Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group, PDB code: 7i18:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 7i18
Go back to
Fluorine Binding Sites List in 7i18
Fluorine binding site 1 out
of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:32.4
occ:0.25
|
F
|
A:R9D501
|
0.0
|
32.4
|
0.2
|
F
|
A:R9D501
|
0.0
|
32.4
|
0.2
|
C7
|
A:R9D501
|
1.4
|
32.1
|
0.2
|
C7
|
A:R9D501
|
1.4
|
32.1
|
0.2
|
C8
|
A:R9D501
|
2.3
|
31.9
|
0.2
|
C8
|
A:R9D501
|
2.3
|
31.9
|
0.2
|
C6
|
A:R9D501
|
2.4
|
31.2
|
0.2
|
C6
|
A:R9D501
|
2.4
|
31.2
|
0.2
|
C
|
A:ASP187
|
3.0
|
26.6
|
0.2
|
C
|
A:ASP187
|
3.0
|
26.6
|
0.2
|
C
|
A:ASP187
|
3.0
|
27.3
|
0.2
|
C
|
A:ASP187
|
3.0
|
27.3
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.2
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.2
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.7
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.7
|
0.2
|
O
|
A:ASP187
|
3.3
|
26.2
|
0.2
|
O
|
A:ASP187
|
3.3
|
26.2
|
0.2
|
N
|
A:ARG188
|
3.3
|
27.9
|
0.2
|
N
|
A:ARG188
|
3.3
|
27.9
|
0.2
|
N
|
A:ARG188
|
3.4
|
27.0
|
0.2
|
N
|
A:ARG188
|
3.4
|
27.0
|
0.2
|
CB
|
A:ASP187
|
3.5
|
25.4
|
0.2
|
CB
|
A:ASP187
|
3.5
|
25.4
|
0.2
|
O
|
A:ASP187
|
3.5
|
26.7
|
0.2
|
O
|
A:ASP187
|
3.5
|
26.7
|
0.2
|
CB
|
A:ASP187
|
3.6
|
26.0
|
0.2
|
CB
|
A:ASP187
|
3.6
|
26.0
|
0.2
|
C9
|
A:R9D501
|
3.6
|
32.1
|
0.2
|
C9
|
A:R9D501
|
3.6
|
32.1
|
0.2
|
C5
|
A:R9D501
|
3.6
|
33.1
|
0.2
|
C5
|
A:R9D501
|
3.6
|
33.1
|
0.2
|
CD2
|
A:HIS41
|
3.8
|
24.8
|
0.2
|
CD2
|
A:HIS41
|
3.8
|
24.8
|
0.2
|
CA
|
A:ARG188
|
4.0
|
29.9
|
0.2
|
CA
|
A:ARG188
|
4.0
|
29.9
|
0.2
|
CA
|
A:ARG188
|
4.1
|
28.6
|
0.2
|
CA
|
A:ARG188
|
4.1
|
28.6
|
0.2
|
C4
|
A:R9D501
|
4.1
|
33.7
|
0.2
|
C4
|
A:R9D501
|
4.1
|
33.7
|
0.2
|
CG
|
A:HIS41
|
4.2
|
25.0
|
0.2
|
CG
|
A:HIS41
|
4.2
|
25.0
|
0.2
|
C
|
A:ARG188
|
4.2
|
30.3
|
0.2
|
C
|
A:ARG188
|
4.2
|
30.3
|
0.2
|
CB
|
A:HIS41
|
4.3
|
25.4
|
0.2
|
CB
|
A:HIS41
|
4.3
|
25.4
|
0.2
|
C
|
A:ARG188
|
4.3
|
28.9
|
0.2
|
C
|
A:ARG188
|
4.3
|
28.9
|
0.2
|
SD
|
A:MET165
|
4.3
|
34.5
|
0.2
|
SD
|
A:MET165
|
4.3
|
34.5
|
0.2
|
NE2
|
A:GLN189
|
4.3
|
41.4
|
0.2
|
NE2
|
A:GLN189
|
4.3
|
41.4
|
0.2
|
CB
|
A:HIS41
|
4.4
|
30.6
|
0.2
|
CB
|
A:HIS41
|
4.4
|
30.6
|
0.2
|
CG
|
A:HIS41
|
4.4
|
31.3
|
0.2
|
CG
|
A:HIS41
|
4.4
|
31.3
|
0.2
|
CD2
|
A:HIS41
|
4.5
|
32.9
|
0.2
|
CD2
|
A:HIS41
|
4.5
|
32.9
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.1
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.1
|
0.2
|
SD
|
A:MET165
|
4.5
|
36.4
|
0.2
|
SD
|
A:MET165
|
4.5
|
36.4
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.5
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.5
|
0.2
|
O
|
A:ARG188
|
4.5
|
29.2
|
0.2
|
O
|
A:ARG188
|
4.5
|
29.2
|
0.2
|
CG
|
A:GLN189
|
4.6
|
40.5
|
0.2
|
CG
|
A:GLN189
|
4.6
|
40.5
|
0.2
|
O
|
A:ARG188
|
4.6
|
27.6
|
0.2
|
O
|
A:ARG188
|
4.6
|
27.6
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.5
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.5
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.4
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.4
|
0.2
|
O
|
A:VAL186
|
4.6
|
25.9
|
1.0
|
NE2
|
A:HIS41
|
4.7
|
26.0
|
0.2
|
NE2
|
A:HIS41
|
4.7
|
26.0
|
0.2
|
CG
|
A:ASP187
|
4.8
|
25.3
|
0.2
|
CG
|
A:ASP187
|
4.8
|
25.3
|
0.2
|
CE
|
A:MET49
|
4.8
|
64.8
|
0.2
|
CE
|
A:MET49
|
4.8
|
64.8
|
0.2
|
N
|
A:GLN189
|
4.8
|
33.0
|
0.2
|
N
|
A:GLN189
|
4.8
|
33.0
|
0.2
|
N
|
A:GLN189
|
4.8
|
31.8
|
0.2
|
N
|
A:GLN189
|
4.8
|
31.8
|
0.2
|
CG
|
A:ASP187
|
4.9
|
26.1
|
0.2
|
CG
|
A:ASP187
|
4.9
|
26.1
|
0.2
|
CB
|
A:MET165
|
4.9
|
30.9
|
0.2
|
CB
|
A:MET165
|
4.9
|
30.9
|
0.2
|
CB
|
A:MET165
|
5.0
|
29.5
|
0.2
|
CB
|
A:MET165
|
5.0
|
29.5
|
0.2
|
|
Fluorine binding site 2 out
of 2 in 7i18
Go back to
Fluorine Binding Sites List in 7i18
Fluorine binding site 2 out
of 2 in the Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pandda Analysis Group Deposition -- Main Protease (Sars-Cov-2) in Complex with Fragment D04 From the F2X-Entry Screen in Orthorhombic Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:32.4
occ:0.25
|
F
|
A:R9D501
|
0.0
|
32.4
|
0.2
|
F
|
A:R9D501
|
0.0
|
32.4
|
0.2
|
C7
|
A:R9D501
|
1.4
|
32.1
|
0.2
|
C7
|
A:R9D501
|
1.4
|
32.1
|
0.2
|
C8
|
A:R9D501
|
2.3
|
31.9
|
0.2
|
C8
|
A:R9D501
|
2.3
|
31.9
|
0.2
|
C6
|
A:R9D501
|
2.4
|
31.2
|
0.2
|
C6
|
A:R9D501
|
2.4
|
31.2
|
0.2
|
C
|
A:ASP187
|
3.0
|
26.6
|
0.2
|
C
|
A:ASP187
|
3.0
|
26.6
|
0.2
|
C
|
A:ASP187
|
3.0
|
27.3
|
0.2
|
C
|
A:ASP187
|
3.0
|
27.3
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.2
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.2
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.7
|
0.2
|
CA
|
A:ASP187
|
3.1
|
26.7
|
0.2
|
O
|
A:ASP187
|
3.3
|
26.2
|
0.2
|
O
|
A:ASP187
|
3.3
|
26.2
|
0.2
|
N
|
A:ARG188
|
3.3
|
27.9
|
0.2
|
N
|
A:ARG188
|
3.3
|
27.9
|
0.2
|
N
|
A:ARG188
|
3.4
|
27.0
|
0.2
|
N
|
A:ARG188
|
3.4
|
27.0
|
0.2
|
CB
|
A:ASP187
|
3.5
|
25.4
|
0.2
|
CB
|
A:ASP187
|
3.5
|
25.4
|
0.2
|
O
|
A:ASP187
|
3.5
|
26.7
|
0.2
|
O
|
A:ASP187
|
3.5
|
26.7
|
0.2
|
CB
|
A:ASP187
|
3.6
|
26.0
|
0.2
|
CB
|
A:ASP187
|
3.6
|
26.0
|
0.2
|
C9
|
A:R9D501
|
3.6
|
32.1
|
0.2
|
C9
|
A:R9D501
|
3.6
|
32.1
|
0.2
|
C5
|
A:R9D501
|
3.6
|
33.1
|
0.2
|
C5
|
A:R9D501
|
3.6
|
33.1
|
0.2
|
CD2
|
A:HIS41
|
3.8
|
24.8
|
0.2
|
CD2
|
A:HIS41
|
3.8
|
24.8
|
0.2
|
CA
|
A:ARG188
|
4.0
|
29.9
|
0.2
|
CA
|
A:ARG188
|
4.0
|
29.9
|
0.2
|
CA
|
A:ARG188
|
4.1
|
28.6
|
0.2
|
CA
|
A:ARG188
|
4.1
|
28.6
|
0.2
|
C4
|
A:R9D501
|
4.1
|
33.7
|
0.2
|
C4
|
A:R9D501
|
4.1
|
33.7
|
0.2
|
CG
|
A:HIS41
|
4.2
|
25.0
|
0.2
|
CG
|
A:HIS41
|
4.2
|
25.0
|
0.2
|
C
|
A:ARG188
|
4.2
|
30.3
|
0.2
|
C
|
A:ARG188
|
4.2
|
30.3
|
0.2
|
CB
|
A:HIS41
|
4.3
|
25.4
|
0.2
|
CB
|
A:HIS41
|
4.3
|
25.4
|
0.2
|
C
|
A:ARG188
|
4.3
|
28.9
|
0.2
|
C
|
A:ARG188
|
4.3
|
28.9
|
0.2
|
SD
|
A:MET165
|
4.3
|
34.5
|
0.2
|
SD
|
A:MET165
|
4.3
|
34.5
|
0.2
|
NE2
|
A:GLN189
|
4.3
|
41.4
|
0.2
|
NE2
|
A:GLN189
|
4.3
|
41.4
|
0.2
|
CB
|
A:HIS41
|
4.4
|
30.6
|
0.2
|
CB
|
A:HIS41
|
4.4
|
30.6
|
0.2
|
CG
|
A:HIS41
|
4.4
|
31.3
|
0.2
|
CG
|
A:HIS41
|
4.4
|
31.3
|
0.2
|
CD2
|
A:HIS41
|
4.5
|
32.9
|
0.2
|
CD2
|
A:HIS41
|
4.5
|
32.9
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.1
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.1
|
0.2
|
SD
|
A:MET165
|
4.5
|
36.4
|
0.2
|
SD
|
A:MET165
|
4.5
|
36.4
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.5
|
0.2
|
N
|
A:ASP187
|
4.5
|
26.5
|
0.2
|
O
|
A:ARG188
|
4.5
|
29.2
|
0.2
|
O
|
A:ARG188
|
4.5
|
29.2
|
0.2
|
CG
|
A:GLN189
|
4.6
|
40.5
|
0.2
|
CG
|
A:GLN189
|
4.6
|
40.5
|
0.2
|
O
|
A:ARG188
|
4.6
|
27.6
|
0.2
|
O
|
A:ARG188
|
4.6
|
27.6
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.5
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.5
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.4
|
0.2
|
OH
|
A:TYR54
|
4.6
|
27.4
|
0.2
|
O
|
A:VAL186
|
4.6
|
25.9
|
1.0
|
NE2
|
A:HIS41
|
4.7
|
26.0
|
0.2
|
NE2
|
A:HIS41
|
4.7
|
26.0
|
0.2
|
CG
|
A:ASP187
|
4.8
|
25.3
|
0.2
|
CG
|
A:ASP187
|
4.8
|
25.3
|
0.2
|
CE
|
A:MET49
|
4.8
|
64.8
|
0.2
|
CE
|
A:MET49
|
4.8
|
64.8
|
0.2
|
N
|
A:GLN189
|
4.8
|
33.0
|
0.2
|
N
|
A:GLN189
|
4.8
|
33.0
|
0.2
|
N
|
A:GLN189
|
4.8
|
31.8
|
0.2
|
N
|
A:GLN189
|
4.8
|
31.8
|
0.2
|
CG
|
A:ASP187
|
4.9
|
26.1
|
0.2
|
CG
|
A:ASP187
|
4.9
|
26.1
|
0.2
|
CB
|
A:MET165
|
4.9
|
30.9
|
0.2
|
CB
|
A:MET165
|
4.9
|
30.9
|
0.2
|
CB
|
A:MET165
|
5.0
|
29.5
|
0.2
|
CB
|
A:MET165
|
5.0
|
29.5
|
0.2
|
|
Reference:
T.Barthel,
J.Wollenhaupt,
L.S.Benz,
P.Reincke,
L.Zhang,
F.Lennartz,
H.Tabermann,
U.Mueller,
A.Meente,
R.Hilgenfeld,
M.S.Weiss.
Orthorhombic Sars-Cov-2 Main Protease Crystals Provide Higher Success Rate in Fragment Screening To Be Published.
Page generated: Tue Jul 15 20:24:31 2025
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