Fluorine in PDB 8hom: Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
Enzymatic activity of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
All present enzymatic activity of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir:
3.4.22.69;
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir, PDB code: 8hom
was solved by
M.Lin,
X.Liu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.25 /
1.56
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
97.02,
81.493,
51.545,
90,
114.61,
90
|
R / Rfree (%)
|
17 /
19.6
|
Other elements in 8hom:
The structure of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
(pdb code 8hom). 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 Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir, PDB code: 8hom:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 8hom
Go back to
Fluorine Binding Sites List in 8hom
Fluorine binding site 1 out
of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
 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 Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:31.6
occ:1.00
|
F28
|
A:7YY401
|
0.0
|
31.6
|
1.0
|
C27
|
A:7YY401
|
1.4
|
28.7
|
1.0
|
C26
|
A:7YY401
|
2.4
|
21.9
|
1.0
|
C29
|
A:7YY401
|
2.4
|
30.0
|
1.0
|
NE2
|
A:GLN189
|
2.7
|
60.0
|
1.0
|
C25
|
A:7YY401
|
2.7
|
23.0
|
1.0
|
CD
|
A:GLN189
|
3.4
|
60.5
|
1.0
|
O
|
A:HOH521
|
3.5
|
41.2
|
1.0
|
O
|
A:HOH557
|
3.6
|
32.7
|
1.0
|
C34
|
A:7YY401
|
3.6
|
22.7
|
1.0
|
C30
|
A:7YY401
|
3.6
|
29.5
|
1.0
|
O
|
A:HOH652
|
3.7
|
54.5
|
1.0
|
OE1
|
A:GLN189
|
3.7
|
59.8
|
1.0
|
C32
|
A:7YY401
|
4.1
|
24.7
|
1.0
|
N24
|
A:7YY401
|
4.1
|
21.1
|
1.0
|
NE2
|
A:HIS41
|
4.6
|
30.4
|
1.0
|
CG
|
A:GLN189
|
4.6
|
50.1
|
1.0
|
O36
|
A:7YY401
|
4.6
|
25.1
|
1.0
|
F31
|
A:7YY401
|
4.8
|
35.8
|
1.0
|
CB
|
A:MET165
|
4.8
|
25.3
|
1.0
|
N12
|
A:7YY401
|
4.9
|
25.5
|
1.0
|
C35
|
A:7YY401
|
4.9
|
22.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 8hom
Go back to
Fluorine Binding Sites List in 8hom
Fluorine binding site 2 out
of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
 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 Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:35.8
occ:1.00
|
F31
|
A:7YY401
|
0.0
|
35.8
|
1.0
|
C30
|
A:7YY401
|
1.4
|
29.5
|
1.0
|
C32
|
A:7YY401
|
2.4
|
24.7
|
1.0
|
C29
|
A:7YY401
|
2.4
|
30.0
|
1.0
|
F33
|
A:7YY401
|
2.7
|
26.6
|
1.0
|
CB
|
A:ASP187
|
3.0
|
24.8
|
1.0
|
CA
|
A:ASP187
|
3.0
|
24.6
|
1.0
|
C
|
A:ASP187
|
3.1
|
29.3
|
1.0
|
O
|
A:ASP187
|
3.4
|
28.7
|
1.0
|
ND1
|
A:HIS41
|
3.5
|
25.5
|
1.0
|
C27
|
A:7YY401
|
3.6
|
28.7
|
1.0
|
C34
|
A:7YY401
|
3.6
|
22.7
|
1.0
|
N
|
A:ARG188
|
3.7
|
29.3
|
1.0
|
CG
|
A:HIS41
|
3.7
|
22.9
|
1.0
|
CE1
|
A:HIS41
|
3.9
|
28.9
|
1.0
|
C26
|
A:7YY401
|
4.1
|
21.9
|
1.0
|
SD
|
A:MET165
|
4.1
|
28.8
|
1.0
|
CB
|
A:HIS41
|
4.2
|
24.7
|
1.0
|
CD2
|
A:HIS41
|
4.2
|
27.9
|
1.0
|
NE2
|
A:HIS41
|
4.3
|
30.4
|
1.0
|
OH
|
A:TYR54
|
4.3
|
25.9
|
1.0
|
CG
|
A:ASP187
|
4.4
|
24.8
|
1.0
|
O
|
A:HOH594
|
4.4
|
22.5
|
1.0
|
N
|
A:ASP187
|
4.4
|
24.3
|
1.0
|
CA
|
A:ARG188
|
4.5
|
33.5
|
1.0
|
F28
|
A:7YY401
|
4.8
|
31.6
|
1.0
|
O
|
A:VAL186
|
4.8
|
26.6
|
1.0
|
CB
|
A:MET165
|
4.8
|
25.3
|
1.0
|
OD2
|
A:ASP187
|
4.9
|
23.2
|
1.0
|
ND1
|
A:HIS164
|
5.0
|
21.4
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 8hom
Go back to
Fluorine Binding Sites List in 8hom
Fluorine binding site 3 out
of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir
 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 Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:26.6
occ:1.00
|
F33
|
A:7YY401
|
0.0
|
26.6
|
1.0
|
C32
|
A:7YY401
|
1.4
|
24.7
|
1.0
|
C30
|
A:7YY401
|
2.4
|
29.5
|
1.0
|
C34
|
A:7YY401
|
2.4
|
22.7
|
1.0
|
F31
|
A:7YY401
|
2.7
|
35.8
|
1.0
|
O
|
A:HIS164
|
3.3
|
23.6
|
1.0
|
CB
|
A:HIS41
|
3.4
|
24.7
|
1.0
|
CG
|
A:HIS41
|
3.5
|
22.9
|
1.0
|
C26
|
A:7YY401
|
3.6
|
21.9
|
1.0
|
C29
|
A:7YY401
|
3.6
|
30.0
|
1.0
|
CD2
|
A:HIS41
|
3.6
|
27.9
|
1.0
|
SG
|
A:CYS145
|
3.7
|
22.7
|
1.0
|
C
|
A:HIS164
|
3.8
|
21.0
|
1.0
|
CB
|
A:HIS164
|
3.8
|
20.1
|
1.0
|
CA
|
A:HIS164
|
4.0
|
18.4
|
1.0
|
O
|
A:HOH594
|
4.0
|
22.5
|
1.0
|
ND1
|
A:HIS164
|
4.1
|
21.4
|
1.0
|
C27
|
A:7YY401
|
4.1
|
28.7
|
1.0
|
ND1
|
A:HIS41
|
4.2
|
25.5
|
1.0
|
CG
|
A:HIS164
|
4.3
|
20.0
|
1.0
|
NE2
|
A:HIS41
|
4.4
|
30.4
|
1.0
|
CB
|
A:MET165
|
4.6
|
25.3
|
1.0
|
CL2
|
A:7YY401
|
4.6
|
25.2
|
1.0
|
N
|
A:MET165
|
4.7
|
21.3
|
1.0
|
CE1
|
A:HIS41
|
4.7
|
28.9
|
1.0
|
CB
|
A:ASP187
|
4.7
|
24.8
|
1.0
|
CB
|
A:PRO39
|
4.9
|
20.7
|
1.0
|
CA
|
A:HIS41
|
4.9
|
23.4
|
1.0
|
C25
|
A:7YY401
|
4.9
|
23.0
|
1.0
|
N24
|
A:7YY401
|
5.0
|
21.1
|
1.0
|
|
Reference:
M.Lin,
X.Liu.
Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir To Be Published.
Page generated: Fri Aug 2 20:12:20 2024
|