Fluorine in PDB 7mb2: Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144:
3.4.22.69;
Protein crystallography data
The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144, PDB code: 7mb2
was solved by
G.J.Lockbaum,
C.A.Schiffer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.20 /
1.89
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.62,
104.5,
52.51,
90,
104.05,
90
|
R / Rfree (%)
|
16.7 /
21
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
(pdb code 7mb2). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the
Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144, PDB code: 7mb2:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 7mb2
Go back to
Fluorine Binding Sites List in 7mb2
Fluorine binding site 1 out
of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:35.8
occ:1.00
|
F39
|
A:YVM401
|
0.0
|
35.8
|
1.0
|
C33
|
A:YVM401
|
1.3
|
28.5
|
1.0
|
C34
|
A:YVM401
|
2.5
|
29.1
|
1.0
|
C38
|
A:YVM401
|
2.5
|
32.6
|
1.0
|
HB2
|
A:GLN192
|
2.5
|
40.5
|
1.0
|
H341
|
A:YVM401
|
2.7
|
35.0
|
1.0
|
HD23
|
A:LEU167
|
2.7
|
45.6
|
1.0
|
H381
|
A:YVM401
|
2.7
|
39.3
|
1.0
|
HE21
|
A:GLN192
|
2.8
|
35.3
|
1.0
|
HE3
|
A:MET165
|
2.9
|
37.8
|
1.0
|
HD22
|
A:LEU167
|
3.0
|
45.6
|
1.0
|
NE2
|
A:GLN192
|
3.1
|
29.3
|
1.0
|
CD2
|
A:LEU167
|
3.1
|
37.9
|
1.0
|
HD21
|
A:LEU167
|
3.2
|
45.6
|
1.0
|
HE22
|
A:GLN192
|
3.4
|
35.3
|
1.0
|
CB
|
A:GLN192
|
3.4
|
33.6
|
1.0
|
HG3
|
A:GLN192
|
3.5
|
39.0
|
1.0
|
CD
|
A:GLN192
|
3.5
|
31.0
|
1.0
|
CG
|
A:GLN192
|
3.7
|
32.4
|
1.0
|
CE
|
A:MET165
|
3.7
|
31.4
|
1.0
|
H
|
A:GLN192
|
3.8
|
43.1
|
1.0
|
O
|
A:THR190
|
3.8
|
38.0
|
1.0
|
HE1
|
A:MET165
|
3.8
|
37.8
|
1.0
|
C35
|
A:YVM401
|
3.9
|
30.0
|
1.0
|
C37
|
A:YVM401
|
3.9
|
28.2
|
1.0
|
O
|
A:HOH511
|
3.9
|
41.3
|
1.0
|
HB3
|
A:GLN192
|
4.0
|
40.5
|
1.0
|
HA
|
A:LEU167
|
4.1
|
38.3
|
1.0
|
N
|
A:GLN192
|
4.3
|
35.8
|
1.0
|
HG3
|
A:MET165
|
4.3
|
34.7
|
1.0
|
OE1
|
A:GLN192
|
4.3
|
25.0
|
1.0
|
CA
|
A:GLN192
|
4.3
|
37.5
|
1.0
|
C36
|
A:YVM401
|
4.4
|
23.6
|
1.0
|
SD
|
A:MET165
|
4.4
|
33.5
|
1.0
|
HE2
|
A:MET165
|
4.4
|
37.8
|
1.0
|
HD3
|
A:PRO168
|
4.5
|
49.3
|
1.0
|
O
|
A:GLN192
|
4.5
|
38.5
|
1.0
|
H
|
A:THR190
|
4.6
|
44.0
|
1.0
|
CG
|
A:LEU167
|
4.6
|
35.1
|
1.0
|
H351
|
A:YVM401
|
4.6
|
36.1
|
1.0
|
H371
|
A:YVM401
|
4.6
|
34.0
|
1.0
|
HG2
|
A:GLN192
|
4.6
|
39.0
|
1.0
|
O
|
A:ARG188
|
4.7
|
24.7
|
1.0
|
C
|
A:GLN192
|
4.8
|
37.8
|
1.0
|
HD1
|
A:PHE185
|
4.8
|
32.6
|
1.0
|
CG
|
A:MET165
|
4.9
|
28.8
|
1.0
|
HG
|
A:LEU167
|
4.9
|
42.3
|
1.0
|
HB2
|
A:MET165
|
5.0
|
29.4
|
1.0
|
HA
|
A:GLN189
|
5.0
|
44.5
|
1.0
|
CA
|
A:LEU167
|
5.0
|
31.8
|
1.0
|
|
Fluorine binding site 2 out
of 2 in 7mb2
Go back to
Fluorine Binding Sites List in 7mb2
Fluorine binding site 2 out
of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:38.5
occ:1.00
|
F39
|
B:YVM401
|
0.0
|
38.5
|
1.0
|
C33
|
B:YVM401
|
1.4
|
25.2
|
1.0
|
HB2
|
B:GLN192
|
2.5
|
36.1
|
1.0
|
C38
|
B:YVM401
|
2.5
|
29.4
|
1.0
|
C34
|
B:YVM401
|
2.5
|
31.1
|
1.0
|
H381
|
B:YVM401
|
2.7
|
35.4
|
1.0
|
H341
|
B:YVM401
|
2.7
|
37.4
|
1.0
|
HD23
|
B:LEU167
|
2.8
|
36.0
|
1.0
|
HE3
|
B:MET165
|
2.9
|
41.4
|
1.0
|
HE21
|
B:GLN192
|
3.0
|
31.8
|
1.0
|
NE2
|
B:GLN192
|
3.1
|
26.4
|
1.0
|
HD21
|
B:LEU167
|
3.1
|
36.0
|
1.0
|
CD
|
B:GLN192
|
3.2
|
24.6
|
1.0
|
HG3
|
B:GLN192
|
3.2
|
35.3
|
1.0
|
CD2
|
B:LEU167
|
3.2
|
29.9
|
1.0
|
HD22
|
B:LEU167
|
3.2
|
36.0
|
1.0
|
CB
|
B:GLN192
|
3.3
|
30.0
|
1.0
|
CG
|
B:GLN192
|
3.4
|
29.3
|
1.0
|
HE22
|
B:GLN192
|
3.4
|
31.8
|
1.0
|
H
|
B:GLN192
|
3.5
|
26.7
|
1.0
|
CE
|
B:MET165
|
3.6
|
34.4
|
1.0
|
HE1
|
B:MET165
|
3.7
|
41.4
|
1.0
|
O
|
B:THR190
|
3.7
|
24.7
|
1.0
|
OE1
|
B:GLN192
|
3.7
|
30.6
|
1.0
|
C35
|
B:YVM401
|
3.9
|
25.2
|
1.0
|
C37
|
B:YVM401
|
3.9
|
29.3
|
1.0
|
HB3
|
B:GLN192
|
3.9
|
36.1
|
1.0
|
N
|
B:GLN192
|
4.0
|
22.2
|
1.0
|
O
|
B:HOH579
|
4.1
|
34.0
|
1.0
|
CA
|
B:GLN192
|
4.1
|
31.1
|
1.0
|
HG3
|
B:MET165
|
4.3
|
35.9
|
1.0
|
HG2
|
B:GLN192
|
4.3
|
35.3
|
1.0
|
SD
|
B:MET165
|
4.4
|
36.0
|
1.0
|
HA
|
B:LEU167
|
4.4
|
31.7
|
1.0
|
O
|
B:GLN192
|
4.4
|
33.9
|
1.0
|
C36
|
B:YVM401
|
4.4
|
28.6
|
1.0
|
HE2
|
B:MET165
|
4.4
|
41.4
|
1.0
|
HD1
|
B:PHE185
|
4.5
|
32.4
|
1.0
|
H351
|
B:YVM401
|
4.6
|
30.4
|
1.0
|
C
|
B:GLN192
|
4.6
|
26.2
|
1.0
|
H371
|
B:YVM401
|
4.6
|
35.2
|
1.0
|
HD3
|
B:PRO168
|
4.7
|
39.3
|
1.0
|
CG
|
B:LEU167
|
4.7
|
31.9
|
1.0
|
O
|
B:ARG188
|
4.9
|
25.8
|
1.0
|
CG
|
B:MET165
|
4.9
|
29.8
|
1.0
|
HA
|
B:ALA191
|
4.9
|
34.5
|
1.0
|
HA
|
B:GLN189
|
4.9
|
35.0
|
1.0
|
HA
|
B:GLN192
|
4.9
|
37.5
|
1.0
|
C
|
B:THR190
|
4.9
|
23.4
|
1.0
|
HG
|
B:LEU167
|
4.9
|
38.4
|
1.0
|
|
Reference:
G.J.Lockbaum,
C.A.Schiffer.
Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144 To Be Published.
Page generated: Fri Aug 2 09:25:54 2024
|