Fluorine in PDB 7mb1: Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143
Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143
All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143:
3.4.22.69;
Protein crystallography data
The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143, PDB code: 7mb1
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)
|
29.52 /
1.43
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.874,
104.874,
52.462,
90,
104.12,
90
|
R / Rfree (%)
|
18.8 /
21.4
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143
(pdb code 7mb1). 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 SM143, PDB code: 7mb1:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 7mb1
Go back to
Fluorine Binding Sites List in 7mb1
Fluorine binding site 1 out
of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143
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 SM143 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:25.6
occ:1.00
|
F39
|
A:YVJ401
|
0.0
|
25.6
|
1.0
|
C33
|
A:YVJ401
|
1.3
|
21.1
|
1.0
|
HB2
|
A:GLN192
|
2.3
|
21.9
|
1.0
|
C38
|
A:YVJ401
|
2.5
|
18.4
|
1.0
|
C34
|
A:YVJ401
|
2.5
|
19.2
|
1.0
|
H381
|
A:YVJ401
|
2.7
|
22.1
|
1.0
|
H341
|
A:YVJ401
|
2.7
|
23.1
|
1.0
|
HE3
|
A:MET165
|
2.8
|
31.1
|
1.0
|
HD23
|
A:LEU167
|
3.0
|
24.3
|
1.0
|
HD22
|
A:LEU167
|
3.1
|
24.3
|
1.0
|
HE21
|
A:GLN192
|
3.1
|
21.6
|
1.0
|
NE2
|
A:GLN192
|
3.2
|
17.9
|
1.0
|
CB
|
A:GLN192
|
3.2
|
18.2
|
1.0
|
HD21
|
A:LEU167
|
3.3
|
24.3
|
1.0
|
CD2
|
A:LEU167
|
3.3
|
20.2
|
1.0
|
CD
|
A:GLN192
|
3.3
|
16.1
|
1.0
|
HG3
|
A:GLN192
|
3.3
|
22.3
|
1.0
|
H
|
A:GLN192
|
3.4
|
19.4
|
1.0
|
CG
|
A:GLN192
|
3.5
|
18.6
|
1.0
|
HE22
|
A:GLN192
|
3.5
|
21.6
|
1.0
|
HE2
|
A:MET165
|
3.6
|
31.1
|
1.0
|
CE
|
A:MET165
|
3.6
|
25.9
|
1.0
|
HB3
|
A:GLN192
|
3.8
|
21.9
|
1.0
|
O
|
A:THR190
|
3.8
|
17.3
|
1.0
|
C37
|
A:YVJ401
|
3.8
|
17.8
|
1.0
|
C35
|
A:YVJ401
|
3.8
|
17.4
|
1.0
|
N
|
A:GLN192
|
4.0
|
16.1
|
1.0
|
OE1
|
A:GLN192
|
4.0
|
17.0
|
1.0
|
CA
|
A:GLN192
|
4.1
|
17.5
|
1.0
|
O
|
A:HOH660
|
4.2
|
21.7
|
1.0
|
HE1
|
A:MET165
|
4.3
|
31.1
|
1.0
|
O
|
A:GLN192
|
4.3
|
22.6
|
1.0
|
C36
|
A:YVJ401
|
4.4
|
15.9
|
1.0
|
HA
|
A:LEU167
|
4.4
|
19.6
|
1.0
|
HG2
|
A:GLN192
|
4.4
|
22.3
|
1.0
|
HD1
|
A:PHE185
|
4.5
|
21.8
|
1.0
|
SD
|
A:MET165
|
4.5
|
27.0
|
1.0
|
H371
|
A:YVJ401
|
4.6
|
21.4
|
1.0
|
H351
|
A:YVJ401
|
4.6
|
20.9
|
1.0
|
C
|
A:GLN192
|
4.6
|
20.5
|
1.0
|
HG3
|
A:MET165
|
4.6
|
21.0
|
1.0
|
HD3
|
A:PRO168
|
4.7
|
21.6
|
1.0
|
CG
|
A:LEU167
|
4.8
|
18.0
|
1.0
|
HA
|
A:ALA191
|
4.8
|
21.1
|
1.0
|
HA
|
A:GLN192
|
4.9
|
21.1
|
1.0
|
HB2
|
A:MET165
|
4.9
|
20.1
|
1.0
|
C
|
A:ALA191
|
5.0
|
20.2
|
1.0
|
|
Fluorine binding site 2 out
of 2 in 7mb1
Go back to
Fluorine Binding Sites List in 7mb1
Fluorine binding site 2 out
of 2 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143
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 SM143 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:31.0
occ:1.00
|
F39
|
B:YVJ401
|
0.0
|
31.0
|
1.0
|
C33
|
B:YVJ401
|
1.3
|
20.2
|
1.0
|
C34
|
B:YVJ401
|
2.5
|
19.8
|
1.0
|
C38
|
B:YVJ401
|
2.5
|
22.8
|
1.0
|
HB2
|
B:GLN192
|
2.6
|
31.1
|
1.0
|
H341
|
B:YVJ401
|
2.7
|
23.8
|
1.0
|
H381
|
B:YVJ401
|
2.7
|
27.4
|
1.0
|
HE21
|
B:GLN192
|
2.8
|
28.3
|
1.0
|
HD23
|
B:LEU167
|
2.9
|
35.3
|
1.0
|
NE2
|
B:GLN192
|
3.0
|
23.6
|
1.0
|
HE3
|
B:MET165
|
3.0
|
27.3
|
1.0
|
HD22
|
B:LEU167
|
3.1
|
35.3
|
1.0
|
HD21
|
B:LEU167
|
3.2
|
35.3
|
1.0
|
CD2
|
B:LEU167
|
3.2
|
29.4
|
1.0
|
HG3
|
B:GLN192
|
3.3
|
32.5
|
1.0
|
HE22
|
B:GLN192
|
3.4
|
28.3
|
1.0
|
CD
|
B:GLN192
|
3.4
|
23.8
|
1.0
|
CB
|
B:GLN192
|
3.4
|
25.9
|
1.0
|
CG
|
B:GLN192
|
3.5
|
27.0
|
1.0
|
CE
|
B:MET165
|
3.8
|
22.7
|
1.0
|
O
|
B:THR190
|
3.8
|
32.4
|
1.0
|
HE1
|
B:MET165
|
3.9
|
27.3
|
1.0
|
C37
|
B:YVJ401
|
3.9
|
23.1
|
1.0
|
C35
|
B:YVJ401
|
3.9
|
19.6
|
1.0
|
HB3
|
B:GLN192
|
4.0
|
31.1
|
1.0
|
H
|
B:GLN192
|
4.0
|
34.9
|
1.0
|
OE1
|
B:GLN192
|
4.2
|
20.4
|
1.0
|
HG3
|
B:MET165
|
4.3
|
19.7
|
1.0
|
SD
|
B:MET165
|
4.3
|
24.1
|
1.0
|
HA
|
B:LEU167
|
4.4
|
26.4
|
1.0
|
C36
|
B:YVJ401
|
4.4
|
19.2
|
1.0
|
O
|
B:ARG188
|
4.4
|
23.3
|
1.0
|
H
|
B:THR190
|
4.4
|
33.4
|
1.0
|
N
|
B:GLN192
|
4.5
|
29.1
|
1.0
|
CA
|
B:GLN192
|
4.5
|
26.7
|
1.0
|
HG2
|
B:GLN192
|
4.5
|
32.5
|
1.0
|
O
|
B:HOH615
|
4.5
|
36.1
|
1.0
|
HD1
|
B:PHE185
|
4.6
|
30.0
|
1.0
|
HE2
|
B:MET165
|
4.6
|
27.3
|
1.0
|
H351
|
B:YVJ401
|
4.6
|
23.6
|
1.0
|
H371
|
B:YVJ401
|
4.6
|
27.8
|
1.0
|
O
|
B:GLN192
|
4.7
|
34.0
|
1.0
|
CG
|
B:LEU167
|
4.7
|
24.6
|
1.0
|
CG
|
B:MET165
|
4.8
|
16.4
|
1.0
|
HD3
|
B:PRO168
|
4.8
|
33.6
|
1.0
|
HB2
|
B:MET165
|
4.8
|
23.4
|
1.0
|
HA
|
B:GLN189
|
4.8
|
30.5
|
1.0
|
HB3
|
B:PHE185
|
5.0
|
24.3
|
1.0
|
O
|
B:VAL186
|
5.0
|
17.0
|
1.0
|
C
|
B:GLN192
|
5.0
|
29.1
|
1.0
|
HD2
|
B:PRO168
|
5.0
|
33.6
|
1.0
|
|
Reference:
G.J.Lockbaum,
C.A.Schiffer.
Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143 To Be Published.
Page generated: Fri Aug 2 09:25:32 2024
|