Fluorine in PDB 8gtw: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
Enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26:
3.4.22.69;
Protein crystallography data
The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26, PDB code: 8gtw
was solved by
H.X.Su,
T.Q.Nie,
H.Xie,
M.J.Li,
Y.C.Xu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.56 /
1.85
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.616,
81.708,
89.079,
90,
97.19,
90
|
R / Rfree (%)
|
19.8 /
22.7
|
Other elements in 8gtw:
The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
(pdb code 8gtw). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26, PDB code: 8gtw:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8gtw
Go back to
Fluorine Binding Sites List in 8gtw
Fluorine binding site 1 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 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 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:83.6
occ:1.00
|
F1
|
A:K9U401
|
0.0
|
83.6
|
1.0
|
C24
|
A:K9U401
|
1.3
|
81.8
|
1.0
|
F2
|
A:K9U401
|
2.1
|
83.1
|
1.0
|
F3
|
A:K9U401
|
2.1
|
83.4
|
1.0
|
C23
|
A:K9U401
|
2.3
|
75.7
|
1.0
|
CE
|
A:MET49
|
3.2
|
82.7
|
1.0
|
SD
|
A:MET49
|
3.6
|
82.6
|
1.0
|
C22
|
A:K9U401
|
3.7
|
68.8
|
1.0
|
C2
|
A:K9U401
|
3.8
|
42.9
|
1.0
|
O
|
A:HOH521
|
4.2
|
43.9
|
1.0
|
C3
|
A:K9U401
|
4.2
|
44.4
|
1.0
|
OG1
|
A:THR25
|
4.5
|
50.1
|
1.0
|
C10
|
A:K9U401
|
4.7
|
39.8
|
1.0
|
O
|
A:HOH585
|
4.7
|
49.1
|
1.0
|
N4
|
A:K9U401
|
4.7
|
62.2
|
1.0
|
C21
|
A:K9U401
|
4.9
|
51.3
|
1.0
|
C1
|
A:K9U401
|
4.9
|
42.0
|
1.0
|
O
|
A:CYS44
|
5.0
|
57.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8gtw
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Fluorine Binding Sites List in 8gtw
Fluorine binding site 2 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 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 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:83.1
occ:1.00
|
F2
|
A:K9U401
|
0.0
|
83.1
|
1.0
|
C24
|
A:K9U401
|
1.3
|
81.8
|
1.0
|
F1
|
A:K9U401
|
2.1
|
83.6
|
1.0
|
F3
|
A:K9U401
|
2.1
|
83.4
|
1.0
|
C23
|
A:K9U401
|
2.4
|
75.7
|
1.0
|
C22
|
A:K9U401
|
3.0
|
68.8
|
1.0
|
OG1
|
A:THR25
|
3.4
|
50.1
|
1.0
|
CG2
|
A:THR25
|
4.4
|
47.2
|
1.0
|
N4
|
A:K9U401
|
4.4
|
62.2
|
1.0
|
CB
|
A:THR25
|
4.5
|
49.1
|
1.0
|
CE
|
A:MET49
|
4.7
|
82.7
|
1.0
|
O
|
A:HOH585
|
4.8
|
49.1
|
1.0
|
O
|
A:HOH521
|
5.0
|
43.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8gtw
Go back to
Fluorine Binding Sites List in 8gtw
Fluorine binding site 3 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:83.4
occ:1.00
|
F3
|
A:K9U401
|
0.0
|
83.4
|
1.0
|
C24
|
A:K9U401
|
1.3
|
81.8
|
1.0
|
F2
|
A:K9U401
|
2.1
|
83.1
|
1.0
|
F1
|
A:K9U401
|
2.1
|
83.6
|
1.0
|
C23
|
A:K9U401
|
2.3
|
75.7
|
1.0
|
C22
|
A:K9U401
|
2.9
|
68.8
|
1.0
|
N4
|
A:K9U401
|
3.9
|
62.2
|
1.0
|
O3
|
A:K9U401
|
4.1
|
51.6
|
1.0
|
C21
|
A:K9U401
|
4.1
|
51.3
|
1.0
|
SD
|
A:MET49
|
4.5
|
82.6
|
1.0
|
CE
|
A:MET49
|
4.5
|
82.7
|
1.0
|
C2
|
A:K9U401
|
5.0
|
42.9
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8gtw
Go back to
Fluorine Binding Sites List in 8gtw
Fluorine binding site 4 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:82.6
occ:1.00
|
F1
|
B:K9U401
|
0.0
|
82.6
|
1.0
|
C24
|
B:K9U401
|
1.3
|
81.5
|
1.0
|
F2
|
B:K9U401
|
2.1
|
82.6
|
1.0
|
F3
|
B:K9U401
|
2.1
|
82.5
|
1.0
|
C23
|
B:K9U401
|
2.4
|
76.0
|
1.0
|
C22
|
B:K9U401
|
2.9
|
69.6
|
1.0
|
C2
|
B:K9U401
|
3.8
|
43.7
|
1.0
|
CE
|
B:MET49
|
3.8
|
81.9
|
1.0
|
N4
|
B:K9U401
|
4.0
|
64.0
|
1.0
|
C10
|
B:K9U401
|
4.0
|
44.1
|
1.0
|
OG1
|
B:THR25
|
4.2
|
52.0
|
1.0
|
CG2
|
B:THR25
|
4.2
|
49.2
|
1.0
|
C21
|
B:K9U401
|
4.3
|
55.8
|
1.0
|
C3
|
B:K9U401
|
4.4
|
44.6
|
1.0
|
C9
|
B:K9U401
|
4.6
|
47.3
|
1.0
|
C1
|
B:K9U401
|
4.8
|
42.3
|
1.0
|
N1
|
B:K9U401
|
4.8
|
43.3
|
1.0
|
O3
|
B:K9U401
|
4.8
|
57.5
|
1.0
|
CB
|
B:THR25
|
4.9
|
51.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8gtw
Go back to
Fluorine Binding Sites List in 8gtw
Fluorine binding site 5 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:82.6
occ:1.00
|
F2
|
B:K9U401
|
0.0
|
82.6
|
1.0
|
C24
|
B:K9U401
|
1.3
|
81.5
|
1.0
|
F1
|
B:K9U401
|
2.1
|
82.6
|
1.0
|
F3
|
B:K9U401
|
2.1
|
82.5
|
1.0
|
C23
|
B:K9U401
|
2.4
|
76.0
|
1.0
|
C22
|
B:K9U401
|
3.0
|
69.6
|
1.0
|
OG1
|
B:THR25
|
3.6
|
52.0
|
1.0
|
N4
|
B:K9U401
|
4.4
|
64.0
|
1.0
|
CG2
|
B:THR25
|
4.4
|
49.2
|
1.0
|
CB
|
B:THR25
|
4.5
|
51.7
|
1.0
|
CE
|
B:MET49
|
4.9
|
81.9
|
1.0
|
CA
|
B:THR25
|
4.9
|
53.2
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8gtw
Go back to
Fluorine Binding Sites List in 8gtw
Fluorine binding site 6 out
of 6 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound Jzd-26 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:82.5
occ:1.00
|
F3
|
B:K9U401
|
0.0
|
82.5
|
1.0
|
C24
|
B:K9U401
|
1.3
|
81.5
|
1.0
|
F1
|
B:K9U401
|
2.1
|
82.6
|
1.0
|
F2
|
B:K9U401
|
2.1
|
82.6
|
1.0
|
C23
|
B:K9U401
|
2.4
|
76.0
|
1.0
|
CE
|
B:MET49
|
3.2
|
81.9
|
1.0
|
C22
|
B:K9U401
|
3.7
|
69.6
|
1.0
|
SD
|
B:MET49
|
4.3
|
82.1
|
1.0
|
N4
|
B:K9U401
|
4.8
|
64.0
|
1.0
|
C2
|
B:K9U401
|
4.9
|
43.7
|
1.0
|
CA
|
B:SER46
|
4.9
|
77.9
|
1.0
|
N
|
B:SER46
|
5.0
|
77.4
|
1.0
|
|
Reference:
Y.C.Xu,
Y.Zang,
Y.Zhou.
Development of Novel Inhibitors Against Sars-Cov-2 3CLPRO To Be Published.
Page generated: Wed Jul 16 05:07:10 2025
|