Fluorine in PDB 6w2a: 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Enzymatic activity of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
All present enzymatic activity of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J:
3.4.19.12;
3.4.22.69;
Protein crystallography data
The structure of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J, PDB code: 6w2a
was solved by
M.M.Kashipathy,
S.Lovell,
K.P.Battaile,
A.D.Rathnayake,
J.Zheng,
Y.Kim,
H.N.Nguyen,
K.O.Chang,
W.C.Groutas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.93 /
1.65
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.004,
99.999,
59.269,
90.00,
108.31,
90.00
|
R / Rfree (%)
|
17.2 /
20.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
(pdb code 6w2a). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J, PDB code: 6w2a:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 1 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:51.6
occ:0.50
|
F01
|
A:VDJ401
|
0.0
|
51.6
|
0.5
|
F01
|
A:QYS402
|
0.0
|
51.6
|
0.5
|
C02
|
A:VDJ401
|
1.4
|
46.5
|
0.5
|
C02
|
A:QYS402
|
1.4
|
46.5
|
0.5
|
F03
|
A:VDJ401
|
2.1
|
48.2
|
0.5
|
F03
|
A:QYS402
|
2.1
|
48.2
|
0.5
|
C31
|
A:VDJ401
|
2.4
|
43.3
|
0.5
|
C31
|
A:QYS402
|
2.4
|
43.3
|
0.5
|
C04
|
A:VDJ401
|
2.4
|
42.9
|
0.5
|
C04
|
A:QYS402
|
2.4
|
42.9
|
0.5
|
C30
|
A:QYS402
|
3.7
|
38.7
|
0.5
|
C30
|
A:VDJ401
|
3.7
|
38.7
|
0.5
|
C05
|
A:QYS402
|
3.7
|
38.5
|
0.5
|
C05
|
A:VDJ401
|
3.7
|
38.5
|
0.5
|
CB
|
A:ALA191
|
3.9
|
37.1
|
1.0
|
C06
|
A:QYS402
|
4.2
|
37.9
|
0.5
|
C06
|
A:VDJ401
|
4.2
|
37.9
|
0.5
|
CG
|
A:PRO168
|
4.4
|
36.9
|
1.0
|
CA
|
A:ALA191
|
4.4
|
29.5
|
1.0
|
CB
|
A:PRO168
|
4.6
|
30.6
|
1.0
|
N
|
A:ALA191
|
4.8
|
30.4
|
1.0
|
CA
|
A:PRO168
|
4.9
|
27.0
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 2 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:48.2
occ:0.50
|
F03
|
A:VDJ401
|
0.0
|
48.2
|
0.5
|
F03
|
A:QYS402
|
0.0
|
48.2
|
0.5
|
C02
|
A:QYS402
|
1.3
|
46.5
|
0.5
|
C02
|
A:VDJ401
|
1.3
|
46.5
|
0.5
|
F01
|
A:QYS402
|
2.1
|
51.6
|
0.5
|
F01
|
A:VDJ401
|
2.1
|
51.6
|
0.5
|
C31
|
A:QYS402
|
2.4
|
43.3
|
0.5
|
C31
|
A:VDJ401
|
2.4
|
43.3
|
0.5
|
C04
|
A:VDJ401
|
2.4
|
42.9
|
0.5
|
C04
|
A:QYS402
|
2.4
|
42.9
|
0.5
|
C30
|
A:QYS402
|
2.9
|
38.7
|
0.5
|
C30
|
A:VDJ401
|
2.9
|
38.7
|
0.5
|
C05
|
A:VDJ401
|
3.0
|
38.5
|
0.5
|
C05
|
A:QYS402
|
3.0
|
38.5
|
0.5
|
CG
|
A:PRO168
|
3.0
|
36.9
|
1.0
|
CD
|
A:PRO168
|
3.2
|
26.0
|
1.0
|
N
|
A:PRO168
|
3.5
|
25.7
|
1.0
|
C06
|
A:QYS402
|
3.6
|
37.9
|
0.5
|
C06
|
A:VDJ401
|
3.6
|
37.9
|
0.5
|
CB
|
A:PRO168
|
3.6
|
30.6
|
1.0
|
CA
|
A:PRO168
|
3.6
|
27.0
|
1.0
|
CB
|
A:ALA191
|
3.6
|
37.1
|
1.0
|
CA
|
A:ALA191
|
3.6
|
29.5
|
1.0
|
O
|
A:HOH554
|
3.9
|
28.2
|
1.0
|
C
|
A:LEU167
|
4.2
|
27.8
|
1.0
|
N
|
A:ALA191
|
4.4
|
30.4
|
1.0
|
O
|
A:THR190
|
4.7
|
29.7
|
1.0
|
C07
|
A:QYS402
|
4.7
|
34.1
|
0.5
|
C07
|
A:VDJ401
|
4.8
|
34.1
|
0.5
|
O
|
A:LEU167
|
4.8
|
28.6
|
1.0
|
C
|
A:ALA191
|
4.8
|
28.1
|
1.0
|
O
|
A:GLU166
|
4.8
|
28.5
|
1.0
|
CA
|
A:LEU167
|
4.8
|
21.4
|
1.0
|
C
|
A:THR190
|
4.8
|
30.8
|
1.0
|
N
|
A:GLN192
|
4.8
|
23.8
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 3 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:51.6
occ:0.50
|
F01
|
A:QYS402
|
0.0
|
51.6
|
0.5
|
F01
|
A:VDJ401
|
0.0
|
51.6
|
0.5
|
C02
|
A:VDJ401
|
1.4
|
46.5
|
0.5
|
C02
|
A:QYS402
|
1.4
|
46.5
|
0.5
|
F03
|
A:VDJ401
|
2.1
|
48.2
|
0.5
|
F03
|
A:QYS402
|
2.1
|
48.2
|
0.5
|
C31
|
A:VDJ401
|
2.4
|
43.3
|
0.5
|
C31
|
A:QYS402
|
2.4
|
43.3
|
0.5
|
C04
|
A:VDJ401
|
2.4
|
42.9
|
0.5
|
C04
|
A:QYS402
|
2.4
|
42.9
|
0.5
|
C30
|
A:QYS402
|
3.7
|
38.7
|
0.5
|
C30
|
A:VDJ401
|
3.7
|
38.7
|
0.5
|
C05
|
A:QYS402
|
3.7
|
38.5
|
0.5
|
C05
|
A:VDJ401
|
3.7
|
38.5
|
0.5
|
CB
|
A:ALA191
|
3.9
|
37.1
|
1.0
|
C06
|
A:QYS402
|
4.2
|
37.9
|
0.5
|
C06
|
A:VDJ401
|
4.2
|
37.9
|
0.5
|
CG
|
A:PRO168
|
4.4
|
36.9
|
1.0
|
CA
|
A:ALA191
|
4.4
|
29.5
|
1.0
|
CB
|
A:PRO168
|
4.6
|
30.6
|
1.0
|
N
|
A:ALA191
|
4.8
|
30.4
|
1.0
|
CA
|
A:PRO168
|
4.9
|
27.0
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 4 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:48.2
occ:0.50
|
F03
|
A:QYS402
|
0.0
|
48.2
|
0.5
|
F03
|
A:VDJ401
|
0.0
|
48.2
|
0.5
|
C02
|
A:QYS402
|
1.3
|
46.5
|
0.5
|
C02
|
A:VDJ401
|
1.3
|
46.5
|
0.5
|
F01
|
A:QYS402
|
2.1
|
51.6
|
0.5
|
F01
|
A:VDJ401
|
2.1
|
51.6
|
0.5
|
C31
|
A:QYS402
|
2.4
|
43.3
|
0.5
|
C31
|
A:VDJ401
|
2.4
|
43.3
|
0.5
|
C04
|
A:VDJ401
|
2.4
|
42.9
|
0.5
|
C04
|
A:QYS402
|
2.4
|
42.9
|
0.5
|
C30
|
A:QYS402
|
2.9
|
38.7
|
0.5
|
C30
|
A:VDJ401
|
2.9
|
38.7
|
0.5
|
C05
|
A:VDJ401
|
3.0
|
38.5
|
0.5
|
C05
|
A:QYS402
|
3.0
|
38.5
|
0.5
|
CG
|
A:PRO168
|
3.0
|
36.9
|
1.0
|
CD
|
A:PRO168
|
3.2
|
26.0
|
1.0
|
N
|
A:PRO168
|
3.5
|
25.7
|
1.0
|
C06
|
A:QYS402
|
3.6
|
37.9
|
0.5
|
C06
|
A:VDJ401
|
3.6
|
37.9
|
0.5
|
CB
|
A:PRO168
|
3.6
|
30.6
|
1.0
|
CB
|
A:ALA191
|
3.6
|
37.1
|
1.0
|
CA
|
A:PRO168
|
3.6
|
27.0
|
1.0
|
CA
|
A:ALA191
|
3.6
|
29.5
|
1.0
|
O
|
A:HOH554
|
3.9
|
28.2
|
1.0
|
C
|
A:LEU167
|
4.2
|
27.8
|
1.0
|
N
|
A:ALA191
|
4.4
|
30.4
|
1.0
|
O
|
A:THR190
|
4.7
|
29.7
|
1.0
|
C07
|
A:QYS402
|
4.7
|
34.1
|
0.5
|
C07
|
A:VDJ401
|
4.8
|
34.1
|
0.5
|
C
|
A:ALA191
|
4.8
|
28.1
|
1.0
|
O
|
A:LEU167
|
4.8
|
28.6
|
1.0
|
O
|
A:GLU166
|
4.8
|
28.5
|
1.0
|
CA
|
A:LEU167
|
4.8
|
21.4
|
1.0
|
C
|
A:THR190
|
4.8
|
30.8
|
1.0
|
N
|
A:GLN192
|
4.8
|
23.8
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 5 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:64.0
occ:0.50
|
F01
|
B:QYS401
|
0.0
|
64.0
|
0.5
|
F01
|
B:VDJ402
|
0.0
|
64.0
|
0.5
|
C02
|
B:QYS401
|
1.4
|
58.5
|
0.5
|
C02
|
B:VDJ402
|
1.4
|
58.5
|
0.5
|
F03
|
B:VDJ402
|
2.1
|
63.5
|
0.5
|
F03
|
B:QYS401
|
2.1
|
63.5
|
0.5
|
C31
|
B:QYS401
|
2.4
|
56.8
|
0.5
|
C31
|
B:VDJ402
|
2.4
|
56.8
|
0.5
|
C04
|
B:QYS401
|
2.4
|
59.5
|
0.5
|
C04
|
B:VDJ402
|
2.4
|
59.5
|
0.5
|
C05
|
B:QYS401
|
3.1
|
48.9
|
0.5
|
C05
|
B:VDJ402
|
3.1
|
48.9
|
0.5
|
C30
|
B:QYS401
|
3.5
|
52.8
|
0.5
|
C30
|
B:VDJ402
|
3.5
|
52.8
|
0.5
|
C06
|
B:VDJ402
|
3.6
|
48.1
|
0.5
|
C06
|
B:QYS401
|
3.6
|
48.1
|
0.5
|
CB
|
B:ALA191
|
4.4
|
53.8
|
1.0
|
CA
|
B:ALA191
|
4.7
|
56.6
|
1.0
|
N
|
B:ALA191
|
4.7
|
63.5
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 6 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:63.5
occ:0.50
|
F03
|
B:QYS401
|
0.0
|
63.5
|
0.5
|
F03
|
B:VDJ402
|
0.0
|
63.5
|
0.5
|
C02
|
B:QYS401
|
1.3
|
58.5
|
0.5
|
C02
|
B:VDJ402
|
1.3
|
58.5
|
0.5
|
F01
|
B:QYS401
|
2.1
|
64.0
|
0.5
|
F01
|
B:VDJ402
|
2.1
|
64.0
|
0.5
|
C31
|
B:VDJ402
|
2.4
|
56.8
|
0.5
|
C31
|
B:QYS401
|
2.4
|
56.8
|
0.5
|
C04
|
B:QYS401
|
2.4
|
59.5
|
0.5
|
C04
|
B:VDJ402
|
2.4
|
59.5
|
0.5
|
CG
|
B:PRO168
|
3.3
|
46.3
|
1.0
|
CB
|
B:ALA191
|
3.5
|
53.8
|
1.0
|
CB
|
B:PRO168
|
3.5
|
39.2
|
1.0
|
C30
|
B:VDJ402
|
3.5
|
52.8
|
0.5
|
C30
|
B:QYS401
|
3.5
|
52.8
|
0.5
|
C05
|
B:QYS401
|
3.7
|
48.9
|
0.5
|
C05
|
B:VDJ402
|
3.7
|
48.9
|
0.5
|
CA
|
B:PRO168
|
3.8
|
40.5
|
1.0
|
CA
|
B:ALA191
|
3.8
|
56.6
|
1.0
|
CD
|
B:PRO168
|
4.0
|
46.4
|
1.0
|
N
|
B:PRO168
|
4.0
|
36.2
|
1.0
|
C06
|
B:VDJ402
|
4.2
|
48.1
|
0.5
|
C06
|
B:QYS401
|
4.2
|
48.1
|
0.5
|
N
|
B:ALA191
|
4.5
|
63.5
|
1.0
|
O
|
B:HOH588
|
4.5
|
39.5
|
1.0
|
C
|
B:LEU167
|
4.8
|
33.5
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 7 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:64.0
occ:0.50
|
F01
|
B:VDJ402
|
0.0
|
64.0
|
0.5
|
F01
|
B:QYS401
|
0.0
|
64.0
|
0.5
|
C02
|
B:QYS401
|
1.4
|
58.5
|
0.5
|
C02
|
B:VDJ402
|
1.4
|
58.5
|
0.5
|
F03
|
B:VDJ402
|
2.1
|
63.5
|
0.5
|
F03
|
B:QYS401
|
2.1
|
63.5
|
0.5
|
C31
|
B:QYS401
|
2.4
|
56.8
|
0.5
|
C31
|
B:VDJ402
|
2.4
|
56.8
|
0.5
|
C04
|
B:QYS401
|
2.4
|
59.5
|
0.5
|
C04
|
B:VDJ402
|
2.4
|
59.5
|
0.5
|
C05
|
B:QYS401
|
3.0
|
48.9
|
0.5
|
C05
|
B:VDJ402
|
3.1
|
48.9
|
0.5
|
C30
|
B:QYS401
|
3.4
|
52.8
|
0.5
|
C30
|
B:VDJ402
|
3.5
|
52.8
|
0.5
|
C06
|
B:VDJ402
|
3.5
|
48.1
|
0.5
|
C06
|
B:QYS401
|
3.5
|
48.1
|
0.5
|
CB
|
B:ALA191
|
4.5
|
53.8
|
1.0
|
CA
|
B:ALA191
|
4.7
|
56.6
|
1.0
|
N
|
B:ALA191
|
4.7
|
63.5
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6w2a
Go back to
Fluorine Binding Sites List in 6w2a
Fluorine binding site 8 out
of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:63.5
occ:0.50
|
F03
|
B:VDJ402
|
0.0
|
63.5
|
0.5
|
F03
|
B:QYS401
|
0.0
|
63.5
|
0.5
|
C02
|
B:QYS401
|
1.3
|
58.5
|
0.5
|
C02
|
B:VDJ402
|
1.3
|
58.5
|
0.5
|
F01
|
B:QYS401
|
2.1
|
64.0
|
0.5
|
F01
|
B:VDJ402
|
2.1
|
64.0
|
0.5
|
C31
|
B:VDJ402
|
2.4
|
56.8
|
0.5
|
C04
|
B:QYS401
|
2.4
|
59.5
|
0.5
|
C04
|
B:VDJ402
|
2.4
|
59.5
|
0.5
|
C31
|
B:QYS401
|
2.4
|
56.8
|
0.5
|
CG
|
B:PRO168
|
3.3
|
46.3
|
1.0
|
CB
|
B:ALA191
|
3.4
|
53.8
|
1.0
|
C30
|
B:VDJ402
|
3.5
|
52.8
|
0.5
|
C30
|
B:QYS401
|
3.5
|
52.8
|
0.5
|
CB
|
B:PRO168
|
3.5
|
39.2
|
1.0
|
C05
|
B:QYS401
|
3.7
|
48.9
|
0.5
|
C05
|
B:VDJ402
|
3.7
|
48.9
|
0.5
|
CA
|
B:ALA191
|
3.8
|
56.6
|
1.0
|
CA
|
B:PRO168
|
3.8
|
40.5
|
1.0
|
CD
|
B:PRO168
|
4.1
|
46.4
|
1.0
|
N
|
B:PRO168
|
4.1
|
36.2
|
1.0
|
C06
|
B:VDJ402
|
4.2
|
48.1
|
0.5
|
C06
|
B:QYS401
|
4.2
|
48.1
|
0.5
|
N
|
B:ALA191
|
4.5
|
63.5
|
1.0
|
O
|
B:HOH588
|
4.6
|
39.5
|
1.0
|
C
|
B:LEU167
|
4.8
|
33.5
|
1.0
|
|
Reference:
A.D.Rathnayake,
J.Zheng,
Y.Kim,
K.D.Perera,
S.Mackin,
D.K.Meyerholz,
M.M.Kashipathy,
K.P.Battaile,
S.Lovell,
S.Perlman,
W.C.Groutas,
K.O.Chang.
3C-Like Protease Inhibitors Block Coronavirus Replication in Vitro and Improve Survival in Mers-Cov-Infected Mice. Sci Transl Med V. 12 2020.
ISSN: ESSN 1946-6242
PubMed: 32747425
DOI: 10.1126/SCITRANSLMED.ABC5332
Page generated: Fri Aug 2 03:33:46 2024
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