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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:

Chlorine (Cl) 4 atoms

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

Go back to 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: Thu Dec 28 04:33:09 2023

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