Fluorine in PDB 8igx: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432)

All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432):
3.4.22.69;

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432), PDB code: 8igx was solved by H.X.Su, W.F.Zhao, H.Xie, T.Q.Nie, 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)	21.43 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.578, 62.831, 105.323, 90, 90, 90
R / Rfree (%)	17.6 / 21.3

The binding sites of Fluorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432) (pdb code 8igx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432), PDB code: 8igx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432)


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 9 (Simnotrelvir, SIM0417, SSD8432) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:35.0 occ:1.00 F1 A:PQL401 0.0 35.0 1.0 C20 A:PQL401 1.3 33.4 1.0 F2 A:PQL401 2.1 31.3 1.0 F3 A:PQL401 2.1 33.0 1.0 C19 A:PQL401 2.4 25.5 1.0 N5 A:PQL401 2.9 20.6 1.0 O A:GLU166 3.1 22.6 1.0 O A:HOH638 3.2 48.2 1.0 O A:HOH581 3.2 34.5 1.0 O4 A:PQL401 3.2 27.8 1.0 CD A:PRO168 3.7 27.5 1.0 CA A:LEU167 3.8 24.8 1.0 C A:GLU166 4.1 20.1 1.0 CD2 A:LEU167 4.2 33.7 1.0 C14 A:PQL401 4.3 19.8 1.0 N A:LEU167 4.3 25.0 1.0 C16 A:PQL401 4.3 25.1 1.0 N A:PRO168 4.3 32.8 1.0 C A:LEU167 4.4 29.7 1.0 CG A:PRO168 4.5 33.9 1.0 O A:GLN192 4.5 51.8 1.0 O A:THR190 4.7 38.5 1.0 CB A:LEU167 4.7 21.4 1.0 C15 A:PQL401 4.8 22.7 1.0 C18 A:PQL401 4.9 21.4 1.0 CG A:LEU167 5.0 25.6 1.0 CB A:GLN192 5.0 41.7 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432)


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 9 (Simnotrelvir, SIM0417, SSD8432) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:31.3 occ:1.00 F2 A:PQL401 0.0 31.3 1.0 C20 A:PQL401 1.3 33.4 1.0 F1 A:PQL401 2.1 35.0 1.0 F3 A:PQL401 2.1 33.0 1.0 C19 A:PQL401 2.4 25.5 1.0 N5 A:PQL401 2.8 20.6 1.0 O A:GLU166 3.1 22.6 1.0 CD2 A:LEU167 3.1 33.7 1.0 CE A:MET165 3.3 32.8 1.0 O4 A:PQL401 3.3 27.8 1.0 C A:GLU166 3.8 20.1 1.0 NE2 A:GLN192 3.9 27.3 1.0 CA A:LEU167 4.0 24.8 1.0 CB A:MET165 4.1 22.0 1.0 CG A:LEU167 4.2 25.6 1.0 N A:LEU167 4.2 25.0 1.0 C14 A:PQL401 4.2 19.8 1.0 CD A:GLN192 4.4 33.1 1.0 CB A:LEU167 4.5 21.4 1.0 N A:GLU166 4.6 16.6 1.0 CB A:GLN192 4.6 41.7 1.0 O3 A:PQL401 4.6 20.0 1.0 C13 A:PQL401 4.7 21.1 1.0 SD A:MET165 4.7 32.0 1.0 CG A:MET165 4.7 31.5 1.0 O A:HOH581 4.7 34.5 1.0 CG A:GLN192 4.8 38.5 1.0 CA A:GLU166 4.9 16.7 1.0 O A:HOH638 4.9 48.2 1.0 OE1 A:GLN192 5.0 32.7 1.0 CD A:PRO168 5.0 27.5 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Compound 9 (Simnotrelvir, SIM0417, SSD8432)


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 9 (Simnotrelvir, SIM0417, SSD8432) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.0 occ:1.00 F3 A:PQL401 0.0 33.0 1.0 C20 A:PQL401 1.3 33.4 1.0 F2 A:PQL401 2.1 31.3 1.0 F1 A:PQL401 2.1 35.0 1.0 C19 A:PQL401 2.4 25.5 1.0 O4 A:PQL401 2.6 27.8 1.0 O A:THR190 3.0 38.5 1.0 NE2 A:GLN192 3.2 27.3 1.0 O A:HOH638 3.3 48.2 1.0 N5 A:PQL401 3.6 20.6 1.0 CG A:GLN192 3.7 38.5 1.0 CD A:GLN192 3.7 33.1 1.0 CB A:GLN192 3.7 41.7 1.0 CE A:MET165 4.1 32.8 1.0 N A:GLN192 4.2 45.6 1.0 C A:THR190 4.2 34.8 1.0 N A:THR190 4.2 26.1 1.0 O A:ARG188 4.3 24.0 1.0 CD2 A:LEU167 4.4 33.7 1.0 CA A:GLN192 4.5 46.5 1.0 O A:GLN192 4.6 51.8 1.0 OE1 A:GLN192 4.7 32.7 1.0 O A:GLU166 4.7 22.6 1.0 C14 A:PQL401 4.8 19.8 1.0 CA A:THR190 4.9 26.9 1.0 C A:GLN192 4.9 49.9 1.0 CA A:GLN189 5.0 23.1 1.0 C A:ALA191 5.0 40.5 1.0

X.Jiang, H.Su. Discovery of Oral Simnotrelvir, An Approved Sars-Cov-2 3C-Like Protease Inhibitor For the Treatment of Covid-19 To Be Published.