Fluorine in PDB 8igy: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir

All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir:
3.4.22.69;

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir, PDB code: 8igy 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)	27.81 / 1.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.582, 63.619, 105.282, 90, 90, 90
R / Rfree (%)	18.7 / 20.6

The binding sites of Fluorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir (pdb code 8igy). 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 Nirmatrelvir, PDB code: 8igy:
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 Nirmatrelvir


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 Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:46.1 occ:1.00 F1 A:4WI401 0.0 46.1 1.0 C22 A:4WI401 1.3 40.9 1.0 F2 A:4WI401 2.1 42.2 1.0 F3 A:4WI401 2.1 42.8 1.0 C21 A:4WI401 2.4 34.4 1.0 O4 A:4WI401 2.9 32.4 1.0 N4 A:4WI401 3.3 28.4 1.0 O A:THR190 3.5 31.1 1.0 N A:GLN192 3.9 32.1 1.0 O A:HOH602 4.0 34.0 1.0 O A:GLN192 4.1 31.6 1.0 O A:GLU166 4.1 20.7 1.0 CD A:PRO168 4.3 31.8 1.0 C A:THR190 4.3 32.0 1.0 CA A:ALA191 4.4 34.6 1.0 CD2 A:LEU167 4.6 26.7 1.0 C14 A:4WI401 4.6 24.2 1.0 C A:ALA191 4.6 33.2 1.0 CB A:GLN192 4.6 29.6 1.0 CA A:GLN192 4.7 30.9 1.0 C16 A:4WI401 4.8 21.4 1.0 CA A:LEU167 4.8 27.1 1.0 N A:ALA191 4.8 34.2 1.0 C A:GLN192 4.8 31.4 1.0 CG A:GLN192 5.0 29.0 1.0 CG A:PRO168 5.0 33.1 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir


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 Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.2 occ:1.00 F2 A:4WI401 0.0 42.2 1.0 C22 A:4WI401 1.3 40.9 1.0 F3 A:4WI401 2.1 42.8 1.0 F1 A:4WI401 2.1 46.1 1.0 C21 A:4WI401 2.4 34.4 1.0 O A:GLU166 2.6 20.7 1.0 N4 A:4WI401 2.6 28.4 1.0 CD2 A:LEU167 3.3 26.7 1.0 C A:GLU166 3.4 21.9 1.0 O4 A:4WI401 3.5 32.4 1.0 CA A:LEU167 3.6 27.1 1.0 N A:LEU167 3.9 23.7 1.0 C14 A:4WI401 4.1 24.2 1.0 CG A:LEU167 4.1 26.3 1.0 CB A:LEU167 4.3 27.6 1.0 CD A:PRO168 4.5 31.8 1.0 N A:GLU166 4.5 20.7 1.0 SD A:MET165 4.6 33.5 1.0 CA A:GLU166 4.6 21.3 1.0 C13 A:4WI401 4.6 23.8 1.0 O3 A:4WI401 4.6 22.4 1.0 CG A:MET165 4.7 28.9 1.0 C A:LEU167 4.7 30.4 1.0 O A:GLN192 4.8 31.6 1.0 CB A:MET165 4.8 25.4 1.0 CE A:MET165 4.9 34.3 1.0 C17 A:4WI401 4.9 22.2 1.0 C15 A:4WI401 4.9 21.7 1.0 O A:THR190 4.9 31.1 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with Nirmatrelvir


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 Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.8 occ:1.00 F3 A:4WI401 0.0 42.8 1.0 C22 A:4WI401 1.3 40.9 1.0 F2 A:4WI401 2.1 42.2 1.0 F1 A:4WI401 2.1 46.1 1.0 C21 A:4WI401 2.4 34.4 1.0 O4 A:4WI401 2.8 32.4 1.0 O A:THR190 3.1 31.1 1.0 NE2 A:GLN192 3.2 27.5 1.0 N4 A:4WI401 3.4 28.4 1.0 CD A:GLN192 3.7 28.0 1.0 O A:ARG188 3.8 24.7 1.0 CG A:GLN192 3.9 29.0 1.0 CB A:GLN192 4.0 29.6 1.0 CD2 A:LEU167 4.2 26.7 1.0 C A:THR190 4.3 32.0 1.0 N A:GLN192 4.3 32.1 1.0 N A:THR190 4.4 28.6 1.0 SD A:MET165 4.4 33.5 1.0 OE1 A:GLN192 4.6 28.4 1.0 O A:GLU166 4.6 20.7 1.0 C14 A:4WI401 4.6 24.2 1.0 CA A:GLN192 4.7 30.9 1.0 CE A:MET165 4.8 34.3 1.0 O A:GLN192 4.9 31.6 1.0 C A:ARG188 4.9 24.6 1.0 CA A:GLN189 4.9 25.1 1.0 O A:HOH602 5.0 34.0 1.0 C A:ALA191 5.0 33.2 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.