Fluorine in PDB 8hoz: Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir, PDB code: 8hoz was solved by M.Lin, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.32 / 2.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.667, 63.546, 104.671, 90, 90, 90
R / Rfree (%)	23 / 25.8

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir (pdb code 8hoz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir, PDB code: 8hoz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) 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 Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.0 occ:0.91 F1 A:4WI401 0.0 40.0 0.9 C22 A:4WI401 1.4 39.9 0.9 F2 A:4WI401 2.2 40.3 0.9 F3 A:4WI401 2.2 40.6 0.9 C21 A:4WI401 2.4 39.3 0.9 N4 A:4WI401 2.8 38.7 0.9 O A:GLU166 2.8 38.7 1.0 CD A:PRO168 3.4 40.5 1.0 CA A:LEU167 3.4 39.2 1.0 O4 A:4WI401 3.5 39.9 0.9 C A:GLU166 3.8 38.3 1.0 N A:PRO168 4.0 40.1 1.0 C A:LEU167 4.0 39.7 1.0 N A:LEU167 4.1 38.6 1.0 CD2 A:LEU167 4.1 40.6 1.0 C14 A:4WI401 4.2 38.6 0.9 O A:GLN192 4.2 41.6 1.0 CG A:PRO168 4.3 39.8 1.0 CB A:LEU167 4.4 39.5 1.0 CG A:LEU167 4.6 39.5 1.0 C23 A:4WI401 4.6 38.0 0.9 O A:THR190 4.6 41.1 1.0 C15 A:4WI401 4.9 38.4 0.9 O A:LEU167 5.0 39.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) 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 Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.3 occ:0.91 F2 A:4WI401 0.0 40.3 0.9 C22 A:4WI401 1.4 39.9 0.9 F1 A:4WI401 2.2 40.0 0.9 F3 A:4WI401 2.2 40.6 0.9 C21 A:4WI401 2.4 39.3 0.9 O4 A:4WI401 3.0 39.9 0.9 SD A:MET165 3.1 40.6 1.0 CD2 A:LEU167 3.3 40.6 1.0 O A:GLU166 3.3 38.7 1.0 N4 A:4WI401 3.4 38.7 0.9 CE A:MET165 3.6 39.3 1.0 CG A:LEU167 4.0 39.5 1.0 NE2 A:GLN192 4.1 40.4 1.0 C A:GLU166 4.1 38.3 1.0 CA A:LEU167 4.1 39.2 1.0 CB A:GLN192 4.1 41.2 1.0 CG A:MET165 4.1 37.9 1.0 CD A:GLN192 4.4 40.8 1.0 N A:LEU167 4.4 38.6 1.0 CB A:LEU167 4.5 39.5 1.0 C14 A:4WI401 4.6 38.6 0.9 O A:THR190 4.7 41.1 1.0 CG A:GLN192 4.7 40.9 1.0 CB A:MET165 4.7 38.2 1.0 O A:GLN192 4.7 41.6 1.0 CD A:PRO168 4.9 40.5 1.0 C13 A:4WI401 4.9 38.3 0.9 OE1 A:GLN192 5.0 40.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) 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 Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.6 occ:0.91 F3 A:4WI401 0.0 40.6 0.9 C22 A:4WI401 1.4 39.9 0.9 F1 A:4WI401 2.2 40.0 0.9 F2 A:4WI401 2.2 40.3 0.9 C21 A:4WI401 2.4 39.3 0.9 O A:THR190 2.6 41.1 1.0 O4 A:4WI401 2.7 39.9 0.9 N4 A:4WI401 3.6 38.7 0.9 N A:GLN192 3.7 41.2 1.0 C A:THR190 3.8 41.1 1.0 CB A:GLN192 3.8 41.2 1.0 NE2 A:GLN192 4.0 40.4 1.0 O A:GLN192 4.2 41.6 1.0 CG A:GLN192 4.2 40.9 1.0 N A:THR190 4.2 42.1 1.0 CA A:GLN192 4.2 41.2 1.0 CD A:GLN192 4.5 40.8 1.0 C A:ALA191 4.6 41.6 1.0 C A:GLN192 4.6 41.5 1.0 O A:ARG188 4.6 41.2 1.0 O A:GLU166 4.7 38.7 1.0 CA A:THR190 4.7 41.8 1.0 CD2 A:LEU167 4.7 40.6 1.0 N A:ALA191 4.7 41.1 1.0 CA A:ALA191 4.7 41.3 1.0 C14 A:4WI401 4.8 38.6 0.9 SD A:MET165 4.9 40.6 1.0 CD A:PRO168 4.9 40.5 1.0

M.Lin, X.Liu. Crystal Structure of Sars-Cov-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir To Be Published.