Fluorine in PDB 9bo6: Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir:
3.4.22.69;

The structure of Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo6 was solved by C.Papini, J.Kenneson, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 1.61
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.372, 63.359, 105.736, 90, 90, 90
R / Rfree (%)	19.1 / 22.3

The binding sites of Fluorine atom in the Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir (pdb code 9bo6). 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 A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease 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 A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:34.5 occ:1.00 F1 A:4WI401 0.0 34.5 1.0 C22 A:4WI401 1.3 36.0 1.0 F3 A:4WI401 2.1 36.0 1.0 F2 A:4WI401 2.2 37.6 1.0 C21 A:4WI401 2.3 29.9 1.0 H16 A:4WI401 2.5 24.1 1.0 N4 A:4WI401 2.8 20.1 1.0 O A:GLU166 3.0 23.1 1.0 CD2 A:LEU167 3.3 30.3 1.0 O4 A:4WI401 3.3 33.5 1.0 CE A:MET165 3.4 33.7 1.0 C A:GLU166 3.7 23.8 1.0 SD A:MET165 3.7 39.1 1.0 CB A:MET165 3.8 26.4 1.0 CA A:LEU167 4.0 22.9 1.0 N A:LEU167 4.1 19.6 1.0 C14 A:4WI401 4.2 17.9 1.0 N A:GLU166 4.4 21.0 1.0 CG A:LEU167 4.4 31.1 1.0 CG A:MET165 4.5 36.4 1.0 C13 A:4WI401 4.5 24.3 1.0 O3 A:4WI401 4.5 22.1 1.0 H17 A:4WI401 4.5 28.7 1.0 NE2 A:GLN192 4.6 24.9 1.0 H15 A:4WI401 4.7 21.6 1.0 CA A:GLU166 4.7 22.3 1.0 H20 A:4WI401 4.7 30.1 1.0 CB A:LEU167 4.7 27.8 1.0 H26 A:4WI401 4.8 29.5 1.0 CB A:GLN192 4.9 27.7 1.0 C A:MET165 4.9 20.4 1.0 CA A:MET165 5.0 21.6 1.0 CG2 A:VAL173 5.0 23.1 1.0 CD A:GLN192 5.0 27.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease 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 A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:37.6 occ:1.00 F2 A:4WI401 0.0 37.6 1.0 C22 A:4WI401 1.3 36.0 1.0 F1 A:4WI401 2.2 34.5 1.0 F3 A:4WI401 2.2 36.0 1.0 C21 A:4WI401 2.2 29.9 1.0 O4 A:4WI401 2.5 33.5 1.0 O A:THR190 2.9 34.2 1.0 NE2 A:GLN192 3.3 24.9 1.0 N4 A:4WI401 3.5 20.1 1.0 H16 A:4WI401 3.8 24.1 1.0 CB A:GLN192 3.8 27.7 1.0 CD A:GLN192 3.8 27.7 1.0 CG A:GLN192 3.8 32.0 1.0 O A:ARG188 4.0 25.4 1.0 C A:THR190 4.1 38.9 1.0 CE A:MET165 4.2 33.7 1.0 N A:THR190 4.2 30.7 1.0 O A:HOH694 4.3 46.2 1.0 SD A:MET165 4.3 39.1 1.0 N A:GLN192 4.4 35.2 1.0 CD2 A:LEU167 4.5 30.3 1.0 CA A:GLN192 4.6 28.0 1.0 C14 A:4WI401 4.7 17.9 1.0 H15 A:4WI401 4.7 21.6 1.0 OE1 A:GLN192 4.7 29.4 1.0 O A:GLU166 4.8 23.1 1.0 CA A:THR190 4.9 41.6 1.0 O A:GLN192 4.9 31.9 1.0 H26 A:4WI401 4.9 29.5 1.0 CA A:GLN189 4.9 27.6 1.0 H20 A:4WI401 4.9 30.1 1.0 C A:ALA191 5.0 31.9 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of A173V/L50F Sars-Cov-2 Main Protease 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 A173V/L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.0 occ:1.00 F3 A:4WI401 0.0 36.0 1.0 C22 A:4WI401 1.3 36.0 1.0 F1 A:4WI401 2.1 34.5 1.0 F2 A:4WI401 2.2 37.6 1.0 C21 A:4WI401 2.3 29.9 1.0 H16 A:4WI401 2.8 24.1 1.0 N4 A:4WI401 2.9 20.1 1.0 O4 A:4WI401 3.2 33.5 1.0 O A:GLU166 3.2 23.1 1.0 O A:HOH694 3.5 46.2 1.0 H20 A:4WI401 3.6 30.1 1.0 CA A:LEU167 3.8 22.9 1.0 CD2 A:LEU167 3.9 30.3 1.0 CD A:PRO168 4.1 46.6 1.0 C A:GLU166 4.2 23.8 1.0 N A:PRO168 4.2 52.0 1.0 O A:THR190 4.3 34.2 1.0 C14 A:4WI401 4.3 17.9 1.0 O A:GLN192 4.3 31.9 1.0 C A:LEU167 4.3 40.5 1.0 N A:LEU167 4.4 19.6 1.0 C17 A:4WI401 4.5 25.1 1.0 H15 A:4WI401 4.6 21.6 1.0 CB A:LEU167 4.6 27.8 1.0 H22 A:4WI401 4.7 30.1 1.0 H17 A:4WI401 4.7 28.7 1.0 CB A:GLN192 4.7 27.7 1.0 N A:GLN192 4.8 35.2 1.0 CG A:LEU167 4.9 31.1 1.0 C15 A:4WI401 4.9 25.0 1.0

J.R.Kenneson, C.Papini, S.Tang, K.Huynh, C.H.Zhang, W.L.Jorgensen, K.S.Anderson. Exploring Possible Drug-Resistant Variants of Sars-Cov-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, MPRO61 Acs Bio Med Chem Au 2025.
ISSN: ESSN 2694-2437
DOI: 10.1021/ACSBIOMEDCHEMAU.4C00109