Fluorine in PDB 9bo7: Crystal Structure of L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

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

The structure of Crystal Structure of L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo7 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)	40.75 / 1.54
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.497, 64.164, 105.49, 90, 90, 90
R / Rfree (%)	18.9 / 22.4

The binding sites of Fluorine atom in the Crystal Structure of L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir (pdb code 9bo7). 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 L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of 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 L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:23.1 occ:1.00 F1 A:4WI401 0.0 23.1 1.0 C22 A:4WI401 1.3 21.2 1.0 F3 A:4WI401 2.2 27.4 1.0 F2 A:4WI401 2.2 23.9 1.0 C21 A:4WI401 2.3 16.4 1.0 H16 A:4WI401 2.5 15.6 1.0 N4 A:4WI401 2.7 13.0 1.0 O A:GLU166 2.8 13.2 1.0 O4 A:4WI401 3.3 18.7 1.0 CD2 A:LEU167 3.5 16.1 1.0 C A:GLU166 3.5 12.0 1.0 CE A:MET165 3.9 28.1 1.0 CA A:LEU167 4.0 15.0 1.0 CG A:MET165 4.0 18.0 1.0 N A:LEU167 4.0 15.4 1.0 CG A:LEU167 4.0 16.8 1.0 CB A:MET165 4.1 14.7 1.0 C14 A:4WI401 4.1 12.9 1.0 SD A:MET165 4.2 25.6 1.0 N A:GLU166 4.3 12.6 1.0 O A:HOH668 4.3 24.2 1.0 O3 A:4WI401 4.4 14.1 1.0 C13 A:4WI401 4.4 15.5 1.0 H19 A:4WI401 4.4 18.7 1.0 H28 A:4WI401 4.5 21.3 1.0 CB A:LEU167 4.6 15.9 1.0 CA A:GLU166 4.6 16.9 1.0 H22 A:4WI401 4.6 20.6 1.0 H15 A:4WI401 4.7 15.5 1.0 C A:MET165 4.8 10.7 1.0 O A:HOH793 4.9 26.4 1.0 CB A:GLN192 4.9 16.5 1.0 NE2 A:GLN192 4.9 17.8 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of 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 L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:23.9 occ:1.00 F2 A:4WI401 0.0 23.9 1.0 C22 A:4WI401 1.3 21.2 1.0 F1 A:4WI401 2.2 23.1 1.0 F3 A:4WI401 2.2 27.4 1.0 C21 A:4WI401 2.3 16.4 1.0 O4 A:4WI401 2.6 18.7 1.0 O A:THR190 3.0 22.6 1.0 NE2 A:GLN192 3.5 17.8 1.0 N4 A:4WI401 3.5 13.0 1.0 CB A:GLN192 3.7 16.5 1.0 H16 A:4WI401 3.8 15.6 1.0 CG A:GLN192 3.8 19.3 1.0 CD A:GLN192 3.8 17.9 1.0 O A:ARG188 3.9 17.6 1.0 O A:HOH674 4.1 24.6 1.0 C A:THR190 4.2 20.0 1.0 N A:THR190 4.2 15.4 1.0 N A:GLN192 4.2 19.1 1.0 CD2 A:LEU167 4.4 16.1 1.0 CA A:GLN192 4.5 15.2 1.0 O A:HOH793 4.5 26.4 1.0 CE A:MET165 4.5 28.1 1.0 O A:GLN192 4.6 18.0 1.0 O A:HOH592 4.7 25.2 1.0 H28 A:4WI401 4.7 21.3 1.0 OE1 A:GLN192 4.7 17.0 1.0 O A:GLU166 4.7 13.2 1.0 C14 A:4WI401 4.7 12.9 1.0 H15 A:4WI401 4.8 15.5 1.0 CA A:THR190 4.8 16.5 1.0 OG1 A:THR190 4.9 20.1 1.0 H22 A:4WI401 4.9 20.6 1.0 SD A:MET165 4.9 25.6 1.0 C A:GLN192 4.9 17.1 1.0 CA A:GLN189 5.0 17.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of 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 L50F Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.4 occ:1.00 F3 A:4WI401 0.0 27.4 1.0 C22 A:4WI401 1.3 21.2 1.0 F1 A:4WI401 2.2 23.1 1.0 F2 A:4WI401 2.2 23.9 1.0 C21 A:4WI401 2.3 16.4 1.0 O A:HOH793 2.8 26.4 1.0 H16 A:4WI401 2.8 15.6 1.0 N4 A:4WI401 2.9 13.0 1.0 O A:HOH668 3.1 24.2 1.0 O4 A:4WI401 3.2 18.7 1.0 O A:GLU166 3.4 13.2 1.0 O A:HOH592 3.5 25.2 1.0 H22 A:4WI401 3.6 20.6 1.0 O A:HOH674 3.7 24.6 1.0 O A:THR190 4.0 22.6 1.0 O A:GLN192 4.0 18.0 1.0 CD A:PRO168 4.0 17.6 1.0 CA A:LEU167 4.1 15.0 1.0 CD2 A:LEU167 4.1 16.1 1.0 C14 A:4WI401 4.3 12.9 1.0 H19 A:4WI401 4.4 18.7 1.0 C A:GLU166 4.4 12.0 1.0 C17 A:4WI401 4.6 17.2 1.0 N A:GLN192 4.6 19.1 1.0 H15 A:4WI401 4.7 15.5 1.0 N A:LEU167 4.7 15.4 1.0 CB A:GLN192 4.7 16.5 1.0 N A:PRO168 4.7 21.7 1.0 CG A:PRO168 4.8 22.4 1.0 C A:LEU167 4.8 17.4 1.0 C A:GLN192 4.8 17.1 1.0 CG A:LEU167 4.9 16.8 1.0 CB A:LEU167 4.9 15.9 1.0 C15 A:4WI401 5.0 14.9 1.0 CA A:GLN192 5.0 15.2 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