Fluorine in PDB 9cdk: Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61

The structure of Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdk was solved by S.Tang, J.R.Kenneson, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.03 / 1.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.887, 53.558, 44.551, 90, 103.15, 90
R / Rfree (%)	18.3 / 22.4

The structure of Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Fluorine atom in the Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61 (pdb code 9cdk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdk:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61


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 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.2 occ:0.39 F1 A:XEK401 0.0 26.2 0.4 F1 A:XEK401 0.0 26.2 0.5 C6 A:XEK401 1.4 26.4 0.4 C6 A:XEK401 1.4 26.4 0.5 C5 A:XEK401 2.4 25.3 0.5 C5 A:XEK401 2.4 25.3 0.4 C7 A:XEK401 2.4 26.0 0.4 C7 A:XEK401 2.4 26.0 0.5 O2 A:XEK401 2.7 32.6 0.4 O2 A:XEK401 2.7 32.6 0.5 C A:ARG188 2.8 27.0 0.4 C A:ARG188 2.8 27.0 0.6 N A:GLN189 2.9 25.5 1.0 CL1 A:XEK401 2.9 27.6 0.5 CL1 A:XEK401 2.9 27.7 0.4 O A:ARG188 3.0 24.7 0.4 O A:ARG188 3.1 24.6 0.6 N A:ARG188 3.2 21.5 0.6 N A:ARG188 3.3 21.5 0.4 CA A:ARG188 3.3 24.5 0.6 CA A:ARG188 3.3 24.6 0.4 CA A:GLN189 3.5 28.6 1.0 SD A:MET165 3.5 31.0 1.0 C4 A:XEK401 3.6 23.8 0.4 C15 A:XEK401 3.6 24.3 0.4 C4 A:XEK401 3.6 23.8 0.5 C15 A:XEK401 3.6 24.3 0.5 C A:ASP187 3.7 24.7 1.0 C8 A:XEK401 4.0 33.4 0.5 CB A:GLN189 4.0 26.6 1.0 C8 A:XEK401 4.0 33.5 0.4 H3 A:XEK401 4.0 40.1 0.5 C3 A:XEK401 4.1 24.4 0.4 C3 A:XEK401 4.1 24.4 0.5 H3 A:XEK401 4.2 40.2 0.4 O A:ASP187 4.3 22.1 1.0 O A:MET49 4.3 34.5 1.0 CA A:ASP187 4.4 20.0 1.0 H1 A:XEK401 4.4 28.5 0.5 H1 A:XEK401 4.4 28.5 0.4 H8 A:XEK401 4.4 29.2 0.4 H8 A:XEK401 4.4 29.2 0.5 H4 A:XEK401 4.4 42.2 0.5 C9 A:XEK401 4.6 33.0 0.5 CG A:MET165 4.6 28.4 1.0 H2 A:XEK401 4.7 40.2 0.4 H2 A:XEK401 4.7 40.1 0.5 C9 A:XEK401 4.7 35.2 0.4 CL2 A:XEK401 4.7 37.5 0.4 C10 A:XEK401 4.8 35.2 0.5 CB A:ARG188 4.8 25.8 0.6 CB A:ARG188 4.8 25.8 0.4 SD A:MET49 4.9 57.9 1.0 CE A:MET165 4.9 27.3 1.0 CG A:GLN189 4.9 31.4 1.0 C A:GLN189 4.9 24.9 1.0 O A:VAL186 4.9 24.5 1.0 CB A:MET49 5.0 43.4 1.0

Fluorine binding site 2 out of 2 in the Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61


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 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.2 occ:0.48 F1 A:XEK401 0.0 26.2 0.5 F1 A:XEK401 0.0 26.2 0.4 C6 A:XEK401 1.3 26.4 0.4 C6 A:XEK401 1.4 26.4 0.5 C7 A:XEK401 2.3 26.0 0.4 C7 A:XEK401 2.4 26.0 0.5 C5 A:XEK401 2.4 25.3 0.5 C5 A:XEK401 2.4 25.3 0.4 O2 A:XEK401 2.7 32.6 0.4 O2 A:XEK401 2.7 32.6 0.5 C A:ARG188 2.8 27.0 0.4 C A:ARG188 2.8 27.0 0.6 N A:GLN189 2.9 25.5 1.0 CL1 A:XEK401 2.9 27.6 0.5 CL1 A:XEK401 2.9 27.7 0.4 O A:ARG188 3.0 24.7 0.4 O A:ARG188 3.1 24.6 0.6 N A:ARG188 3.2 21.5 0.6 N A:ARG188 3.3 21.5 0.4 CA A:ARG188 3.3 24.5 0.6 CA A:ARG188 3.3 24.6 0.4 SD A:MET165 3.5 31.0 1.0 CA A:GLN189 3.5 28.6 1.0 C15 A:XEK401 3.6 24.3 0.4 C4 A:XEK401 3.6 23.8 0.4 C15 A:XEK401 3.6 24.3 0.5 C4 A:XEK401 3.6 23.8 0.5 C A:ASP187 3.8 24.7 1.0 C8 A:XEK401 3.9 33.4 0.5 C8 A:XEK401 4.0 33.5 0.4 CB A:GLN189 4.0 26.6 1.0 H3 A:XEK401 4.0 40.1 0.5 C3 A:XEK401 4.1 24.4 0.4 H3 A:XEK401 4.1 40.2 0.4 C3 A:XEK401 4.1 24.4 0.5 O A:ASP187 4.3 22.1 1.0 O A:MET49 4.3 34.5 1.0 CA A:ASP187 4.4 20.0 1.0 H8 A:XEK401 4.4 29.2 0.4 H1 A:XEK401 4.4 28.5 0.4 H1 A:XEK401 4.4 28.5 0.5 H8 A:XEK401 4.4 29.2 0.5 H4 A:XEK401 4.4 42.2 0.5 C9 A:XEK401 4.6 33.0 0.5 CG A:MET165 4.6 28.4 1.0 H2 A:XEK401 4.6 40.2 0.4 H2 A:XEK401 4.6 40.1 0.5 C9 A:XEK401 4.7 35.2 0.4 CL2 A:XEK401 4.7 37.5 0.4 C10 A:XEK401 4.7 35.2 0.5 CE A:MET165 4.8 27.3 1.0 CB A:ARG188 4.8 25.8 0.6 CB A:ARG188 4.8 25.8 0.4 CG A:GLN189 4.9 31.4 1.0 C A:GLN189 4.9 24.9 1.0 SD A:MET49 4.9 57.9 1.0 O A:VAL186 4.9 24.5 1.0 C14 A:XEK401 5.0 35.1 0.4

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