Chlorine in PDB 9cdl: Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61

All present enzymatic activity of Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61:
3.4.22.69;

The structure of Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdl was solved by S.Tang, J.R.Kenneson, K.Huynh, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.70 / 1.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.689, 54.545, 44.433, 90, 101.24, 90
R / Rfree (%)	18.5 / 21.1

The structure of Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61 (pdb code 9cdl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdl:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:33.0 occ:0.84 CL1 A:XEK401 0.0 33.0 0.8 C5 A:XEK401 1.7 30.3 0.8 C4 A:XEK401 2.7 25.0 0.8 C6 A:XEK401 2.7 39.8 0.8 H1 A:XEK401 2.8 30.0 0.8 F1 A:XEK401 2.9 34.5 0.8 CE A:MET49 3.1 39.4 1.0 C A:ASP187 3.3 19.7 1.0 CB A:ASP187 3.4 15.9 1.0 CA A:ASP187 3.4 16.6 1.0 O A:ASP187 3.5 19.7 1.0 ND1 A:HIS41 3.7 20.6 1.0 N A:ARG188 3.8 18.5 1.0 C3 A:XEK401 4.0 25.9 0.8 C7 A:XEK401 4.0 40.9 0.8 OH A:TYR54 4.2 18.4 1.0 CG A:HIS41 4.3 20.2 1.0 SD A:MET165 4.3 30.1 1.0 CE1 A:HIS41 4.4 19.9 1.0 CB A:HIS41 4.4 19.6 1.0 C15 A:XEK401 4.5 31.6 0.8 O A:HOH637 4.6 15.3 1.0 CA A:ARG188 4.6 26.0 1.0 SD A:MET49 4.7 46.5 1.0 CG A:ASP187 4.7 19.7 1.0 CB A:MET165 4.7 23.1 1.0 O A:HIS164 4.8 20.4 1.0 N A:ASP187 4.8 16.8 1.0 C A:ARG188 4.9 22.1 1.0

Chlorine binding site 2 out of 2 in the Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Mpro E166V/L50F Double Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:55.8 occ:0.84 CL2 A:XEK401 0.0 55.8 0.8 C14 A:XEK401 1.7 39.6 0.8 H3 A:XEK401 2.6 51.1 0.8 C13 A:XEK401 2.7 38.5 0.8 C9 A:XEK401 2.7 41.6 0.8 H7 A:XEK401 2.8 46.2 0.8 C8 A:XEK401 3.0 42.6 0.8 O2 A:XEK401 3.5 47.1 0.8 NE2 A:GLN192 3.6 26.6 1.0 SD A:MET165 3.7 30.1 1.0 CD2 A:LEU167 3.8 31.1 1.0 H2 A:XEK401 3.9 51.1 0.8 O A:ARG188 4.0 23.4 1.0 C12 A:XEK401 4.0 37.0 0.8 CE A:MET165 4.0 24.7 1.0 C10 A:XEK401 4.0 38.1 0.8 F1 A:XEK401 4.0 34.5 0.8 O A:VAL166 4.1 21.6 1.0 C7 A:XEK401 4.1 40.9 0.8 CG A:MET165 4.2 19.7 1.0 C6 A:XEK401 4.3 39.8 0.8 CD A:GLN192 4.4 28.5 1.0 CA A:LEU167 4.4 22.8 1.0 C11 A:XEK401 4.5 33.8 0.8 O A:THR190 4.6 30.5 1.0 CB A:MET165 4.6 23.1 1.0 CD A:PRO168 4.7 29.4 1.0 C A:VAL166 4.7 20.2 1.0 H6 A:XEK401 4.7 44.3 0.8 H4 A:XEK401 4.7 45.7 0.8 N A:LEU167 4.8 20.5 1.0 CG A:GLN192 4.9 30.3 1.0 C15 A:XEK401 5.0 31.6 0.8 C A:ARG188 5.0 22.1 1.0 CG A:LEU167 5.0 30.9 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