Chlorine in PDB 9cdm: Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61

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

The structure of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdm 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)	31.34 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.665, 54.346, 44.524, 90, 101.11, 90
R / Rfree (%)	19.4 / 23.7

The structure of Sars-Cov-2 Mpro L50F 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 L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 (pdb code 9cdm). 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 L50F Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdm:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Sars-Cov-2 Mpro L50F 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 L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:13.3 occ:0.80 CL1 A:XEK401 0.0 13.3 0.8 C5 A:XEK401 1.7 11.4 0.8 C6 A:XEK401 2.7 16.7 0.8 C4 A:XEK401 2.7 8.6 0.8 H1 A:XEK401 2.8 11.0 0.8 F1 A:XEK401 2.9 11.4 0.8 CB A:ASP187 3.5 5.0 1.0 C A:ASP187 3.5 9.7 1.0 O A:ASP187 3.6 11.2 1.0 CA A:ASP187 3.6 9.6 1.0 ND1 A:HIS41 3.8 4.9 1.0 C7 A:XEK401 4.0 15.2 0.8 C3 A:XEK401 4.0 11.8 0.8 CB A:HIS41 4.1 7.8 1.0 N A:ARG188 4.1 9.6 1.0 OH A:TYR54 4.1 10.3 1.0 CG A:HIS41 4.1 9.0 1.0 SD A:MET49 4.1 40.5 1.0 CE A:MET49 4.2 24.6 1.0 C15 A:XEK401 4.5 11.8 0.8 CE1 A:HIS41 4.5 5.5 1.0 SD A:MET165 4.5 17.6 1.0 O A:HOH612 4.6 4.0 1.0 CA A:ARG188 4.6 15.0 1.0 CG A:ASP187 4.8 7.1 1.0 O A:HIS164 4.9 9.0 1.0 CD2 A:HIS41 4.9 9.5 1.0 C A:ARG188 5.0 16.6 1.0

Chlorine binding site 2 out of 2 in the Sars-Cov-2 Mpro L50F 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 L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:34.4 occ:0.80 CL2 A:XEK401 0.0 34.4 0.8 C14 A:XEK401 1.7 22.6 0.8 H2 A:XEK401 2.6 21.9 0.8 C13 A:XEK401 2.7 22.0 0.8 C9 A:XEK401 2.7 17.0 0.8 H7 A:XEK401 2.8 27.1 0.8 NE2 A:GLN189 3.1 19.7 1.0 C8 A:XEK401 3.1 17.6 0.8 CG A:GLN189 3.2 22.8 1.0 CD A:GLN189 3.4 26.3 1.0 O2 A:XEK401 3.8 18.0 0.8 H3 A:XEK401 3.9 21.9 0.8 C12 A:XEK401 4.0 22.7 0.8 C10 A:XEK401 4.0 17.1 0.8 CB A:GLN189 4.4 20.1 1.0 OE1 A:GLN189 4.4 22.3 1.0 C11 A:XEK401 4.5 16.9 0.8 CD A:PRO168 4.5 12.6 1.0 CA A:GLN189 4.6 19.7 1.0 CG A:PRO168 4.7 16.5 1.0 H6 A:XEK401 4.7 28.0 0.8 H4 A:XEK401 4.8 21.2 0.8 C A:GLN189 4.9 22.0 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