Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Sars-Cov-2 Mpro A173V Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl401 b:27.7 occ:0.39 CL1 A:XEK401 0.0 27.7 0.4 CL1 A:XEK401 0.1 27.6 0.5 C5 A:XEK401 1.7 25.3 0.5 C5 A:XEK401 1.7 25.3 0.4 C4 A:XEK401 2.7 23.8 0.5 C6 A:XEK401 2.7 26.4 0.5 C4 A:XEK401 2.7 23.8 0.4 C6 A:XEK401 2.7 26.4 0.4 H1 A:XEK401 2.8 28.5 0.5 H1 A:XEK401 2.8 28.5 0.4 F1 A:XEK401 2.9 26.2 0.4 F1 A:XEK401 2.9 26.2 0.5 SD A:MET49 3.5 57.9 1.0 O A:ASP187 3.6 22.1 1.0 ND1 A:HIS41 3.6 23.2 1.0 CB A:HIS41 3.6 24.2 1.0 C A:ASP187 3.6 24.7 1.0 CB A:ASP187 3.7 16.8 1.0 OH A:TYR54 3.7 26.3 1.0 CG A:HIS41 3.8 26.1 1.0 CA A:ASP187 3.9 20.0 1.0 C7 A:XEK401 4.0 26.0 0.5 C3 A:XEK401 4.0 24.4 0.5 C7 A:XEK401 4.0 26.0 0.4 C3 A:XEK401 4.0 24.4 0.4 N A:ARG188 4.2 21.5 0.6 N A:ARG188 4.2 21.5 0.4 SD A:MET165 4.3 31.0 1.0 CE1 A:HIS41 4.5 19.9 1.0 C15 A:XEK401 4.5 24.3 0.5 C15 A:XEK401 4.5 24.3 0.4 CE A:MET49 4.6 38.3 1.0 CG A:MET165 4.6 28.4 1.0 CD2 A:HIS41 4.7 28.9 1.0 CA A:ARG188 4.7 24.5 0.6 CA A:ARG188 4.7 24.6 0.4 O A:HOH610 4.8 22.1 1.0 CG A:ASP187 4.8 23.6 1.0 CG A:MET49 4.9 51.4 1.0 H9 A:XEK401 5.0 31.9 0.4 H9 A:XEK401 5.0 31.9 0.5

Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl401 b:27.6 occ:0.48 CL1 A:XEK401 0.0 27.6 0.5 CL1 A:XEK401 0.1 27.7 0.4 C5 A:XEK401 1.7 25.3 0.5 C5 A:XEK401 1.7 25.3 0.4 C6 A:XEK401 2.7 26.4 0.4 C6 A:XEK401 2.7 26.4 0.5 C4 A:XEK401 2.7 23.8 0.5 C4 A:XEK401 2.7 23.8 0.4 H1 A:XEK401 2.8 28.5 0.5 H1 A:XEK401 2.8 28.5 0.4 F1 A:XEK401 2.9 26.2 0.4 F1 A:XEK401 2.9 26.2 0.5 SD A:MET49 3.4 57.9 1.0 O A:ASP187 3.6 22.1 1.0 CB A:HIS41 3.6 24.2 1.0 C A:ASP187 3.7 24.7 1.0 ND1 A:HIS41 3.7 23.2 1.0 OH A:TYR54 3.7 26.3 1.0 CB A:ASP187 3.7 16.8 1.0 CG A:HIS41 3.8 26.1 1.0 CA A:ASP187 4.0 20.0 1.0 C7 A:XEK401 4.0 26.0 0.5 C7 A:XEK401 4.0 26.0 0.4 C3 A:XEK401 4.0 24.4 0.5 C3 A:XEK401 4.0 24.4 0.4 N A:ARG188 4.2 21.5 0.6 N A:ARG188 4.2 21.5 0.4 SD A:MET165 4.4 31.0 1.0 C15 A:XEK401 4.5 24.3 0.5 C15 A:XEK401 4.5 24.3 0.4 CE1 A:HIS41 4.5 19.9 1.0 CE A:MET49 4.5 38.3 1.0 CA A:ARG188 4.7 24.5 0.6 CA A:ARG188 4.7 24.6 0.4 CD2 A:HIS41 4.7 28.9 1.0 CG A:MET165 4.7 28.4 1.0 CG A:MET49 4.8 51.4 1.0 O A:HOH610 4.8 22.1 1.0 CG A:ASP187 4.8 23.6 1.0 CB A:MET49 4.9 43.4 1.0 H9 A:XEK401 5.0 31.9 0.4 H9 A:XEK401 5.0 31.9 0.5

Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl401 b:37.5 occ:0.39 CL2 A:XEK401 0.0 37.5 0.4 H4 A:XEK401 0.3 42.2 0.5 C10 A:XEK401 1.0 35.2 0.5 C14 A:XEK401 1.7 35.1 0.4 C11 A:XEK401 1.9 34.0 0.5 C9 A:XEK401 2.1 33.0 0.5 H5 A:XEK401 2.2 40.8 0.5 H3 A:XEK401 2.6 40.1 0.5 H3 A:XEK401 2.6 40.2 0.4 C13 A:XEK401 2.7 37.0 0.4 C9 A:XEK401 2.7 35.2 0.4 H7 A:XEK401 2.8 44.4 0.4 C8 A:XEK401 2.8 33.4 0.5 C8 A:XEK401 3.1 33.5 0.4 C12 A:XEK401 3.2 38.0 0.5 CE A:MET165 3.2 27.3 1.0 C14 A:XEK401 3.3 37.9 0.5 O2 A:XEK401 3.5 32.6 0.5 CD2 A:LEU167 3.5 24.2 1.0 NE2 A:GLN192 3.6 28.4 1.0 O2 A:XEK401 3.6 32.6 0.4 H2 A:XEK401 3.6 40.1 0.5 C13 A:XEK401 3.7 36.1 0.5 SD A:MET165 3.9 31.0 1.0 H2 A:XEK401 3.9 40.2 0.4 H6 A:XEK401 3.9 45.6 0.5 O A:ARG188 3.9 24.7 0.4 C12 A:XEK401 4.0 33.2 0.4 C10 A:XEK401 4.0 37.0 0.4 O A:ARG188 4.0 24.6 0.6 CD A:GLN192 4.2 33.5 1.0 O A:THR190 4.3 30.3 1.0 C7 A:XEK401 4.5 26.0 0.5 C7 A:XEK401 4.5 26.0 0.4 C11 A:XEK401 4.5 32.7 0.4 CB A:GLN192 4.5 28.4 1.0 O A:GLU166 4.5 21.6 1.0 CD A:PRO168 4.5 26.6 1.0 CG A:GLN192 4.6 35.8 1.0 H7 A:XEK401 4.6 43.4 0.5 CA A:LEU167 4.6 24.9 1.0 F1 A:XEK401 4.7 26.2 0.5 H6 A:XEK401 4.7 39.8 0.4 CB A:MET165 4.7 20.8 1.0 F1 A:XEK401 4.7 26.2 0.4 H4 A:XEK401 4.7 44.4 0.4 CL2 A:XEK401 4.8 39.5 0.5 OE1 A:GLN192 4.9 24.1 1.0 CG A:LEU167 4.9 28.4 1.0 C6 A:XEK401 5.0 26.4 0.5 C6 A:XEK401 5.0 26.4 0.4 N A:THR190 5.0 27.8 1.0

Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl401 b:39.5 occ:0.48 CL2 A:XEK401 0.0 39.5 0.5 H4 A:XEK401 0.7 44.4 0.4 C10 A:XEK401 1.2 37.0 0.4 C14 A:XEK401 1.7 37.9 0.5 C9 A:XEK401 2.1 35.2 0.4 C11 A:XEK401 2.2 32.7 0.4 H2 A:XEK401 2.4 40.2 0.4 H5 A:XEK401 2.5 39.2 0.4 H2 A:XEK401 2.6 40.1 0.5 C13 A:XEK401 2.7 36.1 0.5 C8 A:XEK401 2.7 33.5 0.4 C9 A:XEK401 2.7 33.0 0.5 H7 A:XEK401 2.8 43.4 0.5 C8 A:XEK401 3.1 33.4 0.5 C14 A:XEK401 3.3 35.1 0.4 C12 A:XEK401 3.4 33.2 0.4 H3 A:XEK401 3.5 40.2 0.4 O2 A:XEK401 3.5 32.6 0.4 O2 A:XEK401 3.6 32.6 0.5 CG A:GLN189 3.7 31.4 1.0 C13 A:XEK401 3.8 37.0 0.4 NE2 A:GLN189 3.9 35.4 1.0 H3 A:XEK401 3.9 40.1 0.5 C12 A:XEK401 4.0 38.0 0.5 CD A:GLN189 4.0 34.7 1.0 C10 A:XEK401 4.0 35.2 0.5 O A:HOH691 4.1 34.1 1.0 H6 A:XEK401 4.2 39.8 0.4 H8 A:XEK401 4.3 29.2 0.4 H8 A:XEK401 4.4 29.2 0.5 C11 A:XEK401 4.5 34.0 0.5 CD A:PRO168 4.5 26.6 1.0 O A:GLU166 4.6 21.6 1.0 C7 A:XEK401 4.6 26.0 0.4 C7 A:XEK401 4.7 26.0 0.5 CG A:PRO168 4.7 24.6 1.0 H6 A:XEK401 4.7 45.6 0.5 H4 A:XEK401 4.8 42.2 0.5 H7 A:XEK401 4.8 44.4 0.4 OE1 A:GLN189 4.8 38.7 1.0 CL2 A:XEK401 4.8 37.5 0.4 C15 A:XEK401 4.9 24.3 0.4 C15 A:XEK401 4.9 24.3 0.5 CB A:GLN189 4.9 26.6 1.0

Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl406 b:46.0 occ:1.00 O A:HOH585 2.4 41.5 1.0 NH1 A:ARG4 3.4 40.4 1.0 N A:LYS5 3.4 21.2 1.0 CD A:ARG4 3.5 32.7 1.0 O A:HOH590 3.5 40.7 1.0 CB A:LYS5 3.9 31.2 1.0 CA A:LYS5 4.1 22.8 1.0 O A:LYS5 4.2 40.2 1.0 CA A:ARG4 4.3 24.6 1.0 CZ A:ARG4 4.3 36.9 1.0 C A:ARG4 4.3 22.8 1.0 NE A:ARG4 4.4 40.4 1.0 CB A:ARG4 4.4 23.8 1.0 CG A:ARG4 4.6 24.8 1.0 C A:LYS5 4.6 26.0 1.0 O A:HOH561 5.0 42.3 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