Chlorine in PDB 9bo3: Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61

All present enzymatic activity of Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61:
3.4.22.69;

The structure of Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61, PDB code: 9bo3 was solved by C.Papini, J.Kenneson, C.H.Zhang, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.03 / 2.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.044, 53.668, 44.9, 90, 101.28, 90
R / Rfree (%)	23.8 / 28.7

The structure of Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61 (pdb code 9bo3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61, PDB code: 9bo3:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:51.4 occ:1.00 CL1 A:XEK401 0.0 51.4 1.0 C5 A:XEK401 1.8 52.9 1.0 C6 A:XEK401 2.7 54.5 1.0 C4 A:XEK401 2.8 51.2 1.0 F1 A:XEK401 2.9 53.8 1.0 HB2 A:ASP187 2.9 53.3 1.0 H1 A:XEK401 2.9 61.4 1.0 HB3 A:HIS41 3.1 58.0 1.0 O A:ASP187 3.2 47.1 1.0 HD2 A:HIS41 3.3 53.2 1.0 HB2 A:HIS41 3.4 58.0 1.0 HA A:ASP187 3.5 56.5 1.0 C A:ASP187 3.5 48.0 1.0 CD2 A:HIS41 3.5 44.4 1.0 CB A:HIS41 3.6 48.4 1.0 CG A:HIS41 3.6 46.5 1.0 CB A:ASP187 3.7 44.5 1.0 CA A:ASP187 3.8 47.2 1.0 HH A:TYR54 4.0 54.6 1.0 C7 A:XEK401 4.0 56.9 1.0 C3 A:XEK401 4.1 51.0 1.0 OH A:TYR54 4.1 45.6 1.0 HB3 A:ASP187 4.1 53.3 1.0 HE1 A:MET49 4.2 78.2 1.0 HB3 A:MET165 4.2 58.8 1.0 HA A:ARG188 4.2 66.5 1.0 N A:ARG188 4.3 51.8 1.0 NE2 A:HIS41 4.5 44.9 1.0 ND1 A:HIS41 4.5 48.3 1.0 C15 A:XEK401 4.6 53.2 1.0 HG2 A:MET49 4.6 80.6 1.0 CA A:ARG188 4.7 55.5 1.0 SD A:MET165 4.8 55.1 1.0 CG A:ASP187 4.9 44.6 1.0 HE2 A:HIS41 4.9 53.7 1.0 H A:ARG188 4.9 62.0 1.0 HB3 A:HIS164 4.9 51.1 1.0 CE1 A:HIS41 5.0 47.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of E166V Sars-Cov-2 Main Protease in Complex with Compound MPRO61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:67.5 occ:1.00 CL2 A:XEK401 0.0 67.5 1.0 C14 A:XEK401 1.8 61.9 1.0 H3 A:XEK401 2.6 71.2 1.0 C13 A:XEK401 2.7 64.0 1.0 C9 A:XEK401 2.8 61.6 1.0 H7 A:XEK401 2.9 76.6 1.0 C8 A:XEK401 3.1 59.4 1.0 O A:VAL166 3.1 53.7 1.0 H8 A:XEK401 3.4 63.7 1.0 O2 A:XEK401 3.6 60.2 1.0 OE1 A:GLN189 3.9 66.1 1.0 C12 A:XEK401 4.0 62.0 1.0 H2 A:XEK401 4.1 71.2 1.0 C10 A:XEK401 4.1 60.6 1.0 C15 A:XEK401 4.2 53.2 1.0 C A:VAL166 4.2 52.5 1.0 HD3 A:PRO168 4.4 67.3 1.0 C7 A:XEK401 4.4 56.9 1.0 HA A:LEU167 4.4 63.7 1.0 C11 A:XEK401 4.6 64.1 1.0 HG3 A:GLN189 4.6 74.9 1.0 HA A:PRO168 4.7 66.1 1.0 H A:VAL166 4.7 53.8 1.0 N A:PRO168 4.8 56.1 1.0 C A:LEU167 4.8 55.1 1.0 O1 A:XEK401 4.8 52.3 1.0 H6 A:XEK401 4.9 74.2 1.0 CD A:GLN189 4.9 63.8 1.0 H4 A:XEK401 4.9 72.6 1.0 CA A:LEU167 5.0 53.2 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