Chlorine in PDB 8ur9: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61, PDB code: 8ur9 was solved by C.Papini, 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)	56.91 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.91, 99.895, 104.314, 90, 90, 90
R / Rfree (%)	20.4 / 23.6

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61 (pdb code 8ur9). 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 the Sars-Cov-2 Main Protease in Complex with Compound 61, PDB code: 8ur9:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61


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 the Sars-Cov-2 Main Protease in Complex with Compound 61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:70.9 occ:1.00 CL1 A:XEK401 0.0 70.9 1.0 C5 A:XEK401 1.8 62.8 1.0 C4 A:XEK401 2.7 53.6 1.0 C6 A:XEK401 2.8 67.0 1.0 H1 A:XEK401 2.8 64.4 1.0 F1 A:XEK401 3.0 71.3 1.0 ND1 A:HIS41 3.5 44.5 1.0 CB A:ASP187 3.6 45.2 1.0 CA A:ASP187 3.7 43.2 1.0 C A:ASP187 3.7 53.6 1.0 CG A:HIS41 3.9 47.3 1.0 O A:ASP187 3.9 52.7 1.0 C3 A:XEK401 4.0 54.0 1.0 CE A:MET49 4.0 74.1 1.0 CB A:HIS41 4.0 46.1 1.0 C7 A:XEK401 4.1 69.0 1.0 CE1 A:HIS41 4.2 47.1 1.0 N A:ARG188 4.3 55.1 1.0 C15 A:XEK401 4.5 64.4 1.0 SD A:MET165 4.6 57.7 1.0 CD2 A:HIS41 4.6 45.2 1.0 SD A:MET49 4.6 92.2 1.0 CB A:MET165 4.7 41.7 1.0 OH A:TYR54 4.7 54.8 1.0 NE2 A:HIS41 4.7 46.4 1.0 O A:HIS164 4.8 45.0 1.0 O A:HOH522 4.8 46.1 1.0 CG A:ASP187 4.9 48.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61


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 the Sars-Cov-2 Main Protease in Complex with Compound 61 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:94.2 occ:1.00 CL2 A:XEK401 0.0 94.2 1.0 C14 A:XEK401 1.8 84.1 1.0 H3 A:XEK401 2.5 97.7 1.0 C13 A:XEK401 2.7 81.5 1.0 C9 A:XEK401 2.8 82.9 1.0 H7 A:XEK401 2.9 97.8 1.0 C8 A:XEK401 3.1 81.4 1.0 NE2 A:GLN192 3.7 52.2 1.0 CD2 A:LEU167 3.7 49.8 1.0 H2 A:XEK401 4.0 97.7 1.0 O2 A:XEK401 4.0 79.5 1.0 C12 A:XEK401 4.0 79.6 1.0 C10 A:XEK401 4.1 81.4 1.0 CG A:GLN192 4.1 61.8 1.0 SD A:MET165 4.2 57.7 1.0 O A:ARG188 4.2 55.4 1.0 CD A:GLN192 4.3 56.7 1.0 CD A:PRO168 4.4 63.6 1.0 O A:THR190 4.4 69.0 1.0 O A:GLU166 4.5 46.9 1.0 C11 A:XEK401 4.6 78.2 1.0 F1 A:XEK401 4.6 71.3 1.0 CA A:LEU167 4.6 54.0 1.0 C7 A:XEK401 4.6 69.0 1.0 CE A:MET165 4.7 49.0 1.0 H6 A:XEK401 4.9 95.5 1.0 C6 A:XEK401 4.9 67.0 1.0 H4 A:XEK401 4.9 97.6 1.0 CA A:GLN189 5.0 67.2 1.0

C.Papini, I.Ullah, A.P.Ranjan, S.Zhang, Q.Wu, K.A.Spasov, C.Zhang, W.Mothes, J.M.Crawford, B.D.Lindenbach, P.D.Uchil, P.Kumar, W.L.Jorgensen, K.S.Anderson. Proof-of-Concept Studies with A Computationally Designed M Pro Inhibitor As A Synergistic Combination Regimen Alternative to Paxlovid. Proc.Natl.Acad.Sci.Usa V. 121 13121 2024.
ISSN: ESSN 1091-6490
PubMed: 38621119
DOI: 10.1073/PNAS.2320713121