Chlorine in PDB 8cyu: Crystal Structure of Sars-Cov-2 Mpro with Compound C5

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C5:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Mpro with Compound C5, PDB code: 8cyu was solved by L.J.Worrall, J.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.75 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.29, 102.64, 102.2, 90, 100.25, 90
R / Rfree (%)	21.2 / 24.5

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5 (pdb code 8cyu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5, PDB code: 8cyu:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


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 Sars-Cov-2 Mpro with Compound C5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:35.4 occ:1.00 CL01 A:P5X401 0.0 35.4 1.0 C18 A:P5X401 1.8 31.8 1.0 C09 A:P5X401 2.8 32.1 1.0 C12 A:P5X401 2.8 32.5 1.0 CE A:MET165 3.2 36.8 1.0 CA A:ASP187 3.4 27.5 1.0 CB A:ASP187 3.4 26.5 1.0 O A:HIS164 3.7 23.9 1.0 ND1 A:HIS41 3.7 24.2 1.0 CB A:MET165 3.7 30.1 1.0 CB A:HIS164 3.7 22.4 1.0 CZ A:PHE181 4.0 25.9 1.0 C19 A:P5X401 4.0 31.1 1.0 CE1 A:HIS41 4.1 23.7 1.0 C A:HIS164 4.1 23.5 1.0 S01 A:P5X401 4.2 37.2 1.0 C A:ASP187 4.3 29.3 1.0 O A:VAL186 4.4 27.9 1.0 N A:ASP187 4.4 27.7 1.0 ND1 A:HIS164 4.5 22.6 1.0 CA A:HIS164 4.5 22.2 1.0 CA A:MET165 4.6 27.0 1.0 CE A:MET49 4.6 43.1 1.0 CG A:HIS164 4.6 22.2 1.0 N A:MET165 4.6 24.3 1.0 SD A:MET165 4.6 40.4 1.0 CG A:MET165 4.7 32.5 1.0 O A:HOH601 4.7 22.3 1.0 N A:ARG188 4.7 30.9 1.0 C A:VAL186 4.8 28.1 1.0 CE1 A:PHE181 4.8 26.0 1.0 CE2 A:PHE181 4.9 25.1 1.0 CG A:HIS41 4.9 23.9 1.0 O A:ASP187 4.9 29.2 1.0 CG A:ASP187 4.9 26.6 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


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 Sars-Cov-2 Mpro with Compound C5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:24.9 occ:1.00 CL01 B:P5X401 0.0 24.9 1.0 C18 B:P5X401 1.8 26.3 1.0 C09 B:P5X401 2.7 25.9 1.0 C12 B:P5X401 2.8 27.0 1.0 CB B:ASP187 3.4 25.1 1.0 CA B:ASP187 3.4 25.3 1.0 CB B:MET165 3.6 22.9 1.0 ND1 B:HIS41 3.7 27.6 1.0 O B:HIS164 3.7 19.6 1.0 CB B:HIS164 3.7 17.4 1.0 CE B:MET165 3.8 29.3 1.0 C19 B:P5X401 4.0 27.2 1.0 CZ B:PHE181 4.0 19.9 1.0 CE1 B:HIS41 4.1 28.1 1.0 C B:HIS164 4.2 18.5 1.0 S01 B:P5X401 4.3 28.3 1.0 O B:VAL186 4.3 23.1 1.0 C B:ASP187 4.3 26.9 1.0 N B:ASP187 4.4 24.0 1.0 ND1 B:HIS164 4.5 17.2 1.0 CA B:HIS164 4.5 17.4 1.0 CA B:MET165 4.6 21.2 1.0 CE B:MET49 4.6 33.5 1.0 CG B:HIS164 4.6 16.7 1.0 N B:MET165 4.6 18.8 1.0 CG B:MET165 4.7 26.6 1.0 C B:VAL186 4.7 23.3 1.0 SD B:MET165 4.7 30.0 1.0 O B:HOH603 4.7 16.4 1.0 CE2 B:PHE181 4.7 19.2 1.0 CE1 B:PHE181 4.8 20.4 1.0 N B:ARG188 4.9 28.8 1.0 CG B:ASP187 4.9 25.6 1.0 CG B:HIS41 5.0 26.9 1.0 O B:ASP187 5.0 27.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:29.1 occ:1.00 CL01 C:P5X401 0.0 29.1 1.0 C18 C:P5X401 1.8 28.5 1.0 C09 C:P5X401 2.7 26.7 1.0 C12 C:P5X401 2.8 26.9 1.0 CB C:ASP187 3.4 25.9 1.0 CA C:ASP187 3.4 25.6 1.0 CB C:HIS164 3.7 20.1 1.0 ND1 C:HIS41 3.7 28.6 1.0 CB C:MET165 3.8 27.8 1.0 O C:HIS164 3.9 22.3 1.0 CZ C:PHE181 3.9 22.6 1.0 C19 C:P5X401 4.0 26.9 1.0 C C:HIS164 4.2 21.6 1.0 CE1 C:HIS41 4.2 29.3 1.0 S01 C:P5X401 4.2 31.5 1.0 O C:VAL186 4.2 24.1 1.0 C C:ASP187 4.3 27.7 1.0 CG C:MET165 4.3 29.2 1.0 N C:ASP187 4.4 24.9 1.0 ND1 C:HIS164 4.4 20.3 1.0 CE C:MET49 4.5 31.4 1.0 CG C:HIS164 4.5 19.6 1.0 CA C:HIS164 4.6 20.1 1.0 O C:HOH593 4.6 20.9 1.0 CE C:MET165 4.6 37.0 1.0 C C:VAL186 4.7 24.4 1.0 N C:MET165 4.7 22.4 1.0 CA C:MET165 4.7 24.3 1.0 CE2 C:PHE181 4.7 21.2 1.0 CE1 C:PHE181 4.8 22.7 1.0 SD C:MET165 4.8 34.9 1.0 N C:ARG188 4.8 28.9 1.0 CG C:ASP187 4.8 26.7 1.0 O C:ASP187 4.9 27.5 1.0 CG C:HIS41 5.0 28.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Mpro with Compound C5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:38.3 occ:1.00 CL01 D:P5X401 0.0 38.3 1.0 C18 D:P5X401 1.8 31.3 1.0 C12 D:P5X401 2.8 34.3 1.0 C09 D:P5X401 2.8 33.2 1.0 CB D:ASP187 3.3 24.6 1.0 CA D:ASP187 3.3 25.7 1.0 CE D:MET165 3.5 40.3 1.0 CB D:MET165 3.7 29.1 1.0 CB D:HIS164 3.7 22.0 1.0 O D:HIS164 3.7 22.9 1.0 ND1 D:HIS41 3.7 25.2 1.0 CZ D:PHE181 3.9 24.3 1.0 C19 D:P5X401 4.0 31.4 1.0 C D:HIS164 4.1 23.1 1.0 CE1 D:HIS41 4.1 25.2 1.0 S01 D:P5X401 4.2 39.0 1.0 C D:ASP187 4.2 27.4 1.0 N D:ASP187 4.3 26.0 1.0 O D:VAL186 4.3 27.2 1.0 CA D:HIS164 4.5 21.7 1.0 ND1 D:HIS164 4.5 22.8 1.0 CA D:MET165 4.5 25.9 1.0 O D:HOH620 4.6 19.0 1.0 CG D:HIS164 4.6 22.2 1.0 N D:MET165 4.6 23.3 1.0 CE D:MET49 4.6 37.4 1.0 CG D:MET165 4.7 32.4 1.0 CE1 D:PHE181 4.7 24.3 1.0 C D:VAL186 4.7 26.8 1.0 N D:ARG188 4.7 29.0 1.0 CE2 D:PHE181 4.8 23.7 1.0 CG D:ASP187 4.8 24.7 1.0 O D:ASP187 4.9 27.2 1.0 SD D:MET165 4.9 44.4 1.0 CG D:HIS41 4.9 24.7 1.0

J.Perez-Vargas, L.J.Worrall, A.D.Olmstead, A.T.Ton, J.Lee, I.Villanueva, C.A.H.Thompson, S.Dudek, S.Ennis, J.R.Smith, T.Shapira, J.De Guzman, S.Gang, F.Ban, M.Vuckovic, M.Bielecki, S.Kovacic, C.Kenward, C.Y.Hong, D.G.Gordon, P.N.Levett, M.Krajden, R.Leduc, P.L.Boudreault, M.Niikura, M.Paetzel, R.N.Young, A.Cherkasov, N.C.J.Strynadka, F.Jean. A Novel Class of Broad-Spectrum Active-Site-Directed 3C-Like Protease Inhibitors with Nanomolar Antiviral Activity Against Highly Immune-Evasive Sars-Cov-2 Omicron Subvariants. Emerg Microbes Infect V. 12 46594 2023.
ISSN: ESSN 2222-1751
PubMed: 37555275
DOI: 10.1080/22221751.2023.2246594