Chlorine in PDB 7vvt: Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor

All present enzymatic activity of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor:
3.4.22.69;

The structure of Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor, PDB code: 7vvt was solved by H.Su, T.Nie, M.Li, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.25 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.992, 90.12, 103.175, 90, 90, 90
R / Rfree (%)	23.4 / 25.3

The binding sites of Chlorine atom in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor (pdb code 7vvt). 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 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor, PDB code: 7vvt:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor


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 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:63.2 occ:1.00 CL1 A:80X401 0.0 63.2 1.0 C11 A:80X401 1.7 63.4 1.0 C12 A:80X401 2.7 62.6 1.0 C10 A:80X401 2.7 62.9 1.0 SD A:MET165 3.7 52.5 1.0 C A:ASP187 3.8 42.8 1.0 N A:ARG188 3.8 45.0 1.0 O A:ARG188 3.8 45.4 1.0 CA A:ASP187 3.9 40.2 1.0 C A:ARG188 3.9 46.6 1.0 CB A:MET165 3.9 48.0 1.0 CG A:GLN189 3.9 58.6 1.0 C9 A:80X401 4.0 61.8 1.0 C7 A:80X401 4.0 62.2 1.0 CA A:ARG188 4.3 45.7 1.0 O A:ASP187 4.3 43.6 1.0 CB A:ASP187 4.4 39.1 1.0 N A:GLN189 4.4 48.0 1.0 CG A:MET165 4.4 50.0 1.0 C8 A:80X401 4.5 61.6 1.0 O A:VAL186 4.6 38.2 1.0 CA A:GLN189 4.8 50.9 1.0 OE1 A:GLN189 4.8 63.7 1.0 O A:HIS164 4.8 40.6 1.0 CD A:GLN189 4.9 61.5 1.0 CB A:GLN189 5.0 55.0 1.0

Chlorine binding site 2 out of 2 in the Sars-Cov-2 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor


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 3CL Protease (3CLPRO) in Complex with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:86.7 occ:1.00 CL1 B:80X401 0.0 86.7 1.0 C11 B:80X401 1.7 86.6 1.0 C12 B:80X401 2.7 85.4 1.0 C10 B:80X401 2.7 87.2 1.0 N B:ARG188 3.4 58.3 1.0 SD B:MET165 3.4 64.3 1.0 C B:ARG188 3.5 74.0 1.0 O B:ARG188 3.6 75.0 1.0 C B:ASP187 3.6 53.2 1.0 N B:GLN189 3.7 82.9 1.0 CA B:ASP187 3.7 47.7 1.0 CA B:ARG188 3.8 64.6 1.0 C9 B:80X401 4.0 86.9 1.0 C7 B:80X401 4.0 85.3 1.0 CB B:MET165 4.1 57.8 1.0 O B:ASP187 4.2 53.5 1.0 CA B:GLN189 4.2 90.7 1.0 O B:VAL186 4.3 40.3 1.0 CG B:MET165 4.4 60.2 1.0 CB B:ASP187 4.5 45.9 1.0 C8 B:80X401 4.5 86.5 1.0 CB B:GLN189 4.8 93.3 1.0 CD2 B:HIS41 4.8 40.7 1.0 N B:ASP187 4.9 44.2 1.0 O2 B:80X401 5.0 82.8 1.0 CE B:MET165 5.0 66.6 1.0

M.Xiong, T.Nie, Q.Shao, M.Li, H.Su, Y.Xu. In Silico Screening-Based Discovery of Novel Covalent Inhibitors of the Sars-Cov-2 3CL Protease. Eur.J.Med.Chem. V. 231 14130 2022.
ISSN: ISSN 0223-5234
PubMed: 35114541
DOI: 10.1016/J.EJMECH.2022.114130