Chlorine in PDB 7l11: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5, PDB code: 7l11 was solved by M.G.Deshmukh, J.A.Ippolito, E.A.Stone, 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)	72.46 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.888, 101.192, 103.82, 90, 90, 90
R / Rfree (%)	20.5 / 23.2

The binding sites of Chlorine atom in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5 (pdb code 7l11). 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(2019-Ncov) Main Protease in Complex with Compound 5, PDB code: 7l11:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5


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(2019-Ncov) Main Protease in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:24.6 occ:1.00 CL1 A:XF1400 0.0 24.6 1.0 C20 A:XF1400 1.8 23.8 1.0 C21 A:XF1400 2.7 19.0 1.0 C19 A:XF1400 2.8 19.5 1.0 C A:ASP187 3.4 20.6 1.0 O A:ASP187 3.4 19.6 1.0 CB A:HIS41 3.7 20.0 1.0 CE A:MET49 3.7 31.6 1.0 N A:ARG188 3.8 21.4 1.0 OH A:TYR54 3.8 16.9 1.0 CB A:ASP187 3.8 17.5 1.0 CA A:ASP187 3.8 18.9 1.0 CG A:HIS41 3.9 18.9 1.0 CD2 A:HIS41 4.0 21.1 1.0 CA A:ARG188 4.0 23.4 1.0 C22 A:XF1400 4.1 22.4 1.0 C18 A:XF1400 4.1 18.7 1.0 C26 A:XF1400 4.6 21.2 1.0 C A:ARG188 4.6 24.7 1.0 ND1 A:HIS41 4.6 20.1 1.0 SD A:MET165 4.7 25.6 1.0 CG A:MET165 4.8 21.6 1.0 NE2 A:HIS41 4.8 23.0 1.0 CG A:ASP187 5.0 18.6 1.0 SD A:MET49 5.0 43.0 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 5


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(2019-Ncov) Main Protease in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl400 b:27.8 occ:1.00 CL1 B:XF1400 0.0 27.8 1.0 C20 B:XF1400 1.8 25.4 1.0 C21 B:XF1400 2.7 22.0 1.0 C19 B:XF1400 2.8 25.1 1.0 C B:ASP187 3.4 20.6 1.0 O B:ASP187 3.5 20.5 1.0 N B:ARG188 3.7 19.9 1.0 CA B:ASP187 3.7 18.6 1.0 CB B:HIS41 3.7 17.9 1.0 CD2 B:HIS41 3.7 20.1 1.0 CG B:HIS41 3.8 18.4 1.0 CB B:ASP187 3.8 17.4 1.0 CG B:MET49 3.8 29.3 1.0 SD B:MET49 3.8 41.8 1.0 C22 B:XF1400 4.0 23.9 1.0 C18 B:XF1400 4.1 22.0 1.0 CA B:ARG188 4.1 22.9 1.0 OH B:TYR54 4.2 17.8 1.0 C B:ARG188 4.2 25.9 1.0 N B:GLN189 4.4 24.4 1.0 SD B:MET165 4.5 26.6 1.0 C26 B:XF1400 4.6 21.3 1.0 CG B:MET165 4.6 22.4 1.0 NE2 B:HIS41 4.6 21.3 1.0 ND1 B:HIS41 4.7 21.8 1.0 O B:ARG188 4.7 23.7 1.0 CE B:MET49 4.8 27.1 1.0 CB B:MET49 4.9 33.6 1.0

C.H.Zhang, E.A.Stone, M.Deshmukh, J.A.Ippolito, M.M.Ghahremanpour, J.Tirado-Rives, K.A.Spasov, S.Zhang, Y.Takeo, S.N.Kudalkar, Z.Liang, F.Isaacs, B.Lindenbach, S.J.Miller, K.S.Anderson, W.L.Jorgensen. Potent Noncovalent Inhibitors of the Main Protease of Sars-Cov-2 From Molecular Sculpting of the Drug Perampanel Guided By Free Energy Perturbation Calculations Acs Central Science 2021.
DOI: 10.1021/ACSCENTSCI.1C00039