Chlorine in PDB 7m8n: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 16

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 16:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 16, PDB code: 7m8n was solved by M.G.Deshmukh, J.A.Ippolito, 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)	29.50 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.306, 100.947, 104.137, 90, 90, 90
R / Rfree (%)	19.7 / 22.9

The binding sites of Chlorine atom in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 16 (pdb code 7m8n). 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 16, PDB code: 7m8n:
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 16


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 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:29.2 occ:1.00 CL1 A:YSP401 0.0 29.2 1.0 C27 A:YSP401 1.8 25.3 1.0 C26 A:YSP401 2.7 22.4 1.0 H20 A:YSP401 2.8 27.0 1.0 C28 A:YSP401 2.8 21.1 1.0 H21 A:YSP401 2.9 25.4 1.0 C A:ASP187 3.4 20.4 1.0 O A:ASP187 3.6 21.3 1.0 CA A:ASP187 3.7 17.9 1.0 CB A:ASP187 3.7 17.4 1.0 CB A:HIS41 3.7 20.6 1.0 N A:ARG188 3.7 20.0 1.0 CD2 A:HIS41 3.8 18.7 1.0 CG A:HIS41 3.8 20.0 1.0 OH A:TYR54 3.9 21.8 1.0 CE A:MET49 3.9 32.0 1.0 C15 A:YSP401 4.1 20.8 1.0 C17 A:YSP401 4.1 23.9 1.0 CA A:ARG188 4.3 19.6 1.0 NE2 A:HIS41 4.6 23.3 1.0 ND1 A:HIS41 4.6 22.6 1.0 C16 A:YSP401 4.6 23.6 1.0 SD A:MET165 4.7 27.6 1.0 C A:ARG188 4.8 23.9 1.0 CG A:ASP187 4.9 20.1 1.0 O A:HOH559 5.0 16.8 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 16


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 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:33.4 occ:1.00 CL1 B:YSP401 0.0 33.4 1.0 C27 B:YSP401 1.8 26.8 1.0 C26 B:YSP401 2.7 27.3 1.0 H20 B:YSP401 2.7 32.8 1.0 C28 B:YSP401 2.8 23.9 1.0 H21 B:YSP401 2.9 28.7 1.0 C B:ASP187 3.4 23.7 1.0 O B:ASP187 3.4 21.9 1.0 CB B:HIS41 3.6 19.8 1.0 CG B:HIS41 3.7 21.2 1.0 CD2 B:HIS41 3.7 21.2 1.0 N B:ARG188 3.8 22.8 1.0 CE B:MET49 3.9 37.6 1.0 CA B:ASP187 3.9 19.0 1.0 CB B:ASP187 3.9 18.8 1.0 OH B:TYR54 4.0 22.6 1.0 C15 B:YSP401 4.0 21.7 1.0 C17 B:YSP401 4.1 26.1 1.0 CE B:MET165 4.1 20.2 1.0 CA B:ARG188 4.2 24.4 1.0 SD B:MET49 4.3 62.2 1.0 ND1 B:HIS41 4.4 22.8 1.0 NE2 B:HIS41 4.6 22.3 1.0 CG B:MET49 4.6 45.5 1.0 C16 B:YSP401 4.6 21.5 1.0 C B:ARG188 4.6 24.8 1.0 N B:GLN189 4.9 26.7 1.0 CE1 B:HIS41 4.9 26.4 1.0 O B:HOH533 4.9 15.0 1.0

M.G.Deshmukh, J.A.Ippolito, C.-H.Zhang, E.A.Stone, R.A.Reilly, S.J.Miller, W.L.Jorgensen, K.S.Anderson. Structure-Guided Design of A Perampanel-Derived Pharmacophore Targeting the Sars-Cov-2 Main Protease Structure 2021.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2021.06.002