Chlorine in PDB 7m8p: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23, PDB code: 7m8p 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)	72.43 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.181, 100.606, 104.355, 90, 90, 90
R / Rfree (%)	18.5 / 23.1

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23 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(2019-Ncov) Main Protease in Complex with Compound 23 (pdb code 7m8p). 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 23, PDB code: 7m8p:
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 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:58.7 occ:1.00 CL1 A:YSJ401 0.0 58.7 1.0 C1 A:YSJ401 1.8 50.4 1.0 C27 A:YSJ401 2.7 55.1 1.0 C2 A:YSJ401 2.8 43.0 1.0 F1 A:YSJ401 2.8 54.7 1.0 H1 A:YSJ401 3.0 51.6 1.0 C A:ASP187 3.6 42.1 1.0 CB A:ASP187 3.7 38.0 1.0 CA A:ASP187 3.7 39.4 1.0 CD2 A:HIS41 3.8 38.2 1.0 O A:ASP187 3.8 38.8 1.0 CB A:HIS41 3.8 35.9 1.0 CG A:HIS41 3.8 36.4 1.0 N A:ARG188 4.0 42.7 1.0 C19 A:YSJ401 4.0 56.0 1.0 C3 A:YSJ401 4.1 43.0 1.0 OH A:TYR54 4.3 36.2 1.0 CA A:ARG188 4.4 43.2 1.0 SD A:MET165 4.5 49.8 1.0 NE2 A:HIS41 4.5 40.4 1.0 ND1 A:HIS41 4.6 37.4 1.0 C18 A:YSJ401 4.6 53.9 1.0 SD A:MET49 4.6 73.8 1.0 O A:HOH551 4.8 30.5 1.0 CG A:ASP187 4.9 40.5 1.0 C A:ARG188 4.9 45.5 1.0 CB A:MET165 4.9 38.4 1.0 CE1 A:HIS41 5.0 40.8 1.0 CE A:MET49 5.0 64.9 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 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:74.9 occ:1.00 CL2 A:YSJ401 0.0 74.9 1.0 C22 A:YSJ401 1.8 55.7 1.0 H13 A:YSJ401 2.6 69.6 1.0 C21 A:YSJ401 2.7 55.7 1.0 C23 A:YSJ401 2.8 52.8 1.0 H14 A:YSJ401 2.9 63.4 1.0 C20 A:YSJ401 3.0 58.0 1.0 O4 A:YSJ401 3.4 60.7 1.0 NE2 A:GLN192 3.5 42.4 1.0 SD A:MET165 3.8 49.8 1.0 CD2 A:LEU167 3.9 48.7 1.0 H12 A:YSJ401 4.0 69.6 1.0 C26 A:YSJ401 4.0 58.1 1.0 C24 A:YSJ401 4.0 52.5 1.0 C19 A:YSJ401 4.1 56.0 1.0 F1 A:YSJ401 4.1 54.7 1.0 CD A:GLN192 4.2 50.2 1.0 O A:ARG188 4.3 41.1 1.0 CE A:MET165 4.3 41.3 1.0 C27 A:YSJ401 4.3 55.1 1.0 O A:GLU166 4.3 41.4 1.0 CG A:GLN192 4.4 49.9 1.0 CG A:MET165 4.5 36.2 1.0 C25 A:YSJ401 4.5 54.5 1.0 CA A:LEU167 4.6 45.3 1.0 CD A:PRO168 4.7 51.4 1.0 O A:THR190 4.8 49.8 1.0 CB A:MET165 4.9 38.4 1.0 H17 A:YSJ401 4.9 69.7 1.0 CA A:GLN189 4.9 48.0 1.0 H15 A:YSJ401 4.9 63.0 1.0 C A:GLU166 4.9 43.1 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