Chlorine in PDB 7l13: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 21

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 21:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 21, PDB code: 7l13 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)	29.53 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.805, 101.22, 104.037, 90, 90, 90
R / Rfree (%)	19.7 / 24.8

The binding sites of Chlorine atom in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 21 (pdb code 7l13). 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 21, PDB code: 7l13:
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 21


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 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:42.9 occ:1.00 CL23 A:XF7401 0.0 42.9 1.0 C7 A:XF7401 1.8 39.4 1.0 C8 A:XF7401 2.8 36.8 1.0 C5 A:XF7401 2.8 30.2 1.0 CE A:MET49 3.3 45.3 1.0 C A:ASP187 3.4 31.8 1.0 O A:ASP187 3.5 27.6 1.0 CD2 A:HIS41 3.6 24.9 1.0 CB A:HIS41 3.7 27.1 1.0 CG A:HIS41 3.7 24.2 1.0 CA A:ASP187 3.7 27.7 1.0 N A:ARG188 3.7 32.6 1.0 CB A:ASP187 3.8 29.8 1.0 OH A:TYR54 4.0 27.6 1.0 C9 A:XF7401 4.1 40.4 1.0 C4 A:XF7401 4.1 33.4 1.0 CA A:ARG188 4.2 32.2 1.0 CE A:MET165 4.3 28.8 1.0 NE2 A:HIS41 4.4 29.1 1.0 ND1 A:HIS41 4.5 28.9 1.0 C12 A:XF7401 4.6 36.6 1.0 C A:ARG188 4.8 35.3 1.0 CE1 A:HIS41 4.9 29.5 1.0 SD A:MET49 4.9 50.5 1.0 CG A:ASP187 5.0 27.2 1.0 O A:HOH559 5.0 25.1 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 21


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 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:56.5 occ:1.00 CL24 A:XF7401 0.0 56.5 1.0 C36 A:XF7401 1.8 42.9 1.0 C11 A:XF7401 2.7 41.5 1.0 C35 A:XF7401 2.8 39.1 1.0 C10 A:XF7401 3.0 37.0 1.0 CE A:MET165 3.3 28.8 1.0 O22 A:XF7401 3.3 43.2 1.0 NE2 A:GLN192 3.3 32.0 1.0 CD2 A:LEU167 3.6 35.8 1.0 C32 A:XF7401 4.0 43.7 1.0 CD A:GLN192 4.1 38.9 1.0 C34 A:XF7401 4.1 40.5 1.0 C9 A:XF7401 4.2 40.4 1.0 SD A:MET165 4.2 46.6 1.0 CG A:GLN192 4.3 34.1 1.0 O A:ARG188 4.4 32.3 1.0 CA A:LEU167 4.4 38.4 1.0 O A:GLU166 4.4 31.9 1.0 CD A:PRO168 4.4 42.3 1.0 O A:THR190 4.5 34.4 1.0 C33 A:XF7401 4.6 45.5 1.0 C8 A:XF7401 4.7 36.8 1.0 CG A:LEU167 4.7 33.9 1.0 CB A:MET165 4.7 29.7 1.0 CG A:MET165 4.8 28.4 1.0 C A:GLU166 4.9 32.3 1.0 N A:LEU167 4.9 36.5 1.0 CB A:LEU167 4.9 33.8 1.0 OE1 A:GLN192 4.9 38.2 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