Chlorine in PDB 7l10: Crystal Structure of the Sars-Cov-2 (2019-Ncov) Main Protease in Complex with Compound 4

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 (2019-Ncov) Main Protease in Complex with Compound 4:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 (2019-Ncov) Main Protease in Complex with Compound 4, PDB code: 7l10 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)	29.63 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.22, 80.869, 54.51, 90, 116.64, 90
R / Rfree (%)	22.4 / 25.1

The binding sites of Chlorine atom in the Crystal Structure of the Sars-Cov-2 (2019-Ncov) Main Protease in Complex with Compound 4 (pdb code 7l10). 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 4, PDB code: 7l10:
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 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:37.5 occ:1.00 CL1 A:XEY400 0.0 37.5 1.0 C1 A:XEY400 1.8 31.2 1.0 C3 A:XEY400 2.7 32.6 1.0 C2 A:XEY400 2.7 26.2 1.0 CE A:MET49 3.3 50.9 1.0 C A:ASP187 3.4 26.6 1.0 O A:ASP187 3.5 28.9 1.0 CB A:HIS41 3.7 26.4 1.0 CA A:ASP187 3.7 22.0 1.0 N A:ARG188 3.7 23.3 1.0 CB A:ASP187 3.7 22.1 1.0 CD2 A:HIS41 3.8 22.9 1.0 CG A:HIS41 3.8 24.6 1.0 C7 A:XEY400 4.0 33.4 1.0 C4 A:XEY400 4.0 26.9 1.0 OH A:TYR54 4.0 26.7 1.0 CA A:ARG188 4.3 33.2 1.0 SD A:MET49 4.5 64.5 1.0 SD A:MET165 4.5 34.2 1.0 CG A:MET165 4.5 24.3 1.0 C6 A:XEY400 4.5 31.2 1.0 NE2 A:HIS41 4.6 25.9 1.0 ND1 A:HIS41 4.7 25.4 1.0 C A:ARG188 4.8 36.5 1.0 O A:ARG188 4.9 32.5 1.0 CG A:ASP187 4.9 22.1 1.0 O A:HOH604 4.9 21.6 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 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl400 b:37.7 occ:1.00 CL2 A:XEY400 0.0 37.7 1.0 C7 A:XEY400 1.8 33.4 1.0 C3 A:XEY400 2.7 32.6 1.0 C6 A:XEY400 2.7 31.2 1.0 OE1 A:GLN189 3.5 57.1 1.0 O A:HOH579 3.5 34.4 1.0 SD A:MET165 4.0 34.2 1.0 C1 A:XEY400 4.0 31.2 1.0 C4 A:XEY400 4.0 26.9 1.0 O A:HOH574 4.1 35.7 1.0 O A:ARG188 4.1 32.5 1.0 CD A:GLN189 4.3 56.0 1.0 O A:GLU166 4.3 28.6 1.0 C2 A:XEY400 4.6 26.2 1.0 CG A:MET165 4.7 24.3 1.0 CB A:MET165 4.7 22.5 1.0 NE2 A:GLN189 4.8 57.9 1.0 CA A:GLN189 4.8 41.4 1.0 O1 A:XEY400 4.9 23.9 1.0 C A:ARG188 4.9 36.5 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