Chlorine in PDB 8acl: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14, PDB code: 8acl was solved by N.Strater, C.Mueller, K.Sylvester, T.Claff, R.H.Weisse, S.Gao, A.E.Tollefson, X.Liu, P.Zhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.671, 81.185, 51.658, 90, 114.52, 90
R / Rfree (%)	13.8 / 17.2

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14 (pdb code 8acl). 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 Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14, PDB code: 8acl:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14


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 Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:17.3 occ:0.83 CL A:LQL401 0.0 17.3 0.8 C12 A:LQL401 1.8 16.1 0.8 C11 A:LQL401 2.7 15.2 0.8 C13 A:LQL401 2.7 17.7 0.8 H13 A:LQL401 2.8 18.3 0.8 HB3 A:MET165 2.9 22.6 0.5 HA A:ASP187 3.0 19.9 1.0 HB3 A:MET165 3.0 10.6 0.5 HD2 A:HIS41 3.0 19.7 1.0 HE2 A:MET165 3.1 13.4 0.5 CL1 A:LQL401 3.2 18.0 0.8 HB2 A:ASP187 3.4 18.3 1.0 H6 A:LQL401 3.4 20.4 0.8 HB3 A:ASP187 3.4 18.3 1.0 HB3 A:HIS164 3.5 14.1 1.0 CD2 A:HIS41 3.5 16.4 1.0 C5 A:LQL401 3.6 16.9 0.8 CB A:ASP187 3.7 15.2 1.0 S A:LQL401 3.7 20.8 0.8 O A:HIS164 3.8 13.4 1.0 CA A:ASP187 3.8 16.5 1.0 CB A:MET165 3.8 18.8 0.5 HG2 A:MET165 3.9 28.6 0.5 CB A:MET165 3.9 8.7 0.5 SD A:MET165 4.0 28.8 0.5 NE2 A:HIS41 4.0 17.3 1.0 C14 A:LQL401 4.0 15.2 0.8 C10 A:LQL401 4.0 14.0 0.8 HB2 A:MET165 4.0 10.6 0.5 HE2 A:HIS41 4.1 20.9 1.0 CE A:MET165 4.1 11.1 0.5 CG A:MET165 4.1 23.8 0.5 HZ A:PHE181 4.2 13.1 1.0 CG A:HIS41 4.2 17.7 1.0 HB3 A:HIS41 4.3 19.9 1.0 HE3 A:MET165 4.3 13.4 0.5 HB2 A:MET165 4.3 22.6 0.5 C A:HIS164 4.3 12.7 1.0 C4 A:LQL401 4.3 16.2 0.8 CB A:HIS164 4.4 11.7 1.0 HD1 A:HIS164 4.5 12.9 1.0 C A:ASP187 4.5 16.0 1.0 C15 A:LQL401 4.5 14.3 0.8 HA A:MET165 4.6 12.0 1.0 HE1 A:MET165 4.6 13.4 0.5 O A:VAL186 4.7 14.0 1.0 CA A:MET165 4.7 10.0 0.5 CA A:MET165 4.7 13.7 0.5 C2 A:LQL401 4.7 16.2 0.8 CB A:HIS41 4.7 16.5 1.0 HB2 A:HIS164 4.7 14.1 1.0 HB2 A:HIS41 4.8 19.9 1.0 CG A:MET165 4.8 7.4 0.5 N A:ASP187 4.8 15.9 1.0 O A:HOH632 4.8 15.5 1.0 N A:MET165 4.8 10.9 1.0 H5 A:LQL401 4.8 19.5 0.8 HG2 A:MET165 4.9 8.9 0.5 H14 A:LQL401 4.9 18.4 0.8 C3 A:LQL401 4.9 13.3 0.8 CE1 A:HIS41 4.9 17.2 1.0 H A:LQL401 5.0 18.7 0.8 CA A:HIS164 5.0 10.5 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14


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 Sars-Cov-2 Main Protease (Mpro) in Complex with the Non-Covalent Inhibitor Gc-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:18.0 occ:0.83 CL1 A:LQL401 0.0 18.0 0.8 C13 A:LQL401 1.7 17.7 0.8 C14 A:LQL401 2.7 15.2 0.8 C12 A:LQL401 2.7 16.1 0.8 HE1 A:MET49 2.8 81.0 1.0 H14 A:LQL401 2.8 18.4 0.8 HB2 A:ASP187 3.0 18.3 1.0 HE2 A:MET49 3.1 81.0 1.0 O A:ASP187 3.1 17.6 1.0 HB2 A:HIS41 3.1 19.9 1.0 HB3 A:HIS41 3.2 19.9 1.0 CL A:LQL401 3.2 17.3 0.8 C A:ASP187 3.3 16.0 1.0 CE A:MET49 3.4 67.5 1.0 HA A:ASP187 3.4 19.9 1.0 H5 A:LQL401 3.4 19.5 0.8 HH A:TYR54 3.5 19.6 1.0 CB A:HIS41 3.5 16.5 1.0 OH A:TYR54 3.6 16.3 1.0 C4 A:LQL401 3.7 16.2 0.8 CA A:ASP187 3.7 16.5 1.0 H6 A:LQL401 3.7 20.4 0.8 CB A:ASP187 3.7 15.2 1.0 HA A:ARG188 3.8 21.2 1.0 C5 A:LQL401 3.8 16.9 0.8 N A:ARG188 3.9 17.0 1.0 HE3 A:MET49 3.9 81.0 1.0 C15 A:LQL401 4.0 14.3 0.8 C11 A:LQL401 4.0 15.2 0.8 CG A:HIS41 4.0 17.7 1.0 HD2 A:HIS41 4.2 19.7 1.0 HB3 A:ASP187 4.2 18.3 1.0 CD2 A:HIS41 4.3 16.4 1.0 CA A:ARG188 4.3 17.6 1.0 H A:ARG188 4.4 20.5 1.0 C10 A:LQL401 4.5 14.0 0.8 SG A:CYS44 4.5 52.1 1.0 C3 A:LQL401 4.5 13.3 0.8 HG A:CYS44 4.8 62.6 1.0 SD A:MET49 4.8 66.7 1.0 HA A:HIS41 4.8 18.5 1.0 H15 A:LQL401 4.8 17.2 0.8 CG A:ASP187 4.8 15.2 1.0 H13 A:LQL401 4.9 18.3 0.8 CA A:HIS41 4.9 15.4 1.0 ND1 A:HIS41 4.9 17.5 1.0 CZ A:TYR54 4.9 14.6 1.0 S A:LQL401 5.0 20.8 0.8 H4 A:LQL401 5.0 16.0 0.8 C A:ARG188 5.0 16.8 1.0

S.Gao, K.Sylvester, L.Song, T.Claff, L.Jing, M.Woodson, R.H.Weisse, Y.Cheng, L.Schakel, M.Petry, M.Gutschow, A.C.Schiedel, N.Strater, D.Kang, S.Xu, K.Toth, J.Tavis, A.E.Tollefson, C.E.Muller, X.Liu, P.Zhan. Discovery and Crystallographic Studies of Trisubstituted Piperazine Derivatives As Non-Covalent Sars-Cov-2 Main Protease Inhibitors with High Target Specificity and Low Toxicity. J.Med.Chem. V. 65 13343 2022.
ISSN: ISSN 0022-2623
PubMed: 36107752
DOI: 10.1021/ACS.JMEDCHEM.2C01146