Chlorine in PDB 7rls: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68:
3.4.22.69;

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68, PDB code: 7rls was solved by A.Kovalevsky, D.W.Kneller, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.34 / 2.00
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.205, 82.175, 91.33, 90, 95.5, 90
R / Rfree (%)	16.2 / 20.1

The binding sites of Chlorine atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68 (pdb code 7rls). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68, PDB code: 7rls:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:39.5 occ:1.00 CL15 A:5YN401 0.0 39.5 1.0 C14 A:5YN401 1.7 40.5 1.0 C13 A:5YN401 2.7 40.2 1.0 C16 A:5YN401 2.7 36.8 1.0 CL17 A:5YN401 3.2 40.9 1.0 N A:ARG188 3.6 27.1 1.0 C A:ASP187 3.7 35.4 1.0 CA A:ASP187 3.8 24.6 1.0 SD A:MET165 3.8 37.9 1.0 C12 A:5YN401 4.0 41.8 1.0 C10 A:5YN401 4.0 35.8 1.0 C A:ARG188 4.0 53.1 1.0 O A:ARG188 4.1 49.5 1.0 CA A:ARG188 4.1 43.6 1.0 CD2 A:HIS41 4.2 30.3 1.0 CB A:ASP187 4.2 21.2 1.0 CB A:MET165 4.3 21.6 1.0 O A:ASP187 4.3 28.8 1.0 CG A:GLN189 4.5 59.2 1.0 N A:GLN189 4.5 61.5 1.0 C11 A:5YN401 4.5 34.5 1.0 O A:VAL186 4.7 28.1 1.0 CG A:HIS41 4.7 32.4 1.0 CG A:MET165 4.8 25.7 1.0 O A:HIS164 4.8 28.3 1.0 NE2 A:HIS41 4.9 29.1 1.0 CD A:GLN189 4.9 62.4 1.0 CB A:HIS41 5.0 26.8 1.0 NE2 A:GLN189 5.0 66.8 1.0

Chlorine binding site 2 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:40.9 occ:1.00 CL17 A:5YN401 0.0 40.9 1.0 C13 A:5YN401 1.7 40.2 1.0 C12 A:5YN401 2.7 41.8 1.0 C14 A:5YN401 2.8 40.5 1.0 CL25 A:5YN401 3.1 42.6 1.0 CL15 A:5YN401 3.2 39.5 1.0 O A:ASP187 3.6 28.8 1.0 OH A:TYR54 3.6 29.9 1.0 CB A:HIS41 3.7 26.8 1.0 CA A:ARG188 3.8 43.6 1.0 C A:ASP187 3.9 35.4 1.0 N A:ARG188 4.0 27.1 1.0 C11 A:5YN401 4.0 34.5 1.0 C16 A:5YN401 4.1 36.8 1.0 CG A:GLN189 4.2 59.2 1.0 N A:GLN189 4.3 61.5 1.0 CG A:HIS41 4.3 32.4 1.0 C A:ARG188 4.3 53.1 1.0 O A:MET49 4.3 60.9 1.0 SG A:CYS44 4.5 51.1 1.0 C10 A:5YN401 4.6 35.8 1.0 CD2 A:HIS41 4.7 30.3 1.0 CA A:MET49 4.8 62.9 1.0 CA A:ASP187 4.8 24.6 1.0 CG A:MET49 4.9 67.6 1.0 CZ A:TYR54 4.9 28.8 1.0 CA A:HIS41 4.9 28.7 1.0 CB A:CYS44 4.9 46.2 1.0 CB A:ASP187 4.9 21.2 1.0 CG A:PRO52 5.0 49.8 1.0 CB A:ARG188 5.0 46.4 1.0

Chlorine binding site 3 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-68 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:42.6 occ:1.00 CL25 A:5YN401 0.0 42.6 1.0 C12 A:5YN401 1.8 41.8 1.0 C11 A:5YN401 2.7 34.5 1.0 C13 A:5YN401 2.7 40.2 1.0 CL17 A:5YN401 3.1 40.9 1.0 CG A:MET49 3.4 67.6 1.0 CB A:CYS44 3.5 46.2 1.0 O A:HOH518 3.8 37.1 1.0 O A:HIS41 4.0 32.5 1.0 C14 A:5YN401 4.0 40.5 1.0 C10 A:5YN401 4.0 35.8 1.0 CB A:HIS41 4.2 26.8 1.0 SG A:CYS44 4.3 51.1 1.0 SD A:MET49 4.4 86.9 1.0 C16 A:5YN401 4.5 36.8 1.0 CB A:MET49 4.6 67.9 1.0 CG A:HIS41 4.6 32.4 1.0 ND1 A:HIS41 4.6 31.0 1.0 CA A:MET49 4.6 62.9 1.0 CA A:CYS44 4.8 40.8 1.0 C A:HIS41 4.9 26.1 1.0 O A:CYS44 4.9 55.2 1.0 C A:CYS44 4.9 53.9 1.0 OE1 A:GLN189 4.9 66.9 1.0 CG A:GLN189 4.9 59.2 1.0 O A:THR45 4.9 67.6 1.0

D.W.Kneller, H.Li, S.Galanie, G.Phillips, A.Labbe, K.L.Weiss, Q.Zhang, M.A.Arnould, A.Clyde, H.Ma, A.Ramanathan, C.B.Jonsson, M.S.Head, L.Coates, J.M.Louis, P.V.Bonnesen, A.Kovalevsky. Structural, Electronic, and Electrostatic Determinants For Inhibitor Binding to Subsites S1 and S2 in Sars-Cov-2 Main Protease. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34705466
DOI: 10.1021/ACS.JMEDCHEM.1C01475