Chlorine in PDB 8udq: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1, PDB code: 8udq was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.24 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.274, 80.979, 51.97, 90, 114.55, 90
R / Rfree (%)	17.4 / 21.7

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1 (pdb code 8udq). 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 3CL Protease with Inhibitor 1, PDB code: 8udq:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1


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 3CL Protease with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:115.4 occ:1.00 CL1 A:WC0401 0.0 115.4 1.0 C5 A:WC0401 1.7 118.5 1.0 C6 A:WC0401 2.7 124.0 1.0 C4 A:WC0401 2.7 110.2 1.0 C3 A:WC0401 3.1 93.0 1.0 C17 A:WC0401 3.4 101.6 1.0 C18 A:WC0401 3.6 99.0 1.0 C2 A:WC0401 3.7 79.2 1.0 C7 A:WC0401 4.0 131.2 1.0 C9 A:WC0401 4.0 117.9 1.0 O A:ARG188 4.0 65.2 1.0 O A:GLU166 4.1 51.8 1.0 CA A:GLN189 4.3 86.6 1.0 SD A:MET165 4.3 79.6 1.0 CB A:MET165 4.3 59.5 1.0 O A:THR190 4.4 89.1 1.0 N2 A:WC0401 4.5 69.3 1.0 CG A:GLN189 4.5 96.8 1.0 C10 A:WC0401 4.5 80.5 1.0 C8 A:WC0401 4.5 125.2 1.0 C16 A:WC0401 4.6 105.3 1.0 CG A:MET165 4.7 65.8 1.0 N A:THR190 4.7 83.0 1.0 N1 A:WC0401 4.8 70.6 1.0 C A:ARG188 4.8 76.3 1.0 O1 A:WC0401 4.9 69.0 1.0 C13 A:WC0401 4.9 97.7 1.0 NE2 A:GLN192 4.9 66.2 1.0 CE A:MET165 4.9 74.8 1.0 C A:GLN189 4.9 84.0 1.0 N A:GLN189 5.0 80.3 1.0 CB A:GLN189 5.0 94.0 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 1


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 3CL Protease with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:142.1 occ:1.00 CL2 A:WC0401 0.0 142.1 1.0 C7 A:WC0401 1.7 131.2 1.0 C6 A:WC0401 2.7 124.0 1.0 C8 A:WC0401 2.7 125.2 1.0 CE A:MET49 3.4 145.8 1.0 C A:ASP187 3.5 56.6 1.0 CA A:ASP187 3.6 54.2 1.0 CB A:ASP187 3.6 54.2 1.0 ND1 A:HIS41 3.6 77.3 1.0 O A:ASP187 3.8 56.4 1.0 CG A:HIS41 3.9 76.3 1.0 N A:ARG188 3.9 63.6 1.0 C5 A:WC0401 4.0 118.5 1.0 C9 A:WC0401 4.0 117.9 1.0 CB A:HIS41 4.1 65.5 1.0 CE1 A:HIS41 4.2 74.3 1.0 SD A:MET49 4.3 144.4 1.0 C4 A:WC0401 4.5 110.2 1.0 CD2 A:HIS41 4.6 79.4 1.0 OH A:TYR54 4.6 70.0 1.0 CA A:ARG188 4.7 74.5 1.0 O A:HOH508 4.7 43.9 1.0 NE2 A:HIS41 4.7 78.2 1.0 SD A:MET165 4.8 79.6 1.0 CG A:ASP187 4.8 60.9 1.0 C A:ARG188 4.9 76.3 1.0 CB A:MET165 4.9 59.5 1.0 O A:HIS164 4.9 52.1 1.0 N A:ASP187 5.0 45.4 1.0

H.Liu, A.Zack, F.Forouhar, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, K.Choi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Small Molecule Non-Covalent Coronavirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening To Be Published.