Chlorine in PDB 8udm: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16, PDB code: 8udm 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)	48.37 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.846, 82.178, 54.583, 90, 117.6, 90
R / Rfree (%)	16.3 / 17.9

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16 (pdb code 8udm). 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 16, PDB code: 8udm:
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 16


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 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:30.5 occ:1.00 CL1 A:WBE401 0.0 30.5 1.0 C5 A:WBE401 1.7 24.8 1.0 C6 A:WBE401 2.7 23.9 1.0 C4 A:WBE401 2.7 26.3 1.0 C3 A:WBE401 3.1 24.7 1.0 C17 A:WBE401 3.4 29.7 1.0 C18 A:WBE401 3.5 29.4 1.0 O A:HOH629 3.6 33.1 1.0 C2 A:WBE401 3.6 21.3 1.0 SD A:MET165 3.8 32.0 1.0 CA A:GLN189 3.9 32.9 1.0 C7 A:WBE401 4.0 37.2 1.0 C9 A:WBE401 4.0 31.4 1.0 O A:ARG188 4.0 26.9 1.0 CB A:MET165 4.1 21.5 1.0 O A:GLU166 4.1 19.6 1.0 CG A:GLN189 4.3 33.7 1.0 N2 A:WBE401 4.3 23.3 1.0 C10 A:WBE401 4.3 23.8 1.0 O A:THR190 4.4 33.6 1.0 CG A:MET165 4.5 20.6 1.0 CB A:GLN189 4.5 34.9 1.0 N A:THR190 4.5 28.8 1.0 C8 A:WBE401 4.5 36.5 1.0 C16 A:WBE401 4.6 37.1 1.0 C A:GLN189 4.6 35.3 1.0 C A:ARG188 4.7 25.0 1.0 N A:GLN189 4.7 30.2 1.0 C13 A:WBE401 4.7 28.1 1.0 N1 A:WBE401 4.8 23.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 16


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 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:49.0 occ:1.00 CL2 A:WBE401 0.0 49.0 1.0 C7 A:WBE401 1.7 37.2 1.0 C6 A:WBE401 2.7 23.9 1.0 C8 A:WBE401 2.7 36.5 1.0 ND1 A:HIS41 3.3 24.9 1.0 CE A:MET49 3.3 78.2 1.0 C A:ASP187 3.4 21.5 1.0 CA A:ASP187 3.6 19.5 1.0 CB A:ASP187 3.6 21.7 1.0 CG A:HIS41 3.7 21.0 1.0 O A:ASP187 3.7 22.8 1.0 N A:ARG188 3.8 21.3 1.0 CE1 A:HIS41 3.9 27.3 1.0 CB A:HIS41 4.0 22.9 1.0 C5 A:WBE401 4.0 24.8 1.0 C9 A:WBE401 4.0 31.4 1.0 CA A:ARG188 4.2 23.8 1.0 C A:ARG188 4.4 25.0 1.0 CD2 A:HIS41 4.4 24.9 1.0 OH A:TYR54 4.4 26.1 1.0 NE2 A:HIS41 4.5 26.5 1.0 C4 A:WBE401 4.5 26.3 1.0 O A:HOH655 4.5 20.0 1.0 O A:HIS164 4.6 18.6 1.0 SD A:MET49 4.6 74.2 1.0 O A:ARG188 4.7 26.9 1.0 CG A:ASP187 4.8 19.3 1.0 N A:GLN189 4.8 30.2 1.0 CB A:MET165 5.0 21.5 1.0 N A:ASP187 5.0 18.8 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 Coronovirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening To Be Published.