Chlorine in PDB 8udy: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25, PDB code: 8udy 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)	43.69 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.306, 81.593, 51.806, 90, 114.87, 90
R / Rfree (%)	17.6 / 21.6

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25 also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25 (pdb code 8udy). 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 25, PDB code: 8udy:
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 25


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 25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:64.2 occ:1.00 CL1 A:WD6401 0.0 64.2 1.0 C5 A:WD6401 1.7 53.6 1.0 C6 A:WD6401 2.7 56.3 1.0 C4 A:WD6401 2.7 56.4 1.0 C3 A:WD6401 3.1 62.0 1.0 C17 A:WD6401 3.4 80.0 1.0 C18 A:WD6401 3.4 75.0 1.0 C2 A:WD6401 3.6 56.2 1.0 SD A:MET165 3.8 66.9 1.0 C7 A:WD6401 4.0 70.6 1.0 O A:GLU166 4.0 54.1 1.0 N2 A:WD6401 4.0 71.1 1.0 CA A:GLN189 4.0 64.9 1.0 C9 A:WD6401 4.0 59.1 1.0 O A:ARG188 4.1 58.2 1.0 CB A:MET165 4.2 44.7 1.0 CG A:MET165 4.2 57.5 1.0 C10 A:WD6401 4.2 68.0 1.0 O A:THR190 4.4 56.4 1.0 C16 A:WD6401 4.4 84.4 1.0 CG A:GLN189 4.5 67.2 1.0 C13 A:WD6401 4.5 77.2 1.0 C8 A:WD6401 4.5 66.7 1.0 N A:THR190 4.6 54.6 1.0 CB A:GLN189 4.6 66.5 1.0 C A:GLN189 4.7 62.9 1.0 C A:ARG188 4.7 58.8 1.0 N A:GLN189 4.8 59.5 1.0 N1 A:WD6401 4.9 56.5 1.0 C A:GLU166 5.0 50.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 25


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 25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:81.8 occ:1.00 CL2 A:WD6401 0.0 81.8 1.0 C7 A:WD6401 1.7 70.6 1.0 C6 A:WD6401 2.7 56.3 1.0 C8 A:WD6401 2.7 66.7 1.0 ND1 A:HIS41 3.4 52.8 1.0 CA A:ASP187 3.4 45.1 1.0 CB A:ASP187 3.4 45.3 1.0 C A:ASP187 3.4 49.3 1.0 N A:ARG188 3.8 46.5 1.0 CG A:HIS41 3.8 52.4 1.0 O A:ASP187 3.8 51.1 1.0 CE1 A:HIS41 3.9 53.0 1.0 C5 A:WD6401 4.0 53.6 1.0 C9 A:WD6401 4.0 59.1 1.0 CB A:HIS41 4.1 49.0 1.0 O A:HIS164 4.3 48.1 1.0 SD A:MET49 4.3 87.6 1.0 CA A:ARG188 4.3 54.5 1.0 CD2 A:HIS41 4.5 54.8 1.0 C4 A:WD6401 4.5 56.4 1.0 NE2 A:HIS41 4.5 54.2 1.0 O A:HOH532 4.6 38.8 1.0 OH A:TYR54 4.6 52.1 1.0 C A:ARG188 4.6 58.8 1.0 CB A:MET165 4.7 44.7 1.0 CG A:ASP187 4.7 44.2 1.0 CE A:MET165 4.8 53.5 1.0 N A:ASP187 4.8 41.8 1.0 O A:ARG188 4.9 58.2 1.0

H.Liu, A.Zask, F.Forouhar, S.Iketani, A.Williams, D.R.Vaz, D.Habashi, K.Choi, S.J.Resnick, S.J.Hong, D.H.Lovett, T.Bai, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Small Molecule Non-Covalent Coronavirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening. Nat Commun V. 16 152 2025.
ISSN: ESSN 2041-1723
PubMed: 39747827
DOI: 10.1038/S41467-024-55421-5