Chlorine in PDB 8ue0: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47, PDB code: 8ue0 was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, K.Choi, 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)	32.71 / 2.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.309, 82.011, 52.202, 90, 115.61, 90
R / Rfree (%)	16.1 / 21.3

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 (pdb code 8ue0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47, PDB code: 8ue0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47


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 47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:81.0 occ:1.00 CL1 A:WDF401 0.0 81.0 1.0 C5 A:WDF401 1.7 74.0 1.0 C6 A:WDF401 2.7 70.4 1.0 C4 A:WDF401 2.7 70.9 1.0 C3 A:WDF401 3.1 63.6 1.0 C17 A:WDF401 3.4 65.8 1.0 C18 A:WDF401 3.5 68.7 1.0 C2 A:WDF401 3.6 61.6 1.0 O A:ARG188 3.9 59.7 1.0 C7 A:WDF401 4.0 81.2 1.0 CG A:MET165 4.0 56.8 1.0 C9 A:WDF401 4.0 72.6 1.0 O A:GLU166 4.1 44.8 1.0 CA A:GLN189 4.1 68.1 1.0 O A:THR190 4.2 64.3 1.0 CB A:MET165 4.2 49.0 1.0 C10 A:WDF401 4.3 56.2 1.0 N2 A:WDF401 4.5 59.7 1.0 C8 A:WDF401 4.5 73.9 1.0 SD A:MET165 4.6 66.7 1.0 CE A:MET165 4.6 53.4 1.0 C A:ARG188 4.6 60.7 1.0 N A:THR190 4.6 68.7 1.0 C16 A:WDF401 4.7 75.6 1.0 N1 A:WDF401 4.7 64.4 1.0 NE2 A:GLN192 4.7 59.1 1.0 N A:GLN189 4.7 63.0 1.0 C A:GLN189 4.8 69.7 1.0 C13 A:WDF401 4.8 68.2 1.0 CB A:GLN189 4.9 73.1 1.0 CG A:GLN189 4.9 75.8 1.0 O1 A:WDF401 4.9 48.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47


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 47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:94.6 occ:1.00 CL2 A:WDF401 0.0 94.6 1.0 C7 A:WDF401 1.7 81.2 1.0 C6 A:WDF401 2.7 70.4 1.0 C8 A:WDF401 2.7 73.9 1.0 C A:ASP187 3.4 54.8 1.0 CA A:ASP187 3.6 46.4 1.0 ND1 A:HIS41 3.6 58.5 1.0 CB A:ASP187 3.7 38.6 1.0 N A:ARG188 3.7 50.3 1.0 O A:ASP187 3.7 56.0 1.0 CG A:HIS41 3.8 61.6 1.0 SD A:MET49 3.9 93.3 1.0 C5 A:WDF401 4.0 74.0 1.0 C9 A:WDF401 4.0 72.6 1.0 CB A:HIS41 4.1 52.1 1.0 CA A:ARG188 4.1 59.0 1.0 CE1 A:HIS41 4.1 58.7 1.0 OH A:TYR54 4.4 58.1 1.0 C A:ARG188 4.4 60.7 1.0 CD2 A:HIS41 4.4 62.6 1.0 C4 A:WDF401 4.5 70.9 1.0 NE2 A:HIS41 4.6 57.8 1.0 SD A:MET165 4.8 66.7 1.0 O A:ARG188 4.8 59.7 1.0 CE A:MET49 4.8 99.6 1.0 O A:HOH528 4.8 46.4 1.0 N A:GLN189 4.8 63.0 1.0 CG A:MET49 4.8 85.5 1.0 CB A:MET165 4.9 49.0 1.0 CG A:ASP187 4.9 49.4 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor 47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:85.8 occ:1.00 OG A:SER81 3.4 61.9 1.0 O A:LYS88 3.6 57.0 1.0 N A:LYS90 4.0 58.4 1.0 CB A:LYS88 4.0 57.0 1.0 CB A:LYS90 4.1 70.3 1.0 N A:SER81 4.1 58.2 1.0 C A:HIS80 4.1 66.5 1.0 C A:LYS88 4.1 59.5 1.0 CB A:SER81 4.2 59.2 1.0 CA A:HIS80 4.2 62.1 1.0 N A:HIS80 4.4 53.7 1.0 O A:GLY79 4.4 60.6 1.0 C A:GLY79 4.4 62.0 1.0 O A:HIS80 4.5 56.0 1.0 CA A:LYS90 4.5 63.4 1.0 C A:LEU89 4.6 63.1 1.0 N A:LEU89 4.7 56.7 1.0 CA A:LYS88 4.7 54.2 1.0 CA A:SER81 4.7 60.5 1.0 CG A:LYS90 4.8 72.9 1.0 CA A:LEU89 4.9 58.1 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