Chlorine in PDB 7xar: Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor

All present enzymatic activity of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor:
3.4.22.69;

The structure of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor, PDB code: 7xar was solved by J.M.M.Caaveiro, J.Ochi, D.Takahashi, T.Ueda, A.Ojida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.027, 63.362, 102.831, 90, 90.4, 90
R / Rfree (%)	17.3 / 20.6

The structure of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor also contains other interesting chemical elements:

Nickel	(Ni)	6 atoms
Fluorine	(F)	4 atoms

The binding sites of Chlorine atom in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor (pdb code 7xar). 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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor, PDB code: 7xar:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:61.1 occ:1.00 O A:HOH514 3.6 41.1 1.0 CA A:ASN84 3.8 19.8 1.0 O A:HOH504 3.8 43.0 1.0 C A:ASN84 4.0 19.8 1.0 NH2 A:ARG40 4.1 19.4 1.0 O A:HOH564 4.1 29.2 1.0 SG A:CYS85 4.2 19.3 1.0 CB A:ASN84 4.2 19.4 1.0 NH1 A:ARG40 4.2 20.9 1.0 OD1 A:ASN84 4.3 22.3 1.0 O A:ASN84 4.3 18.4 1.0 CZ A:ARG40 4.4 20.0 1.0 N A:CYS85 4.5 18.0 1.0 O A:HOH600 4.7 23.0 1.0 CG A:ASN84 4.8 20.1 1.0 O A:HOH591 4.9 23.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:57.8 occ:1.00 O A:HOH700 3.4 32.0 1.0 O A:TRP218 3.4 21.4 1.0 OE1 A:GLU270 3.8 31.2 1.0 CA A:PHE219 4.0 17.4 1.0 O A:PHE219 4.2 17.4 1.0 C A:PHE219 4.2 17.5 1.0 CE3 A:TRP218 4.3 21.7 1.0 O A:HOH542 4.3 20.8 1.0 C A:TRP218 4.4 20.3 1.0 CZ3 A:TRP218 4.4 20.9 1.0 CD A:GLU270 4.6 26.1 1.0 N A:PHE219 4.7 18.6 1.0 O A:LEU220 4.7 22.9 1.0 N A:LEU220 5.0 17.4 1.0

Y.Hirose, N.Shindo, M.Mori, S.Onitsuka, H.Isogai, R.Hamada, T.Hiramoto, J.Ochi, D.Takahashi, T.Ueda, J.M.M.Caaveiro, Y.Yoshida, S.Ohdo, N.Matsunaga, S.Toba, M.Sasaki, Y.Orba, H.Sawa, A.Sato, E.Kawanishi, A.Ojida. Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors For Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease. J.Med.Chem. V. 65 13852 2022.
ISSN: ISSN 0022-2623
PubMed: 36229406
DOI: 10.1021/ACS.JMEDCHEM.2C01081