Chlorine in PDB 8r12: Structure of Compound 8 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

The structure of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease, PDB code: 8r12 was solved by A.Mac Sweeney, J.Hazemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.18 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.01, 100.34, 104.55, 90, 90, 90
R / Rfree (%)	21 / 23.8

The structure of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease (pdb code 8r12). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease, PDB code: 8r12:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:31.7 occ:1.00 CL17 A:XH9401 0.0 31.7 1.0 C16 A:XH9401 1.8 30.1 1.0 C15 A:XH9401 2.7 30.2 1.0 C18 A:XH9401 2.8 29.0 1.0 O B:HOH589 3.4 27.7 1.0 OE2 A:GLU166 3.6 25.8 1.0 O A:HOH672 3.6 31.5 1.0 O B:HOH560 3.7 55.2 1.0 N B:SER1 3.8 24.4 1.0 O A:PHE140 3.8 19.1 1.0 CD A:GLU166 3.9 27.8 1.0 N19 A:XH9401 4.0 28.5 1.0 C14 A:XH9401 4.0 30.3 1.0 OE1 A:GLU166 4.1 31.5 1.0 N A:ASN142 4.1 19.6 1.0 C A:LEU141 4.2 19.6 1.0 CA A:LEU141 4.2 19.0 1.0 CB A:GLU166 4.4 21.4 1.0 C20 A:XH9401 4.5 29.2 1.0 C A:PHE140 4.7 18.4 1.0 CG A:GLU166 4.8 21.8 1.0 O A:HOH665 4.8 45.6 1.0 O A:LEU141 4.8 18.4 1.0 CA A:ASN142 4.8 21.4 1.0 N A:LEU141 4.9 17.7 1.0 OG B:SER1 4.9 36.1 1.0

Chlorine binding site 2 out of 3 in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:20.6 occ:1.00 N A:GLN107 3.2 18.0 1.0 NE2 A:GLN110 3.2 20.8 1.0 CA A:ILE106 3.8 17.3 1.0 CB A:GLN110 3.8 15.7 1.0 CG A:GLN110 3.9 15.9 1.0 CB A:ILE106 3.9 16.9 1.0 CB A:GLN107 4.0 21.1 1.0 C A:ILE106 4.0 18.1 1.0 CD A:GLN110 4.0 18.5 1.0 CG A:GLN107 4.1 26.2 1.0 CA A:GLN107 4.2 18.9 1.0 CG2 A:ILE106 4.2 17.7 1.0 O A:HOH513 4.2 41.3 1.0 O A:GLN107 4.5 18.5 1.0 C A:GLN107 4.8 19.1 1.0 O A:ARG105 4.9 19.4 1.0 O A:HOH723 4.9 25.9 1.0 O A:HOH507 5.0 36.1 1.0

Chlorine binding site 3 out of 3 in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:44.8 occ:1.00 CL17 B:XH9401 0.0 44.8 1.0 C16 B:XH9401 1.8 44.6 1.0 C18 B:XH9401 2.8 44.0 1.0 C15 B:XH9401 2.8 45.3 1.0 O B:HOH553 3.3 33.9 1.0 OE2 B:GLU166 3.4 29.8 1.0 O A:HOH685 3.5 38.1 1.0 O B:HOH645 3.5 43.5 1.0 O B:PHE140 3.8 24.7 1.0 CD B:GLU166 3.8 30.1 1.0 N A:SER1 3.8 23.3 1.0 ND2 B:ASN142 3.9 33.2 0.5 OE1 B:GLU166 3.9 30.1 1.0 N19 B:XH9401 4.0 43.8 1.0 C14 B:XH9401 4.1 45.8 1.0 CA B:LEU141 4.1 25.2 1.0 N B:ASN142 4.2 25.6 1.0 C B:LEU141 4.2 26.0 1.0 CB B:GLU166 4.4 21.8 1.0 C20 B:XH9401 4.5 44.7 1.0 C B:PHE140 4.6 23.3 1.0 CG B:GLU166 4.7 24.0 1.0 N B:LEU141 4.8 24.1 1.0 O B:LEU141 4.8 25.8 1.0 CG B:ASN142 4.9 32.5 0.5 CA B:ASN142 4.9 26.1 0.5 CA B:ASN142 4.9 26.2 0.5

A.Mac Sweeney, J.Hazemann. Identification of Sars-Cov-2 Mpro Inhibitors Through Deep Reinforcement Learning For De Novo Drug Design and Computational Chemistry Approaches To Be Published.