Chlorine in PDB 7vu6: The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3

All present enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3:
3.4.22.69;

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3, PDB code: 7vu6 was solved by S.Yamamoto, J.Yamane, Y.Tachibana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.99 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.468, 99.229, 58.883, 90, 108.05, 90
R / Rfree (%)	22.4 / 27.9

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

Fluorine

(F)

6 atoms

The binding sites of Chlorine atom in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 (pdb code 7vu6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3, PDB code: 7vu6:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:13.8 occ:1.00 CL2 A:7YY501 0.0 13.8 1.0 C22 A:7YY501 1.8 13.9 1.0 C21 A:7YY501 2.7 13.9 1.0 C13 A:7YY501 2.8 13.7 1.0 N12 A:7YY501 3.0 13.9 1.0 N10 A:7YY501 3.2 12.4 1.0 C11 A:7YY501 3.3 13.3 1.0 SG A:CYS145 3.4 12.5 1.0 CB A:CYS145 3.5 11.7 1.0 CD2 A:HIS41 3.8 12.0 1.0 CD2 A:LEU27 3.9 11.8 1.0 C14 A:7YY501 4.0 15.2 1.0 C20 A:7YY501 4.1 15.2 1.0 C34 A:7YY501 4.1 13.8 1.0 C08 A:7YY501 4.1 11.8 1.0 N24 A:7YY501 4.3 13.7 1.0 F33 A:7YY501 4.5 12.3 1.0 CB A:LEU27 4.5 11.2 1.0 C15 A:7YY501 4.5 15.0 1.0 O09 A:7YY501 4.5 12.9 1.0 CG A:HIS41 4.6 12.2 1.0 CB A:HIS41 4.6 12.9 1.0 C32 A:7YY501 4.7 13.7 1.0 CG A:LEU27 4.7 11.6 1.0 O A:HOH638 4.7 22.8 1.0 O A:THR26 4.7 11.1 1.0 NE2 A:HIS41 4.8 13.2 1.0 C26 A:7YY501 4.9 13.6 1.0 O A:HOH703 4.9 20.5 1.0 C25 A:7YY501 4.9 14.3 1.0 N07 A:7YY501 5.0 13.0 1.0

Chlorine binding site 2 out of 2 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:14.2 occ:1.00 CL2 B:7YY501 0.0 14.2 1.0 C22 B:7YY501 1.7 14.4 1.0 C21 B:7YY501 2.7 14.4 1.0 C13 B:7YY501 2.7 14.5 1.0 N12 B:7YY501 2.9 14.2 1.0 N10 B:7YY501 3.0 12.3 1.0 C11 B:7YY501 3.1 12.9 1.0 SG B:CYS145 3.5 12.0 1.0 CB B:CYS145 3.6 9.9 1.0 O B:HOH738 3.7 32.4 1.0 CD2 B:HIS41 3.8 12.6 1.0 C08 B:7YY501 4.0 12.7 1.0 C20 B:7YY501 4.0 14.9 1.0 C14 B:7YY501 4.0 14.6 1.0 C34 B:7YY501 4.0 14.0 1.0 CD2 B:LEU27 4.0 8.6 1.0 N24 B:7YY501 4.1 13.8 1.0 O B:HOH646 4.4 22.5 1.0 O09 B:7YY501 4.4 13.6 1.0 F33 B:7YY501 4.4 12.7 1.0 C15 B:7YY501 4.5 16.0 1.0 CB B:LEU27 4.5 8.6 1.0 C32 B:7YY501 4.6 14.6 1.0 CG B:HIS41 4.7 12.2 1.0 CG B:LEU27 4.7 8.8 1.0 C26 B:7YY501 4.8 14.3 1.0 NE2 B:HIS41 4.8 13.4 1.0 O B:THR26 4.8 10.8 1.0 O B:HOH677 4.8 12.8 1.0 N07 B:7YY501 4.8 13.5 1.0 CB B:HIS41 4.9 11.8 1.0 C25 B:7YY501 4.9 13.9 1.0 C35 B:7YY501 4.9 13.1 1.0

Y.Unoh, S.Uehara, K.Nakahara, H.Nobori, Y.Yamatsu, S.Yamamoto, Y.Maruyama, Y.Taoda, K.Kasamatsu, T.Suto, K.Kouki, A.Nakahashi, S.Kawashima, T.Sanaki, S.Toba, K.Uemura, T.Mizutare, S.Ando, M.Sasaki, Y.Orba, H.Sawa, A.Sato, T.Sato, T.Kato, Y.Tachibana. Discovery of S-217622, A Noncovalent Oral Sars-Cov-2 3CL Protease Inhibitor Clinical Candidate For Treating Covid-19. J.Med.Chem. V. 65 6499 2022.
ISSN: ISSN 0022-2623
PubMed: 35352927
DOI: 10.1021/ACS.JMEDCHEM.2C00117