Fluorine in PDB 8wti: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J, PDB code: 8wti was solved by R.Zeng, X.Zhao, S.Y.Yang, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.01 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.57, 106.37, 54.43, 90, 103.03, 90
R / Rfree (%)	17.2 / 20.1

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J (pdb code 8wti). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J, PDB code: 8wti:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:20.1 occ:1.00 F01 A:X1Z401 0.0 20.1 1.0 C02 A:X1Z401 1.4 15.5 1.0 F03 A:X1Z401 2.2 17.6 1.0 C43 A:X1Z401 2.3 17.5 1.0 C04 A:X1Z401 2.4 15.2 1.0 C42 A:X1Z401 2.9 15.8 1.0 O A:THR190 3.0 19.4 1.0 C05 A:X1Z401 3.0 15.8 1.0 C06 A:X1Z401 3.5 17.7 1.0 NE2 A:GLN192 3.7 17.1 1.0 CG A:GLN192 3.8 23.1 1.0 C A:THR190 3.9 20.7 1.0 N A:THR190 4.0 18.8 1.0 CD A:GLN192 4.3 18.4 1.0 O A:ARG188 4.3 15.4 1.0 N A:GLN192 4.5 18.3 1.0 CA A:GLN189 4.6 16.7 1.0 C07 A:X1Z401 4.6 18.3 1.0 CA A:THR190 4.7 18.9 1.0 C A:GLN189 4.7 19.1 1.0 O A:GLN192 4.7 22.6 1.0 CA A:ALA191 4.8 22.8 1.0 N A:ALA191 4.8 18.1 1.0 O41 A:X1Z401 4.8 17.9 1.0 C A:ALA191 5.0 19.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:17.6 occ:1.00 F03 A:X1Z401 0.0 17.6 1.0 C02 A:X1Z401 1.3 15.5 1.0 F01 A:X1Z401 2.2 20.1 1.0 C43 A:X1Z401 2.3 17.5 1.0 C04 A:X1Z401 2.4 15.2 1.0 CD2 A:LEU167 3.4 17.7 1.0 CD A:PRO168 3.4 24.0 1.0 O A:GLN192 3.5 22.6 1.0 CG A:GLN192 3.7 23.1 1.0 C42 A:X1Z401 3.7 15.8 1.0 C05 A:X1Z401 3.7 15.8 1.0 CA A:LEU167 3.8 17.7 1.0 O A:GLU166 4.1 17.3 1.0 C06 A:X1Z401 4.1 17.7 1.0 CG A:PRO168 4.1 26.3 1.0 CB A:LEU167 4.3 18.4 1.0 N A:PRO168 4.3 20.8 1.0 C A:GLN192 4.4 17.4 1.0 CG A:LEU167 4.5 18.4 1.0 N A:GLN192 4.5 18.3 1.0 O A:THR190 4.5 19.4 1.0 CD A:GLN192 4.5 18.4 1.0 NE2 A:GLN192 4.5 17.1 1.0 C A:LEU167 4.6 20.0 1.0 N A:LEU167 4.7 15.7 1.0 C A:GLU166 4.8 18.5 1.0 CB A:GLN192 4.8 27.4 1.0 CA A:GLN192 4.8 19.6 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:18.1 occ:1.00 F01 B:X1Z401 0.0 18.1 1.0 C02 B:X1Z401 1.4 16.9 1.0 F03 B:X1Z401 2.2 19.3 1.0 C04 B:X1Z401 2.4 17.5 1.0 C43 B:X1Z401 2.4 17.1 1.0 O B:HOH610 3.3 19.4 1.0 CD B:PRO168 3.4 23.3 1.0 O B:GLN192 3.4 19.1 1.0 CD2 B:LEU167 3.4 19.3 1.0 CG B:GLN192 3.7 19.1 1.0 C05 B:X1Z401 3.7 17.7 1.0 C42 B:X1Z401 3.7 15.8 1.0 CA B:LEU167 3.8 16.9 1.0 O B:GLU166 4.0 17.3 1.0 CG B:PRO168 4.0 22.9 1.0 C06 B:X1Z401 4.2 16.8 1.0 N B:PRO168 4.3 20.9 1.0 CB B:LEU167 4.3 17.5 1.0 C B:GLN192 4.4 18.7 1.0 C B:LEU167 4.5 23.2 1.0 CG B:LEU167 4.5 16.8 1.0 NE2 B:GLN192 4.5 17.2 1.0 CD B:GLN192 4.5 15.6 1.0 N B:GLN192 4.5 18.7 1.0 O B:THR190 4.6 19.1 1.0 N B:LEU167 4.7 16.6 1.0 C B:GLU166 4.7 17.3 1.0 CB B:GLN192 4.8 22.7 1.0 CA B:GLN192 4.8 19.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 20J within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:19.3 occ:1.00 F03 B:X1Z401 0.0 19.3 1.0 C02 B:X1Z401 1.4 16.9 1.0 F01 B:X1Z401 2.2 18.1 1.0 C04 B:X1Z401 2.3 17.5 1.0 C43 B:X1Z401 2.4 17.1 1.0 C05 B:X1Z401 3.0 17.7 1.0 C42 B:X1Z401 3.0 15.8 1.0 O B:THR190 3.0 19.1 1.0 C06 B:X1Z401 3.5 16.8 1.0 O B:HOH610 3.7 19.4 1.0 NE2 B:GLN192 3.7 17.2 1.0 CG B:GLN192 3.7 19.1 1.0 C B:THR190 4.1 18.7 1.0 N B:THR190 4.2 16.8 1.0 CD B:GLN192 4.3 15.6 1.0 O B:ARG188 4.4 16.7 1.0 N B:GLN192 4.5 18.7 1.0 C07 B:X1Z401 4.6 17.9 1.0 CA B:GLN189 4.7 16.5 1.0 O B:GLN192 4.7 19.1 1.0 C B:GLN189 4.8 18.6 1.0 O41 B:X1Z401 4.8 20.1 1.0 CA B:THR190 4.8 17.7 1.0 CA B:ALA191 4.8 20.6 1.0 N B:ALA191 4.9 17.3 1.0 C B:ALA191 5.0 21.4 1.0

Q.Huang, B.Quan, Y.Chen, X.Zhao, Y.Zhou, C.Huang, J.Qiao, Y.Wang, Y.Li, S.Yang, J.Lei, L.Li. Discovery of Alpha-Ketoamide Inhibitors of Sars-Cov-2 Main Protease Derived From Quaternized P1 Groups. Bioorg.Chem. V. 143 07001 2024.
ISSN: ISSN 0045-2068
PubMed: 38101266
DOI: 10.1016/J.BIOORG.2023.107001