Fluorine in PDB 8iny: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir, PDB code: 8iny was solved by M.Lin, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.30 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.351, 82.076, 51.476, 90, 114.7, 90
R / Rfree (%)	19.1 / 21.5

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir (pdb code 8iny). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir, PDB code: 8iny:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir


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 Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.2 occ:1.00 F28 A:7YY401 0.0 33.2 1.0 C27 A:7YY401 1.4 31.5 1.0 C26 A:7YY401 2.3 25.2 1.0 C29 A:7YY401 2.4 32.4 1.0 C25 A:7YY401 2.7 25.7 1.0 CG A:GLN189 3.1 45.6 1.0 CA A:GLN189 3.2 41.4 1.0 O A:HOH559 3.3 41.8 1.0 CB A:GLN189 3.3 41.0 1.0 O A:HOH619 3.4 44.5 1.0 O A:HOH573 3.6 30.6 1.0 C34 A:7YY401 3.6 26.3 1.0 C30 A:7YY401 3.6 32.1 1.0 N A:GLN189 3.9 38.0 1.0 O A:ARG188 3.9 41.7 1.0 CD A:GLN189 4.1 49.0 1.0 C32 A:7YY401 4.1 26.9 1.0 N24 A:7YY401 4.1 26.4 1.0 C A:ARG188 4.2 40.9 1.0 C A:GLN189 4.3 50.0 1.0 NE2 A:GLN189 4.4 58.8 1.0 CB A:MET165 4.5 30.1 1.0 O36 A:7YY401 4.6 27.2 1.0 NE2 A:HIS41 4.7 28.3 1.0 N A:THR190 4.8 42.6 1.0 F31 A:7YY401 4.8 35.9 1.0 OE1 A:GLN189 4.9 53.9 1.0 C35 A:7YY401 4.9 25.3 1.0 SD A:MET165 5.0 30.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir


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 Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:35.9 occ:1.00 F31 A:7YY401 0.0 35.9 1.0 C30 A:7YY401 1.4 32.1 1.0 C32 A:7YY401 2.4 26.9 1.0 C29 A:7YY401 2.4 32.4 1.0 F33 A:7YY401 2.7 28.4 1.0 CB A:ASP187 3.0 26.8 1.0 CA A:ASP187 3.0 24.0 1.0 C A:ASP187 3.1 28.1 1.0 O A:ASP187 3.5 31.0 1.0 ND1 A:HIS41 3.5 27.9 1.0 C34 A:7YY401 3.6 26.3 1.0 C27 A:7YY401 3.6 31.5 1.0 N A:ARG188 3.6 29.3 1.0 CG A:HIS41 3.8 26.6 1.0 CE1 A:HIS41 3.9 27.9 1.0 SD A:MET165 4.0 30.5 1.0 C26 A:7YY401 4.1 25.2 1.0 CB A:HIS41 4.2 27.6 1.0 CD2 A:HIS41 4.2 29.2 1.0 NE2 A:HIS41 4.3 28.3 1.0 O A:HOH605 4.3 25.7 1.0 CG A:ASP187 4.4 25.7 1.0 CA A:ARG188 4.4 37.1 1.0 OH A:TYR54 4.4 28.9 1.0 N A:ASP187 4.4 24.5 1.0 C A:ARG188 4.5 40.9 1.0 O A:ARG188 4.5 41.7 1.0 ND1 A:HIS164 4.7 25.9 1.0 O A:VAL186 4.8 26.1 1.0 F28 A:7YY401 4.8 33.2 1.0 CB A:HIS164 4.8 22.8 1.0 OD2 A:ASP187 4.9 23.5 1.0 CB A:MET165 4.9 30.1 1.0 CG A:MET165 5.0 27.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir


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 Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.4 occ:1.00 F33 A:7YY401 0.0 28.4 1.0 C32 A:7YY401 1.4 26.9 1.0 C30 A:7YY401 2.4 32.1 1.0 C34 A:7YY401 2.4 26.3 1.0 F31 A:7YY401 2.7 35.9 1.0 O A:HIS164 3.3 27.0 1.0 CB A:HIS41 3.4 27.6 1.0 CG A:HIS41 3.4 26.6 1.0 SG A:CYS145 3.5 25.5 1.0 CD2 A:HIS41 3.6 29.2 1.0 C29 A:7YY401 3.6 32.4 1.0 C26 A:7YY401 3.6 25.2 1.0 C A:HIS164 3.8 23.6 1.0 CB A:HIS164 3.9 22.8 1.0 ND1 A:HIS164 4.0 25.9 1.0 CA A:HIS164 4.0 19.9 1.0 O A:HOH605 4.1 25.7 1.0 C27 A:7YY401 4.1 31.5 1.0 ND1 A:HIS41 4.1 27.9 1.0 NE2 A:HIS41 4.3 28.3 1.0 CG A:HIS164 4.4 24.1 1.0 CL2 A:7YY401 4.5 28.1 1.0 CE1 A:HIS41 4.6 27.9 1.0 N A:MET165 4.8 23.6 1.0 CB A:PRO39 4.8 24.0 1.0 CA A:HIS41 4.9 28.2 1.0 CB A:ASP187 4.9 26.8 1.0 CB A:MET165 4.9 30.1 1.0 C25 A:7YY401 4.9 25.7 1.0 N24 A:7YY401 5.0 26.4 1.0

M.Lin, X.Liu. Crystal Structure of Sars-Cov-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor Ensitrelvir To Be Published.