Fluorine in PDB 8ftc: Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor

All present enzymatic activity of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor:
3.4.22.69;

The structure of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor, PDB code: 8ftc was solved by P.Chen, M.B.Khan, J.Lu, E.Arutyunova, H.S.Young, M.J.Lemieux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.24 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.564, 63.676, 105.727, 90, 90, 90
R / Rfree (%)	16.8 / 20.6

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

Fluorine binding site 1 out of 2 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.6 occ:1.00 F14 A:Y8O401 0.0 26.6 1.0 C13 A:Y8O401 1.4 18.6 1.0 H131 A:Y8O401 2.0 22.4 1.0 F15 A:Y8O401 2.2 36.6 1.0 H111 A:Y8O401 2.3 14.1 1.0 C12 A:Y8O401 2.3 15.6 1.0 N11 A:Y8O401 2.6 11.7 1.0 O A:GLU166 2.7 14.3 1.0 O A:HOH696 3.2 25.2 1.0 CD2 A:LEU167 3.3 20.0 1.0 O16 A:Y8O401 3.4 18.8 1.0 CE A:MET165 3.7 16.1 1.0 C A:GLU166 3.7 15.0 1.0 CA A:LEU167 3.8 20.2 1.0 O A:HOH716 3.9 27.8 1.0 C06 A:Y8O401 4.1 13.8 1.0 N A:LEU167 4.2 16.0 1.0 CG A:LEU167 4.2 19.5 1.0 H082 A:Y8O401 4.3 19.9 1.0 O A:THR190 4.5 18.7 1.0 CB A:LEU167 4.5 22.2 1.0 H061 A:Y8O401 4.5 16.6 1.0 H093 A:Y8O401 4.6 16.6 1.0 H092 A:Y8O401 4.6 16.6 1.0 CB A:GLN192 4.6 18.8 1.0 C05 A:Y8O401 4.7 12.9 1.0 CD A:PRO168 4.7 35.8 1.0 O17 A:Y8O401 4.8 10.9 1.0 NE2 A:GLN192 4.8 14.2 1.0 N A:GLU166 4.8 9.6 1.0 O A:GLN192 4.8 22.8 1.0 SD A:MET165 4.8 24.4 1.0 C A:LEU167 4.8 30.3 1.0 CA A:GLU166 4.9 14.7 1.0 CG A:MET165 4.9 14.9 1.0 C09 A:Y8O401 4.9 13.7 1.0 C07 A:Y8O401 4.9 13.0 1.0 N A:GLN192 5.0 22.3 1.0 CB A:MET165 5.0 12.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.6 occ:1.00 F15 A:Y8O401 0.0 36.6 1.0 C13 A:Y8O401 1.4 18.6 1.0 H131 A:Y8O401 2.0 22.4 1.0 F14 A:Y8O401 2.2 26.6 1.0 O A:HOH716 2.3 27.8 1.0 C12 A:Y8O401 2.4 15.6 1.0 O16 A:Y8O401 2.9 18.8 1.0 O A:THR190 3.0 18.7 1.0 O A:HOH696 3.2 25.2 1.0 N11 A:Y8O401 3.4 11.7 1.0 N A:GLN192 3.6 22.3 1.0 H111 A:Y8O401 3.6 14.1 1.0 H082 A:Y8O401 3.8 19.9 1.0 O A:HOH694 3.9 18.5 1.0 C A:THR190 3.9 19.8 1.0 CA A:ALA191 4.0 23.0 1.0 C A:ALA191 4.3 20.6 1.0 O A:GLN192 4.3 22.8 1.0 CB A:GLN192 4.4 18.8 1.0 N A:ALA191 4.4 21.9 1.0 O A:GLU166 4.4 14.3 1.0 CA A:GLN192 4.5 21.6 1.0 C06 A:Y8O401 4.6 13.8 1.0 CD2 A:LEU167 4.7 20.0 1.0 H061 A:Y8O401 4.7 16.6 1.0 CD A:PRO168 4.7 35.8 1.0 N A:THR190 4.8 16.0 1.0 C08 A:Y8O401 4.8 16.5 1.0 C A:GLN192 4.9 24.6 1.0 CG A:GLN192 4.9 19.4 1.0 NE2 A:GLN192 5.0 14.2 1.0 CA A:THR190 5.0 21.5 1.0

E.Arutyunova, A.Belovodskiy, P.Chen, M.B.Khan, M.Joyce, H.Saffran, J.Lu, Z.Turner, B.Bai, T.Lamer, H.S.Young, J.C.Vederas, D.L.Tyrrell, M.J.Lemieux, J.A.Nieman. The Effect of Deuteration and Homologation of the Lactam Ring of Nirmatrelvir on Its Biochemical Properties and Oxidative Metabolism Acs Bio Med Chem Au 2023.
ISSN: ESSN 2694-2437
DOI: 10.1021/ACSBIOMEDCHEMAU.3C00039