Fluorine in PDB 8h5f: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5f 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)	27.33 / 1.79
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.373, 63.825, 105.839, 90, 90, 90
R / Rfree (%)	18.4 / 22.7

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir (pdb code 8h5f). 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) L167F Mutant in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5f:
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) L167F Mutant in Complex with Inhibitor Nirmatrelvir


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) L167F Mutant in Complex with Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:35.5 occ:1.00 F1 A:4WI401 0.0 35.5 1.0 C22 A:4WI401 1.4 31.2 1.0 F2 A:4WI401 2.2 30.1 1.0 F3 A:4WI401 2.2 32.6 1.0 C21 A:4WI401 2.3 29.7 1.0 N4 A:4WI401 3.0 22.4 1.0 O4 A:4WI401 3.2 33.3 1.0 CD A:PRO168 3.3 39.2 1.0 CD1 A:PHE167 3.3 36.3 1.0 O A:GLU166 3.3 23.0 1.0 CA A:PHE167 3.6 30.9 1.0 CE1 A:PHE167 3.8 37.5 1.0 CG A:PHE167 4.0 32.4 1.0 CG A:PRO168 4.1 45.3 1.0 C A:GLU166 4.2 23.1 1.0 CB A:PHE167 4.2 33.4 1.0 N A:PRO168 4.3 38.5 1.0 C14 A:4WI401 4.3 24.0 1.0 N A:PHE167 4.4 23.6 1.0 C A:PHE167 4.5 35.1 1.0 C17 A:4WI401 4.5 27.1 1.0 O A:THR190 4.6 30.9 1.0 CE A:MET165 4.9 29.9 1.0 CZ A:PHE167 4.9 39.3 1.0 C15 A:4WI401 4.9 26.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir


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) L167F Mutant in Complex with Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.1 occ:1.00 F2 A:4WI401 0.0 30.1 1.0 C22 A:4WI401 1.4 31.2 1.0 F3 A:4WI401 2.2 32.6 1.0 F1 A:4WI401 2.2 35.5 1.0 C21 A:4WI401 2.3 29.7 1.0 N4 A:4WI401 2.8 22.4 1.0 O A:GLU166 2.9 23.0 1.0 CE A:MET165 3.1 29.9 1.0 CD1 A:PHE167 3.1 36.3 1.0 CE1 A:PHE167 3.2 37.5 1.0 O4 A:4WI401 3.3 33.3 1.0 C A:GLU166 3.4 23.1 1.0 CG A:PHE167 3.5 32.4 1.0 CG A:MET165 3.7 22.2 1.0 CZ A:PHE167 3.7 39.3 1.0 CA A:PHE167 3.7 30.9 1.0 N A:PHE167 3.7 23.6 1.0 CD2 A:PHE167 3.9 36.0 1.0 N A:GLU166 4.0 19.9 1.0 CE2 A:PHE167 4.0 36.3 1.0 CB A:MET165 4.1 21.4 1.0 C14 A:4WI401 4.2 24.0 1.0 CB A:PHE167 4.2 33.4 1.0 SD A:MET165 4.2 28.9 1.0 CA A:GLU166 4.3 20.1 1.0 O3 A:4WI401 4.4 23.3 1.0 C13 A:4WI401 4.5 23.8 1.0 C A:MET165 4.7 20.1 1.0 CD A:PRO168 4.9 39.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir


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) L167F Mutant in Complex with Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.6 occ:1.00 F3 A:4WI401 0.0 32.6 1.0 C22 A:4WI401 1.4 31.2 1.0 F2 A:4WI401 2.2 30.1 1.0 F1 A:4WI401 2.2 35.5 1.0 C21 A:4WI401 2.4 29.7 1.0 O4 A:4WI401 2.7 33.3 1.0 O A:THR190 3.1 30.9 1.0 CE A:MET165 3.2 29.9 1.0 CE1 A:PHE167 3.3 37.5 1.0 CD1 A:PHE167 3.6 36.3 1.0 N4 A:4WI401 3.7 22.4 1.0 NE2 A:GLN192 3.7 29.9 1.0 O A:ARG188 3.9 23.2 1.0 C A:THR190 4.0 29.9 1.0 N A:THR190 4.1 27.6 1.0 CZ A:PHE167 4.1 39.3 1.0 CD A:GLN192 4.5 31.6 1.0 CG A:PHE167 4.6 32.4 1.0 CA A:THR190 4.7 29.7 1.0 CG A:GLN192 4.7 32.8 1.0 CA A:GLN189 4.8 25.9 1.0 O A:GLU166 4.8 23.0 1.0 C14 A:4WI401 4.8 24.0 1.0 N A:ALA191 4.8 31.7 1.0 SD A:MET165 4.8 28.9 1.0 C A:GLN189 4.9 27.2 1.0 CA A:ALA191 4.9 31.7 1.0 C A:ARG188 5.0 21.6 1.0

Y.Duan, H.Zhou, X.Liu, S.Iketani, M.Lin, X.Zhang, Q.Bian, H.Wang, H.Sun, S.J.Hong, B.Culbertson, H.Mohri, M.I.Luck, Y.Zhu, X.Liu, Y.Lu, X.Yang, K.Yang, Y.Sabo, A.Chavez, S.P.Goff, Z.Rao, D.D.Ho, H.Yang. Molecular Mechanisms of Sars-Cov-2 Resistance to Nirmatrelvir. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37696289
DOI: 10.1038/S41586-023-06609-0