Fluorine in PDB 9avq: Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An Inhibitor Nirmatrelvir:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An Inhibitor Nirmatrelvir, PDB code: 9avq was solved by H.Bulut, S.Hattori, H.Hayashi, K.Hasegawa, M.Li, A.Wlodawer, H.Tamamura, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 2.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.74, 64.52, 105.19, 90, 90, 90
R / Rfree (%)	18 / 24.4

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An Inhibitor Nirmatrelvir (pdb code 9avq). 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 A191T Mutant in Complex with An Inhibitor Nirmatrelvir, PDB code: 9avq:
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 A191T Mutant in Complex with An 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 A191T Mutant in Complex with An Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.7 occ:1.00 F1 A:4WI401 0.0 40.7 1.0 C22 A:4WI401 1.3 39.1 1.0 F3 A:4WI401 2.1 38.7 1.0 F2 A:4WI401 2.2 49.9 1.0 C21 A:4WI401 2.3 34.4 1.0 O4 A:4WI401 2.7 32.4 1.0 O A:THR190 2.9 37.7 1.0 CE A:MET165 3.2 27.8 1.0 N4 A:4WI401 3.4 29.3 1.0 NE2 A:GLN192 3.5 26.9 1.0 O A:ARG188 4.0 23.2 1.0 CB A:GLN192 4.1 29.0 1.0 C A:THR190 4.1 33.8 1.0 CG A:GLN192 4.1 27.9 1.0 CD A:GLN192 4.1 27.7 1.0 N A:THR190 4.2 28.8 1.0 N A:GLN192 4.4 33.3 1.0 CD2 A:LEU167 4.4 28.3 1.0 O A:GLU166 4.5 24.2 1.0 C14 A:4WI401 4.7 25.7 1.0 CA A:GLN189 4.8 24.3 1.0 CA A:THR190 4.8 34.1 1.0 CA A:GLN192 4.9 32.8 1.0 C A:THR191 4.9 36.3 1.0 SD A:MET165 5.0 27.6 1.0 C A:GLN189 5.0 25.5 1.0 C A:ARG188 5.0 23.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An 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 A191T Mutant in Complex with An Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.9 occ:1.00 F2 A:4WI401 0.0 49.9 1.0 C22 A:4WI401 1.3 39.1 1.0 F3 A:4WI401 2.1 38.7 1.0 F1 A:4WI401 2.2 40.7 1.0 C21 A:4WI401 2.4 34.4 1.0 O4 A:4WI401 3.0 32.4 1.0 N4 A:4WI401 3.2 29.3 1.0 O A:THR190 3.7 37.7 1.0 O A:GLU166 3.8 24.2 1.0 CD A:PRO168 4.1 42.7 1.0 CG A:PRO168 4.2 42.0 1.0 CA A:LEU167 4.5 27.0 1.0 C14 A:4WI401 4.5 25.7 1.0 N A:PRO168 4.5 40.6 1.0 N A:GLN192 4.6 33.3 1.0 C16 A:4WI401 4.6 25.1 1.0 C A:THR190 4.7 33.8 1.0 C A:LEU167 4.8 32.8 1.0 C A:GLU166 4.8 23.4 1.0 CD2 A:LEU167 4.9 28.3 1.0 CE A:MET165 4.9 27.8 1.0 C15 A:4WI401 5.0 25.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease A191T Mutant in Complex with An 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 A191T Mutant in Complex with An Inhibitor Nirmatrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:38.7 occ:1.00 F3 A:4WI401 0.0 38.7 1.0 C22 A:4WI401 1.3 39.1 1.0 F1 A:4WI401 2.1 40.7 1.0 F2 A:4WI401 2.1 49.9 1.0 C21 A:4WI401 2.4 34.4 1.0 O A:GLU166 2.5 24.2 1.0 N4 A:4WI401 2.7 29.3 1.0 CE A:MET165 3.1 27.8 1.0 C A:GLU166 3.4 23.4 1.0 O4 A:4WI401 3.4 32.4 1.0 CA A:LEU167 3.5 27.0 1.0 CD2 A:LEU167 3.5 28.3 1.0 N A:LEU167 3.8 24.4 1.0 C14 A:4WI401 4.1 25.7 1.0 CG A:LEU167 4.2 28.6 1.0 CB A:LEU167 4.3 27.4 1.0 N A:GLU166 4.4 20.2 1.0 C A:LEU167 4.4 32.8 1.0 CD A:PRO168 4.5 42.7 1.0 CA A:GLU166 4.5 22.2 1.0 N A:PRO168 4.7 40.6 1.0 C13 A:4WI401 4.7 21.2 1.0 O3 A:4WI401 4.7 20.6 1.0 CB A:MET165 4.7 21.1 1.0 CG A:MET165 4.8 23.9 1.0 SD A:MET165 4.8 27.6 1.0 O A:THR190 4.8 37.7 1.0 C23 A:4WI401 4.8 23.6 1.0 C15 A:4WI401 5.0 25.6 1.0 CB A:GLN192 5.0 29.0 1.0

S.Hattori, H.Bulut, H.Hayashi, N.Kishimoto, N.Takamune, K.Hasegawa, K.Murayama, L.Mi, A.Wlodawer, H.Tamamura, S.Misumi, H.Mitsuya. Structural and Virologic Mechanism of Emergence of Main Protease Inhibitor-Resistance in Sars-Cov-2 As Selected with Main Protease Inhibitors To Be Published.