Fluorine in PDB 8ezv: Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A, PDB code: 8ezv was solved by M.Westberg, D.Fernandez, M.Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.67 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.829, 64.071, 104.422, 90, 90, 90
R / Rfree (%)	17.9 / 22

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A (pdb code 8ezv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A, PDB code: 8ezv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:39.0 occ:1.00 F1 A:X6O401 0.0 39.0 1.0 C16 A:X6O401 1.3 35.7 1.0 F3 A:X6O401 2.0 50.0 1.0 F2 A:X6O401 2.1 42.5 1.0 C15 A:X6O401 2.4 32.3 1.0 N2 A:X6O401 2.7 23.3 1.0 O A:GLU166 2.8 20.2 1.0 CD2 A:LEU167 3.2 27.6 1.0 O2 A:X6O401 3.5 35.2 1.0 CA A:LEU167 3.5 26.9 1.0 CE A:MET165 3.6 34.2 1.0 C A:GLU166 3.6 21.4 1.0 O A:HOH651 3.8 35.6 1.0 N A:LEU167 3.9 23.0 1.0 CG A:LEU167 3.9 28.3 1.0 C10 A:X6O401 4.2 21.8 1.0 CB A:LEU167 4.2 26.4 1.0 CD A:PRO168 4.4 32.7 1.0 O A:HOH750 4.5 50.6 1.0 O A:GLN192 4.5 34.4 1.0 CB A:GLN192 4.6 30.0 1.0 C A:LEU167 4.6 29.3 1.0 O A:THR190 4.7 34.1 1.0 C9 A:X6O401 4.8 20.9 1.0 O3 A:X6O401 4.8 21.5 1.0 N A:GLU166 4.8 19.6 1.0 CA A:GLU166 4.8 20.7 1.0 N A:PRO168 4.9 31.2 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.5 occ:1.00 F2 A:X6O401 0.0 42.5 1.0 C16 A:X6O401 1.3 35.7 1.0 F1 A:X6O401 2.1 39.0 1.0 F3 A:X6O401 2.1 50.0 1.0 C15 A:X6O401 2.3 32.3 1.0 O2 A:X6O401 2.7 35.2 1.0 O A:THR190 2.9 34.1 1.0 CE A:MET165 3.3 34.2 1.0 NE2 A:GLN192 3.3 26.9 1.0 N2 A:X6O401 3.4 23.3 1.0 CB A:GLN192 3.6 30.0 1.0 CG A:GLN192 3.7 28.9 1.0 CD A:GLN192 3.7 27.2 1.0 O A:ARG188 4.0 23.9 1.0 N A:GLN192 4.0 35.2 1.0 C A:THR190 4.1 38.8 1.0 CD2 A:LEU167 4.2 27.6 1.0 N A:THR190 4.4 33.8 1.0 CA A:GLN192 4.4 30.4 1.0 OE1 A:GLN192 4.6 27.4 1.0 C10 A:X6O401 4.6 21.8 1.0 O A:HOH750 4.6 50.6 1.0 O A:GLN192 4.7 34.4 1.0 O A:GLU166 4.7 20.2 1.0 O A:HOH689 4.7 33.6 1.0 C A:ALA191 4.8 36.0 1.0 CA A:THR190 4.9 40.3 1.0 C A:GLN192 5.0 31.8 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:50.0 occ:1.00 F3 A:X6O401 0.0 50.0 1.0 C16 A:X6O401 1.3 35.7 1.0 F1 A:X6O401 2.0 39.0 1.0 F2 A:X6O401 2.1 42.5 1.0 C15 A:X6O401 2.4 32.3 1.0 O A:HOH750 2.7 50.6 1.0 O2 A:X6O401 3.0 35.2 1.0 N2 A:X6O401 3.3 23.3 1.0 O A:THR190 3.4 34.1 1.0 O A:HOH651 3.6 35.6 1.0 O A:HOH689 3.8 33.6 1.0 N A:GLN192 3.9 35.2 1.0 O A:GLN192 3.9 34.4 1.0 O A:GLU166 4.2 20.2 1.0 CD A:PRO168 4.2 32.7 1.0 C A:THR190 4.4 38.8 1.0 CB A:GLN192 4.5 30.0 1.0 C10 A:X6O401 4.6 21.8 1.0 CD2 A:LEU167 4.6 27.6 1.0 CA A:GLN192 4.6 30.4 1.0 CA A:ALA191 4.7 41.7 1.0 C14 A:X6O401 4.7 22.2 1.0 CA A:LEU167 4.7 26.9 1.0 C A:GLN192 4.7 31.8 1.0 C A:ALA191 4.7 36.0 1.0 CG A:PRO168 4.8 33.2 1.0 N A:ALA191 4.9 41.3 1.0 CG A:GLN192 5.0 28.9 1.0

M.Westberg, D.Fernandez, M.Z.Lin. Rational Design of A New Class of Protease Inhibitors For the Potential Treatment of Coronavirus Diseases To Be Published.