Fluorine in PDB 8f02: Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4, PDB code: 8f02 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)	37.04 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.649, 63.231, 103.798, 90, 90, 90
R / Rfree (%)	19 / 25.5

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4 (pdb code 8f02). 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 ML2006A4, PDB code: 8f02:
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 ML2006A4


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 ML2006A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:73.4 occ:1.00 F1 A:X6T401 0.0 73.4 1.0 C16 A:X6T401 1.3 61.2 1.0 F2 A:X6T401 2.1 76.9 1.0 F3 A:X6T401 2.2 74.2 1.0 C15 A:X6T401 2.4 52.9 1.0 N2 A:X6T401 2.9 48.4 1.0 O A:GLU166 3.0 48.6 1.0 O2 A:X6T401 3.2 51.9 1.0 CD A:PRO168 3.7 54.4 1.0 CA A:LEU167 3.7 47.9 1.0 C A:GLU166 4.0 42.3 1.0 CD2 A:LEU167 4.3 49.6 1.0 C10 A:X6T401 4.3 48.2 1.0 O A:GLN192 4.3 64.9 1.0 N A:PRO168 4.3 50.4 1.0 C A:LEU167 4.3 53.4 1.0 N A:LEU167 4.4 42.2 1.0 C13 A:X6T401 4.4 45.3 1.0 O A:THR190 4.5 69.5 1.0 CG A:PRO168 4.6 55.5 1.0 CB A:LEU167 4.7 46.0 1.0 C11 A:X6T401 4.8 46.0 1.0 CG A:LEU167 4.8 54.5 1.0 C12 A:X6T401 4.9 47.2 1.0 N A:GLN192 5.0 51.8 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4


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 ML2006A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:76.9 occ:1.00 F2 A:X6T401 0.0 76.9 1.0 C16 A:X6T401 1.3 61.2 1.0 F1 A:X6T401 2.1 73.4 1.0 F3 A:X6T401 2.1 74.2 1.0 C15 A:X6T401 2.3 52.9 1.0 O A:GLU166 2.6 48.6 1.0 N2 A:X6T401 2.7 48.4 1.0 CE A:MET165 3.3 74.7 1.0 O2 A:X6T401 3.3 51.9 1.0 CD2 A:LEU167 3.3 49.6 1.0 C A:GLU166 3.5 42.3 1.0 CA A:LEU167 3.8 47.9 1.0 CG A:LEU167 3.8 54.5 1.0 N A:LEU167 4.0 42.2 1.0 SD A:MET165 4.0 70.7 1.0 C10 A:X6T401 4.1 48.2 1.0 CG A:MET165 4.3 52.0 1.0 N A:GLU166 4.3 43.1 1.0 CB A:MET165 4.3 47.0 1.0 CB A:LEU167 4.4 46.0 1.0 O3 A:X6T401 4.5 41.7 1.0 C9 A:X6T401 4.5 45.6 1.0 CA A:GLU166 4.5 40.9 1.0 NE2 A:GLN192 4.7 52.0 1.0 CD A:PRO168 4.9 54.4 1.0 CB A:GLN192 4.9 54.1 1.0 O A:THR190 4.9 69.5 1.0 O A:GLN192 5.0 64.9 1.0 C A:LEU167 5.0 53.4 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML2006A4


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 ML2006A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:74.2 occ:1.00 F3 A:X6T401 0.0 74.2 1.0 C16 A:X6T401 1.3 61.2 1.0 F2 A:X6T401 2.1 76.9 1.0 F1 A:X6T401 2.2 73.4 1.0 C15 A:X6T401 2.3 52.9 1.0 O2 A:X6T401 2.6 51.9 1.0 O A:THR190 2.8 69.5 1.0 N2 A:X6T401 3.5 48.4 1.0 NE2 A:GLN192 3.7 52.0 1.0 CB A:GLN192 3.8 54.1 1.0 CE A:MET165 4.0 74.7 1.0 CG A:GLN192 4.0 53.8 1.0 N A:GLN192 4.0 51.8 1.0 CD A:GLN192 4.0 54.8 1.0 C A:THR190 4.0 62.3 1.0 CD2 A:LEU167 4.2 49.6 1.0 O A:GLN192 4.3 64.9 1.0 CA A:GLN192 4.4 54.8 1.0 N A:THR190 4.4 59.6 1.0 O A:GLU166 4.4 48.6 1.0 O A:ARG188 4.5 56.3 1.0 C A:ALA191 4.7 49.9 1.0 C10 A:X6T401 4.8 48.2 1.0 C A:GLN192 4.8 53.8 1.0 CA A:ALA191 4.8 50.6 1.0 OE1 A:GLN192 4.9 48.1 1.0 N A:ALA191 4.9 59.5 1.0 CA A:THR190 5.0 65.8 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.