Fluorine in PDB 8f2c: Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A, PDB code: 8f2c 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)	34.98 / 1.95
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.576, 63.846, 104.384, 90, 90, 90
R / Rfree (%)	19.6 / 26.7

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A (pdb code 8f2c). 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 ML3006A, PDB code: 8f2c:
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 ML3006A


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 ML3006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:66.5 occ:1.00 F1 A:X9Z401 0.0 66.5 1.0 C16 A:X9Z401 1.3 57.2 1.0 F3 A:X9Z401 2.1 62.1 1.0 F2 A:X9Z401 2.2 61.6 1.0 C15 A:X9Z401 2.4 50.8 1.0 O2 A:X9Z401 2.9 50.3 1.0 O A:THR190 3.3 48.4 1.0 N2 A:X9Z401 3.3 45.9 1.0 N A:GLN192 3.9 41.7 1.0 O A:GLN192 3.9 49.5 1.0 CD A:PRO168 4.1 50.1 1.0 O A:GLU166 4.2 37.9 1.0 C A:THR190 4.3 48.8 1.0 CA A:ALA191 4.5 48.8 1.0 C14 A:X9Z401 4.5 45.3 1.0 CD2 A:LEU167 4.6 37.4 1.0 CG A:PRO168 4.6 49.0 1.0 CA A:LEU167 4.6 39.3 1.0 CB A:GLN192 4.6 41.8 1.0 C10 A:X9Z401 4.6 43.2 1.0 CA A:GLN192 4.6 42.8 1.0 C A:ALA191 4.6 45.2 1.0 C A:GLN192 4.7 42.0 1.0 N A:ALA191 4.8 46.3 1.0 CE A:MET165 4.9 56.8 1.0 N A:PRO168 4.9 50.2 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A


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 ML3006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:61.6 occ:1.00 F2 A:X9Z401 0.0 61.6 1.0 C16 A:X9Z401 1.3 57.2 1.0 F3 A:X9Z401 2.1 62.1 1.0 F1 A:X9Z401 2.2 66.5 1.0 C15 A:X9Z401 2.3 50.8 1.0 O2 A:X9Z401 2.8 50.3 1.0 CE A:MET165 2.9 56.8 1.0 O A:THR190 3.1 48.4 1.0 N2 A:X9Z401 3.3 45.9 1.0 NE2 A:GLN192 3.3 43.0 1.0 CD A:GLN192 3.7 43.6 1.0 CB A:GLN192 3.8 41.8 1.0 CG A:GLN192 3.9 41.6 1.0 CD2 A:LEU167 4.0 37.4 1.0 O A:ARG188 4.1 42.9 1.0 N A:GLN192 4.3 41.7 1.0 C A:THR190 4.3 48.8 1.0 O A:GLU166 4.4 37.9 1.0 OE1 A:GLN192 4.5 42.0 1.0 N A:THR190 4.5 49.3 1.0 C10 A:X9Z401 4.6 43.2 1.0 CA A:GLN192 4.6 42.8 1.0 O A:GLN192 4.7 49.5 1.0 SD A:MET165 4.7 47.3 1.0 C A:ALA191 5.0 45.2 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML3006A


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 ML3006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:62.1 occ:1.00 F3 A:X9Z401 0.0 62.1 1.0 C16 A:X9Z401 1.3 57.2 1.0 F2 A:X9Z401 2.1 61.6 1.0 F1 A:X9Z401 2.1 66.5 1.0 C15 A:X9Z401 2.3 50.8 1.0 O A:GLU166 2.5 37.9 1.0 N2 A:X9Z401 2.6 45.9 1.0 CD2 A:LEU167 3.3 37.4 1.0 C A:GLU166 3.3 34.7 1.0 CA A:LEU167 3.3 39.3 1.0 CE A:MET165 3.4 56.8 1.0 O2 A:X9Z401 3.5 50.3 1.0 N A:LEU167 3.7 39.2 1.0 CG A:LEU167 3.9 42.2 1.0 C10 A:X9Z401 4.0 43.2 1.0 CB A:LEU167 4.1 38.8 1.0 CD A:PRO168 4.4 50.1 1.0 C A:LEU167 4.4 44.7 1.0 N A:GLU166 4.6 32.5 1.0 CA A:GLU166 4.6 34.8 1.0 O A:GLN192 4.6 49.5 1.0 O3 A:X9Z401 4.6 34.6 1.0 C9 A:X9Z401 4.6 40.6 1.0 N A:PRO168 4.8 50.2 1.0 O A:THR190 4.8 48.4 1.0 C14 A:X9Z401 4.8 45.3 1.0 C11 A:X9Z401 4.8 42.6 1.0 C13 A:X9Z401 4.9 39.8 1.0 CB A:GLN192 5.0 41.8 1.0 CB A:MET165 5.0 41.7 1.0 SD A:MET165 5.0 47.3 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.