Fluorine in PDB 8f2d: Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A, PDB code: 8f2d 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)	37.11 / 1.95
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.396, 64.293, 105.637, 90, 90, 90
R / Rfree (%)	19.6 / 25.2

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A 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 ML4006A (pdb code 8f2d). 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 ML4006A, PDB code: 8f2d:
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 ML4006A


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 ML4006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:46.2 occ:1.00 F1 A:XA8401 0.0 46.2 1.0 C16 A:XA8401 1.3 43.8 1.0 F3 A:XA8401 2.0 54.5 1.0 F2 A:XA8401 2.3 48.6 1.0 C15 A:XA8401 2.4 36.7 1.0 O2 A:XA8401 3.0 35.5 1.0 N2 A:XA8401 3.2 28.4 1.0 CE A:MET165 3.2 34.9 1.0 NE2 A:GLN192 3.6 25.3 1.0 O A:THR190 3.6 28.6 1.0 CD2 A:LEU167 3.8 27.4 1.0 O A:GLU166 3.8 22.5 1.0 CD A:GLN192 4.1 26.9 1.0 O A:ARG188 4.1 23.4 1.0 SD A:MET165 4.3 29.7 1.0 CG A:GLN192 4.4 29.0 1.0 C10 A:XA8401 4.5 26.3 1.0 CA A:LEU167 4.6 29.0 1.0 CB A:GLN192 4.6 29.6 1.0 C A:GLU166 4.6 22.5 1.0 C A:THR190 4.7 25.8 1.0 CG A:MET165 4.7 26.2 1.0 N A:THR190 4.8 26.9 1.0 C9 A:XA8401 4.9 23.3 1.0 OE1 A:GLN192 4.9 28.5 1.0 CB A:MET165 4.9 23.1 1.0 N A:GLN192 4.9 28.5 1.0 CG A:LEU167 4.9 29.9 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A


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 ML4006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:48.6 occ:1.00 F2 A:XA8401 0.0 48.6 1.0 C16 A:XA8401 1.3 43.8 1.0 F3 A:XA8401 2.1 54.5 1.0 F1 A:XA8401 2.3 46.2 1.0 C15 A:XA8401 2.3 36.7 1.0 O2 A:XA8401 2.7 35.5 1.0 O A:THR190 3.0 28.6 1.0 N2 A:XA8401 3.3 28.4 1.0 C A:THR190 3.8 25.8 1.0 CD A:PRO168 3.9 42.4 1.0 CG A:PRO168 3.9 42.5 1.0 CA A:ALA191 4.1 26.9 1.0 N A:GLN192 4.1 28.5 1.0 O A:GLU166 4.2 22.5 1.0 N A:ALA191 4.3 25.8 1.0 C A:ALA191 4.5 26.4 1.0 N A:PRO168 4.5 39.4 1.0 N A:THR190 4.5 26.9 1.0 CA A:LEU167 4.6 29.0 1.0 C10 A:XA8401 4.6 26.3 1.0 CA A:THR190 4.8 30.1 1.0 CD2 A:LEU167 4.8 27.4 1.0 C A:LEU167 4.8 32.6 1.0 O A:GLN192 4.9 34.7 1.0 CG A:GLN192 4.9 29.0 1.0 C14 A:XA8401 4.9 28.6 1.0 CB A:GLN192 4.9 29.6 1.0 NE2 A:GLN192 5.0 25.3 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML4006A


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 ML4006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.5 occ:1.00 F3 A:XA8401 0.0 54.5 1.0 C16 A:XA8401 1.3 43.8 1.0 F1 A:XA8401 2.0 46.2 1.0 F2 A:XA8401 2.1 48.6 1.0 O A:GLU166 2.2 22.5 1.0 C15 A:XA8401 2.3 36.7 1.0 N2 A:XA8401 2.6 28.4 1.0 CA A:LEU167 3.0 29.0 1.0 C A:GLU166 3.1 22.5 1.0 O2 A:XA8401 3.4 35.5 1.0 N A:LEU167 3.5 23.8 1.0 C A:LEU167 3.6 32.6 1.0 CD2 A:LEU167 3.8 27.4 1.0 CD A:PRO168 3.8 42.4 1.0 N A:PRO168 3.9 39.4 1.0 C10 A:XA8401 4.0 26.3 1.0 CB A:LEU167 4.2 28.4 1.0 O A:LEU167 4.4 38.6 1.0 CG A:LEU167 4.4 29.9 1.0 CA A:GLU166 4.4 21.4 1.0 CE A:MET165 4.4 34.9 1.0 CG A:PRO168 4.5 42.5 1.0 N A:GLU166 4.5 19.8 1.0 C9 A:XA8401 4.6 23.3 1.0 O3 A:XA8401 4.7 22.2 1.0 C13 A:XA8401 4.7 28.0 1.0 C11 A:XA8401 4.8 26.7 1.0 O A:THR190 4.8 28.6 1.0 C14 A:XA8401 4.8 28.6 1.0 CA A:PRO168 4.9 41.3 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.