Fluorine in PDB 7sf3: Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M, PDB code: 7sf3 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)	37.30 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.684, 64.44, 105.449, 90, 90, 90
R / Rfree (%)	16.9 / 19.5

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M 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 ML1006M (pdb code 7sf3). 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 ML1006M, PDB code: 7sf3:
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 ML1006M


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 ML1006M within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:51.8 occ:1.00 F1 A:90H401 0.0 51.8 1.0 C16 A:90H401 1.3 37.2 1.0 F3 A:90H401 2.1 43.5 1.0 F2 A:90H401 2.1 47.1 1.0 C15 A:90H401 2.4 31.9 1.0 O2 A:90H401 3.0 33.1 1.0 N2 A:90H401 3.2 20.6 1.0 O A:HOH648 3.3 37.0 1.0 O A:THR190 3.7 32.8 1.0 O A:GLU166 3.9 18.8 1.0 O A:GLN192 3.9 31.9 1.0 CD A:PRO168 4.1 33.5 1.0 N A:GLN192 4.1 31.0 1.0 O A:HOH694 4.2 31.9 1.0 CD2 A:LEU167 4.3 28.8 1.0 CA A:LEU167 4.4 22.9 1.0 CB A:GLN192 4.5 26.6 1.0 C10 A:90H401 4.5 20.2 1.0 C14 A:90H401 4.6 23.7 1.0 C A:THR190 4.7 37.4 1.0 CA A:GLN192 4.7 29.7 1.0 C A:GLN192 4.7 30.3 1.0 CG A:PRO168 4.8 34.4 1.0 CE A:MET165 4.8 34.2 1.0 C A:GLU166 4.9 19.5 1.0 N A:PRO168 5.0 29.8 1.0 C A:ALA191 5.0 33.1 1.0 CA A:ALA191 5.0 37.9 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M


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 ML1006M within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:47.1 occ:1.00 F2 A:90H401 0.0 47.1 1.0 C16 A:90H401 1.3 37.2 1.0 F3 A:90H401 2.1 43.5 1.0 F1 A:90H401 2.1 51.8 1.0 C15 A:90H401 2.4 31.9 1.0 O2 A:90H401 2.7 33.1 1.0 O A:THR190 2.9 32.8 1.0 CE A:MET165 3.2 34.2 1.0 NE2 A:GLN192 3.2 25.3 1.0 N2 A:90H401 3.5 20.6 1.0 CB A:GLN192 3.5 26.6 1.0 CD A:GLN192 3.7 24.0 1.0 CG A:GLN192 3.7 25.3 1.0 N A:GLN192 4.1 31.0 1.0 C A:THR190 4.1 37.4 1.0 O A:ARG188 4.1 23.2 1.0 CD2 A:LEU167 4.2 28.8 1.0 CA A:GLN192 4.3 29.7 1.0 N A:THR190 4.4 32.1 1.0 O A:GLN192 4.6 31.9 1.0 OE1 A:GLN192 4.7 25.9 1.0 O A:GLU166 4.7 18.8 1.0 C10 A:90H401 4.7 20.2 1.0 C A:ALA191 4.8 33.1 1.0 C A:GLN192 4.9 30.3 1.0 SD A:MET165 4.9 33.0 1.0 O A:HOH694 5.0 31.9 1.0 CA A:THR190 5.0 38.4 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006M


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 ML1006M within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:43.5 occ:1.00 F3 A:90H401 0.0 43.5 1.0 C16 A:90H401 1.3 37.2 1.0 F2 A:90H401 2.1 47.1 1.0 F1 A:90H401 2.1 51.8 1.0 C15 A:90H401 2.3 31.9 1.0 N2 A:90H401 2.6 20.6 1.0 O A:GLU166 2.7 18.8 1.0 CE A:MET165 3.1 34.2 1.0 CD2 A:LEU167 3.3 28.8 1.0 O2 A:90H401 3.4 33.1 1.0 C A:GLU166 3.5 19.5 1.0 CA A:LEU167 3.7 22.9 1.0 O A:HOH648 3.8 37.0 1.0 N A:LEU167 3.9 21.1 1.0 CG A:LEU167 3.9 27.9 1.0 C10 A:90H401 4.0 20.2 1.0 CB A:LEU167 4.3 25.8 1.0 C9 A:90H401 4.6 18.8 1.0 N A:GLU166 4.6 16.4 1.0 SD A:MET165 4.6 33.0 1.0 O3 A:90H401 4.6 18.7 1.0 CB A:GLN192 4.6 26.6 1.0 CB A:MET165 4.7 21.2 1.0 CG A:MET165 4.7 23.9 1.0 CD A:PRO168 4.7 33.5 1.0 CA A:GLU166 4.7 17.9 1.0 O A:GLN192 4.8 31.9 1.0 C A:LEU167 4.8 28.5 1.0 O A:THR190 4.8 32.8 1.0 NE2 A:GLN192 4.9 25.3 1.0 C11 A:90H401 5.0 20.0 1.0

M.Westberg, Y.Su, X.Zou, A.Rustagi, A.Beck, L.Ning, D.Fernandez, C.Blish, M.Z.Lin. Rational Design of A New Class of Protease Inhibitors For the Potential Treatment of Coronavirus Diseases To Be Published.