Fluorine in PDB 7sfi: Sars-Cov-2 Main Protease (Mpro) in Complex with ML104

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML104:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML104, PDB code: 7sfi 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)	35.24 / 1.95
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.49, 63.586, 105.64, 90, 90, 90
R / Rfree (%)	19.5 / 23.9

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML104 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML104 (pdb code 7sfi). 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 ML104, PDB code: 7sfi:
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 ML104


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 ML104 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.2 occ:1.00 F1 A:91Z401 0.0 33.2 1.0 C12 A:91Z401 1.4 34.6 1.0 C11 A:91Z401 2.4 32.5 1.0 C13 A:91Z401 2.4 33.2 1.0 N2 A:91Z401 2.7 31.5 1.0 O A:GLU166 2.8 25.4 1.0 C A:GLU166 3.0 26.5 1.0 N A:LEU167 3.3 31.0 1.0 CB A:GLU166 3.4 26.4 1.0 CG A:GLU166 3.4 28.2 1.0 O A:LEU167 3.5 28.6 1.0 C A:LEU167 3.5 34.1 1.0 C14 A:91Z401 3.6 33.1 1.0 O A:HOH564 3.6 38.9 1.0 C16 A:91Z401 3.6 31.9 1.0 CA A:LEU167 3.6 31.4 1.0 CA A:GLU166 3.7 27.5 1.0 C15 A:91Z401 4.1 33.5 1.0 OE1 A:GLU166 4.1 31.4 1.0 C10 A:91Z401 4.1 31.6 1.0 O A:HOH597 4.2 31.6 1.0 N A:PRO168 4.2 37.2 1.0 CD A:GLU166 4.2 27.6 1.0 O A:HOH647 4.5 47.9 1.0 N A:GLU166 4.6 25.9 1.0 O2 A:91Z401 4.6 30.5 1.0 F2 A:91Z401 4.7 30.4 1.0 F3 A:91Z401 4.7 38.1 1.0 CD A:PRO168 4.8 38.7 1.0 C9 A:91Z401 4.9 31.0 1.0 CA A:PRO168 4.9 38.2 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML104


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 ML104 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.4 occ:1.00 F2 A:91Z401 0.0 30.4 1.0 C14 A:91Z401 1.4 33.1 1.0 C15 A:91Z401 2.3 33.5 1.0 C13 A:91Z401 2.4 33.2 1.0 O A:HOH676 3.1 42.2 1.0 CG A:PRO168 3.6 39.5 1.0 C16 A:91Z401 3.6 31.9 1.0 O A:HOH637 3.6 48.0 1.0 C12 A:91Z401 3.6 34.6 1.0 C11 A:91Z401 4.1 32.5 1.0 CD A:PRO168 4.2 38.7 1.0 CB A:PRO168 4.4 37.8 1.0 N A:PRO168 4.5 37.2 1.0 CA A:PRO168 4.6 38.2 1.0 F3 A:91Z401 4.7 38.1 1.0 F1 A:91Z401 4.7 33.2 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML104


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 ML104 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:38.1 occ:1.00 F3 A:91Z401 0.0 38.1 1.0 C16 A:91Z401 1.3 31.9 1.0 C15 A:91Z401 2.3 33.5 1.0 C11 A:91Z401 2.4 32.5 1.0 C10 A:91Z401 2.7 31.6 1.0 N2 A:91Z401 2.9 31.5 1.0 O A:HOH602 3.5 59.7 1.0 C14 A:91Z401 3.6 33.1 1.0 CG A:GLN189 3.6 34.7 1.0 C12 A:91Z401 3.6 34.6 1.0 O A:HOH647 3.9 47.9 1.0 C13 A:91Z401 4.1 33.2 1.0 C9 A:91Z401 4.2 31.0 1.0 CD A:GLN189 4.3 35.1 1.0 O A:HOH637 4.4 48.0 1.0 C8 A:91Z401 4.5 34.0 1.0 O A:HOH597 4.6 31.6 1.0 F2 A:91Z401 4.7 30.4 1.0 CB A:GLN189 4.7 37.3 1.0 F1 A:91Z401 4.7 33.2 1.0 CA A:GLN189 4.8 37.8 1.0 NE2 A:GLN189 4.8 35.9 1.0 N1 A:91Z401 4.8 29.6 1.0 O A:THR190 4.8 50.8 1.0 OE1 A:GLN189 4.9 36.1 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.