Fluorine in PDB 7u92: Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A, PDB code: 7u92 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)	35.04 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.529, 64.264, 104.823, 90, 90, 90
R / Rfree (%)	17.2 / 20.7

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A 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 ML1006A (pdb code 7u92). 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 ML1006A, PDB code: 7u92:
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 ML1006A


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 ML1006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:39.4 occ:1.00 F1 A:M0C401 0.0 39.4 1.0 C16 A:M0C401 1.3 37.9 1.0 F3 A:M0C401 2.2 45.2 1.0 F2 A:M0C401 2.2 42.6 1.0 C15 A:M0C401 2.4 32.9 1.0 O2 A:M0C401 2.7 33.5 1.0 O A:THR190 3.0 35.4 1.0 CE A:MET165 3.1 37.9 1.0 NE2 A:GLN192 3.2 32.9 1.0 N2 A:M0C401 3.4 25.2 1.0 CB A:GLN192 3.7 32.9 1.0 CD A:GLN192 3.7 31.5 1.0 CG A:GLN192 3.8 30.3 1.0 O A:ARG188 4.0 24.8 1.0 CD2 A:LEU167 4.1 29.9 1.0 C A:THR190 4.2 37.5 1.0 N A:GLN192 4.3 34.3 1.0 N A:THR190 4.4 34.2 1.0 CA A:GLN192 4.5 33.7 1.0 O A:GLU166 4.6 21.2 1.0 OE1 A:GLN192 4.7 28.4 1.0 C10 A:M0C401 4.7 25.1 1.0 O A:GLN192 4.7 33.6 1.0 SD A:MET165 4.8 35.8 1.0 O A:HOH662 4.9 36.0 1.0 C A:ALA191 4.9 36.1 1.0 CA A:THR190 5.0 37.6 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A


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 ML1006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.6 occ:1.00 F2 A:M0C401 0.0 42.6 1.0 C16 A:M0C401 1.3 37.9 1.0 F3 A:M0C401 2.1 45.2 1.0 F1 A:M0C401 2.2 39.4 1.0 C15 A:M0C401 2.3 32.9 1.0 O A:GLU166 2.6 21.2 1.0 N2 A:M0C401 2.6 25.2 1.0 CE A:MET165 3.1 37.9 1.0 CD2 A:LEU167 3.3 29.9 1.0 C A:GLU166 3.3 22.6 1.0 O2 A:M0C401 3.4 33.5 1.0 CA A:LEU167 3.6 27.3 1.0 N A:LEU167 3.7 25.4 1.0 C10 A:M0C401 4.0 25.1 1.0 CG A:LEU167 4.0 27.9 1.0 CB A:LEU167 4.3 27.7 1.0 N A:GLU166 4.4 20.7 1.0 C9 A:M0C401 4.5 23.2 1.0 O3 A:M0C401 4.5 23.3 1.0 CA A:GLU166 4.5 21.0 1.0 CB A:MET165 4.5 25.2 1.0 SD A:MET165 4.6 35.8 1.0 CG A:MET165 4.6 28.5 1.0 C A:LEU167 4.7 34.5 1.0 CD A:PRO168 4.7 39.3 1.0 CB A:GLN192 4.9 32.9 1.0 C11 A:M0C401 4.9 25.1 1.0 NE2 A:GLN192 4.9 32.9 1.0 C12 A:M0C401 4.9 26.8 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease (Mpro) in Complex with ML1006A


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 ML1006A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:45.2 occ:1.00 F3 A:M0C401 0.0 45.2 1.0 C16 A:M0C401 1.3 37.9 1.0 F2 A:M0C401 2.1 42.6 1.0 F1 A:M0C401 2.2 39.4 1.0 C15 A:M0C401 2.3 32.9 1.0 O2 A:M0C401 3.0 33.5 1.0 N2 A:M0C401 3.1 25.2 1.0 O A:GLU166 3.7 21.2 1.0 O A:THR190 3.8 35.4 1.0 CD A:PRO168 4.0 39.3 1.0 O A:GLN192 4.1 33.6 1.0 CA A:LEU167 4.2 27.3 1.0 CD2 A:LEU167 4.2 29.9 1.0 O A:HOH662 4.3 36.0 1.0 N A:GLN192 4.3 34.3 1.0 C10 A:M0C401 4.4 25.1 1.0 CB A:GLN192 4.6 32.9 1.0 C A:GLU166 4.7 22.6 1.0 CE A:MET165 4.7 37.9 1.0 C14 A:M0C401 4.7 28.7 1.0 CG A:PRO168 4.7 41.8 1.0 N A:PRO168 4.8 37.5 1.0 C A:THR190 4.8 37.5 1.0 C A:LEU167 4.9 34.5 1.0 CA A:GLN192 4.9 33.7 1.0 N A:LEU167 4.9 25.4 1.0 C A:GLN192 4.9 33.4 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.