Fluorine in PDB 7si9: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332:
3.4.22.69;

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332, PDB code: 7si9 was solved by A.Kovalevsky, D.W.Kneller, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.16 / 2.00
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.544, 81.835, 91.736, 90, 95.34, 90
R / Rfree (%)	17.2 / 20.7

The binding sites of Fluorine atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332 (pdb code 7si9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332, PDB code: 7si9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:60.0 occ:1.00 F33 A:9I7401 0.0 60.0 1.0 C32 A:9I7401 1.4 61.8 1.0 F35 A:9I7401 2.2 75.1 1.0 F34 A:9I7401 2.2 66.8 1.0 C21 A:9I7401 2.4 60.9 1.0 N20 A:9I7401 3.0 58.2 1.0 CD A:PRO168 3.3 48.2 1.0 O22 A:9I7401 3.3 63.2 1.0 O A:GLU166 3.5 30.3 1.0 CA A:LEU167 3.8 34.1 1.0 N A:PRO168 3.9 44.7 1.0 C A:LEU167 4.2 38.4 1.0 CD2 A:LEU167 4.2 39.5 1.0 CG A:PRO168 4.4 45.2 1.0 C15 A:9I7401 4.4 56.4 1.0 O A:THR190 4.4 52.4 1.0 C A:GLU166 4.4 29.1 1.0 O A:GLN192 4.5 51.1 1.0 N A:LEU167 4.6 31.4 1.0 CB A:LEU167 4.7 31.5 1.0 C19 A:9I7401 4.8 51.3 1.0 CB A:PRO168 4.9 44.5 1.0 CA A:PRO168 4.9 44.7 1.0

Fluorine binding site 2 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:66.8 occ:1.00 F34 A:9I7401 0.0 66.8 1.0 C32 A:9I7401 1.3 61.8 1.0 F35 A:9I7401 2.2 75.1 1.0 F33 A:9I7401 2.2 60.0 1.0 C21 A:9I7401 2.4 60.9 1.0 O22 A:9I7401 2.6 63.2 1.0 O A:THR190 3.2 52.4 1.0 NE2 A:GLN192 3.5 36.1 1.0 N20 A:9I7401 3.6 58.2 1.0 CG A:GLN192 3.8 43.2 1.0 O A:ARG188 4.0 41.5 1.0 CE A:MET165 4.0 33.5 1.0 CD A:GLN192 4.0 37.5 1.0 CB A:GLN192 4.3 37.7 1.0 C A:THR190 4.3 59.5 1.0 N A:THR190 4.5 63.3 1.0 N A:GLN192 4.5 52.6 1.0 CD2 A:LEU167 4.5 39.5 1.0 CA A:GLN189 4.6 62.2 1.0 O A:GLU166 4.7 30.3 1.0 C15 A:9I7401 4.8 56.4 1.0 C A:GLN189 4.9 59.8 1.0 O A:GLN192 4.9 51.1 1.0 CA A:GLN192 4.9 41.9 1.0

Fluorine binding site 3 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Pf-07321332 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:75.1 occ:1.00 F35 A:9I7401 0.0 75.1 1.0 C32 A:9I7401 1.3 61.8 1.0 F34 A:9I7401 2.2 66.8 1.0 F33 A:9I7401 2.2 60.0 1.0 C21 A:9I7401 2.4 60.9 1.0 N20 A:9I7401 2.8 58.2 1.0 O A:GLU166 2.8 30.3 1.0 CE A:MET165 3.2 33.5 1.0 O22 A:9I7401 3.3 63.2 1.0 CD2 A:LEU167 3.4 39.5 1.0 C A:GLU166 3.6 29.1 1.0 CA A:LEU167 3.7 34.1 1.0 N A:LEU167 4.0 31.4 1.0 C15 A:9I7401 4.1 56.4 1.0 CB A:MET165 4.2 24.9 1.0 CG A:LEU167 4.2 34.6 1.0 CG A:MET165 4.3 25.7 1.0 SD A:MET165 4.3 44.7 1.0 C14 A:9I7401 4.5 59.7 1.0 CB A:LEU167 4.5 31.5 1.0 N A:GLU166 4.6 24.4 1.0 NE2 A:GLN192 4.6 36.1 1.0 CD A:PRO168 4.6 48.2 1.0 O23 A:9I7401 4.6 45.7 1.0 CA A:GLU166 4.7 22.7 1.0 C A:LEU167 4.8 38.4 1.0

D.W.Kneller, H.Li, S.Galanie, G.Phillips, A.Labbe, K.L.Weiss, Q.Zhang, M.A.Arnould, L.Coates, J.M.Louis, P.V.Bonnesen, A.Kovalevsky. Desing of Hybrid Covalent Inhibitors of Sars-Cov-2 Main Protease Containing A Nitrile Warhead To Be Published.