Fluorine in PDB 8fy6: Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor

All present enzymatic activity of Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor:
3.4.22.69;

The structure of Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor, PDB code: 8fy6 was solved by W.Fried, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.64 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.455, 63.276, 103.843, 90, 90, 90
R / Rfree (%)	18.7 / 22.2

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor (pdb code 8fy6). 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 in Complex with Covalent Inhibitor, PDB code: 8fy6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor


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 in Complex with Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:73.3 occ:1.00 F1 A:OW1401 0.0 73.3 1.0 C17 A:OW1401 1.4 53.8 1.0 F2 A:OW1401 2.2 52.6 1.0 F3 A:OW1401 2.2 66.1 1.0 C16 A:OW1401 2.4 44.9 1.0 O4 A:OW1401 2.6 43.2 1.0 HE3 A:MET165 2.7 62.5 1.0 HB2 A:GLN192 2.7 55.8 1.0 O A:THR190 3.0 49.9 1.0 HE21 A:GLN192 3.1 50.0 1.0 HE1 A:MET165 3.1 62.5 1.0 CE A:MET165 3.2 52.0 1.0 HE2 A:MET165 3.2 62.5 1.0 NE2 A:GLN192 3.4 41.6 1.0 HD13 A:LEU167 3.5 53.4 1.0 N4 A:OW1401 3.5 30.3 1.0 H A:THR190 3.6 53.0 1.0 CB A:GLN192 3.6 46.4 1.0 HG3 A:GLN192 3.7 53.8 1.0 H A:GLN192 3.7 53.8 1.0 HE22 A:GLN192 3.8 50.0 1.0 H20 A:OW1401 3.8 36.5 1.0 CD A:GLN192 3.8 46.4 1.0 CG A:GLN192 3.9 44.8 1.0 O A:ARG188 4.0 35.6 1.0 N A:GLN192 4.1 44.8 1.0 HA A:GLN189 4.2 44.2 1.0 C A:THR190 4.2 48.8 1.0 HB3 A:GLN192 4.3 55.8 1.0 N A:THR190 4.3 44.1 1.0 HD3 A:PRO168 4.3 65.9 1.0 CD1 A:LEU167 4.3 44.5 1.0 HA A:LEU167 4.4 49.3 1.0 CA A:GLN192 4.4 47.6 1.0 HD12 A:LEU167 4.5 53.4 1.0 HD11 A:LEU167 4.5 53.4 1.0 O A:GLN192 4.5 53.4 1.0 O A:GLU166 4.6 34.6 1.0 OE1 A:GLN192 4.7 39.9 1.0 C15 A:OW1401 4.8 39.5 1.0 H19 A:OW1401 4.8 47.5 1.0 HB2 A:MET165 4.8 43.6 1.0 C A:GLN192 4.9 55.0 1.0 HG2 A:GLN192 4.9 53.8 1.0 SD A:MET165 4.9 45.0 1.0 C A:ALA191 4.9 47.4 1.0 HG22 A:THR190 4.9 57.1 1.0 CA A:THR190 4.9 49.9 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor


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 in Complex with Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:52.6 occ:1.00 F2 A:OW1401 0.0 52.6 1.0 C17 A:OW1401 1.4 53.8 1.0 F1 A:OW1401 2.2 73.3 1.0 F3 A:OW1401 2.2 66.1 1.0 C16 A:OW1401 2.4 44.9 1.0 HE3 A:MET165 2.4 62.5 1.0 H20 A:OW1401 2.4 36.5 1.0 HD13 A:LEU167 2.5 53.4 1.0 O A:GLU166 2.5 34.6 1.0 HE2 A:MET165 2.5 62.5 1.0 N4 A:OW1401 2.7 30.3 1.0 HA A:LEU167 2.8 49.3 1.0 CE A:MET165 2.9 52.0 1.0 C A:GLU166 3.3 38.2 1.0 O4 A:OW1401 3.4 43.2 1.0 HB2 A:MET165 3.4 43.6 1.0 CD1 A:LEU167 3.5 44.5 1.0 HE1 A:MET165 3.5 62.5 1.0 HG3 A:MET165 3.5 43.4 1.0 HD22 A:LEU167 3.5 55.3 1.0 CA A:LEU167 3.6 41.1 1.0 HD3 A:PRO168 3.8 65.9 1.0 N A:LEU167 3.8 38.4 1.0 HD11 A:LEU167 3.9 53.4 1.0 HD12 A:LEU167 3.9 53.4 1.0 HB2 A:GLN192 3.9 55.8 1.0 H A:GLU166 4.0 37.9 1.0 CG A:MET165 4.1 36.1 1.0 C15 A:OW1401 4.1 39.5 1.0 N A:GLU166 4.2 31.6 1.0 CB A:MET165 4.2 36.3 1.0 CG A:LEU167 4.2 45.6 1.0 CD2 A:LEU167 4.3 46.0 1.0 SD A:MET165 4.3 45.0 1.0 H28 A:OW1401 4.3 40.6 1.0 CA A:GLU166 4.4 35.5 1.0 CB A:LEU167 4.5 41.9 1.0 HD21 A:LEU167 4.5 55.3 1.0 O3 A:OW1401 4.5 35.7 1.0 C14 A:OW1401 4.6 35.0 1.0 H A:LEU167 4.6 46.1 1.0 C A:LEU167 4.6 41.8 1.0 H19 A:OW1401 4.6 47.5 1.0 CD A:PRO168 4.7 54.9 1.0 H26 A:OW1401 4.8 42.5 1.0 HB3 A:MET165 4.8 43.6 1.0 CB A:GLN192 4.9 46.4 1.0 C A:MET165 4.9 33.2 1.0 HB3 A:LEU167 4.9 50.3 1.0 HE21 A:GLN192 4.9 50.0 1.0 HA A:GLU166 5.0 42.6 1.0 N A:PRO168 5.0 48.6 1.0 NE2 A:GLN192 5.0 41.6 1.0 O A:GLN192 5.0 53.4 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 Main Protease in Complex with Covalent Inhibitor


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 in Complex with Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:66.1 occ:1.00 F3 A:OW1401 0.0 66.1 1.0 C17 A:OW1401 1.4 53.8 1.0 F2 A:OW1401 2.2 52.6 1.0 F1 A:OW1401 2.2 73.3 1.0 C16 A:OW1401 2.4 44.9 1.0 HD3 A:PRO168 2.8 65.9 1.0 H20 A:OW1401 3.0 36.5 1.0 N4 A:OW1401 3.0 30.3 1.0 O4 A:OW1401 3.1 43.2 1.0 HA A:LEU167 3.2 49.3 1.0 O A:GLU166 3.4 34.6 1.0 HD13 A:LEU167 3.5 53.4 1.0 HG3 A:PRO168 3.7 64.5 1.0 CD A:PRO168 3.7 54.9 1.0 H26 A:OW1401 3.8 42.5 1.0 H A:GLN192 3.9 53.8 1.0 HB2 A:GLN192 4.0 55.8 1.0 O A:THR190 4.1 49.9 1.0 CA A:LEU167 4.1 41.1 1.0 O A:GLN192 4.1 53.4 1.0 H28 A:OW1401 4.2 40.6 1.0 HE3 A:MET165 4.2 62.5 1.0 N A:PRO168 4.2 48.6 1.0 CG A:PRO168 4.2 53.7 1.0 HD12 A:LEU167 4.3 53.4 1.0 C15 A:OW1401 4.3 39.5 1.0 CD1 A:LEU167 4.3 44.5 1.0 C A:LEU167 4.4 41.8 1.0 HD2 A:PRO168 4.4 65.9 1.0 C A:GLU166 4.4 38.2 1.0 HE2 A:MET165 4.4 62.5 1.0 H19 A:OW1401 4.6 47.5 1.0 N A:GLN192 4.7 44.8 1.0 C20 A:OW1401 4.7 35.4 1.0 CE A:MET165 4.7 52.0 1.0 N A:LEU167 4.7 38.4 1.0 HG2 A:PRO168 4.8 64.5 1.0 CB A:GLN192 4.9 46.4 1.0 HA A:PRO168 4.9 63.0 1.0 HD11 A:LEU167 4.9 53.4 1.0 C18 A:OW1401 4.9 30.6 1.0 C A:GLN192 5.0 55.0 1.0

C.Ngo, W.Fried, S.Aliyari, J.Feng, C.Qin, S.Zhang, H.Yang, J.Shanaa, P.Feng, G.Cheng, X.S.Chen, C.Zhang. Alkyne As A Latent Warhead to Covalently Target Sars-Cov-2 Main Protease. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37595260
DOI: 10.1021/ACS.JMEDCHEM.3C00810