Fluorine in PDB 7wym: Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor

All present enzymatic activity of Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor:
3.4.22.69;

The structure of Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor, PDB code: 7wym was solved by B.Qin, P.Hou, X.Gao, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.26 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.715, 53.717, 44.775, 90, 101.24, 90
R / Rfree (%)	19.4 / 22.1

The binding sites of Fluorine atom in the Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor (pdb code 7wym). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor, PDB code: 7wym:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:83.2 occ:1.00 F01 A:G7L401 0.0 83.2 1.0 C09 A:G7L401 1.4 84.0 1.0 F03 A:G7L401 2.2 87.0 1.0 F02 A:G7L401 2.2 83.9 1.0 C08 A:G7L401 2.4 81.0 1.0 HG2 A:MET165 2.4 62.1 0.5 HE3 A:MET165 2.9 72.8 0.5 N02 A:G7L401 3.1 76.7 1.0 CG A:MET165 3.1 51.6 0.5 HA A:ASP187 3.2 43.3 1.0 SD A:MET165 3.3 57.1 0.5 HB2 A:ASP187 3.4 43.6 1.0 C07 A:G7L401 3.4 77.9 1.0 HB3 A:MET165 3.5 55.9 0.5 HD2 A:HIS41 3.5 46.7 1.0 HG3 A:MET165 3.5 62.1 0.5 CE A:MET165 3.6 60.5 0.5 HE2 A:MET165 3.7 62.9 0.5 H9 A:G7L401 3.7 93.7 1.0 C A:ASP187 3.7 43.8 1.0 CA A:ASP187 3.8 36.0 1.0 CD2 A:HIS41 3.8 38.8 1.0 N A:ARG188 3.9 48.1 1.0 CB A:ASP187 3.9 36.1 1.0 H A:ARG188 4.1 57.9 1.0 HE1 A:MET165 4.1 72.8 0.5 HA A:ARG188 4.1 61.5 1.0 O A:ASP187 4.1 40.5 1.0 HB2 A:MET165 4.1 55.9 0.5 HB3 A:ASP187 4.2 43.6 1.0 CB A:MET165 4.2 46.4 0.5 C06 A:G7L401 4.3 73.3 1.0 HE2 A:MET165 4.3 72.8 0.5 CG A:HIS41 4.3 47.0 1.0 HB3 A:MET165 4.3 55.9 0.5 NE2 A:HIS41 4.4 36.6 1.0 CB A:MET165 4.4 46.4 0.5 HB3 A:HIS41 4.4 52.2 1.0 CA A:ARG188 4.4 51.1 1.0 HE2 A:HIS41 4.5 44.2 1.0 C A:ARG188 4.5 51.8 1.0 HB2 A:HIS41 4.5 52.2 1.0 CE A:MET165 4.5 52.3 0.5 O A:HIS164 4.6 35.7 1.0 HB3 A:HIS164 4.7 42.8 1.0 S01 A:G7L401 4.7 76.3 1.0 HH A:TYR54 4.7 47.8 1.0 CB A:HIS41 4.7 43.3 1.0 O A:ARG188 4.7 45.5 1.0 HA A:MET165 4.8 48.9 1.0 HG2 A:MET49 4.9 93.4 1.0 HE1 A:MET165 4.9 62.9 0.5 SD A:MET165 4.9 62.1 0.5 OH A:TYR54 4.9 39.7 1.0

Fluorine binding site 2 out of 3 in the Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:83.9 occ:1.00 F02 A:G7L401 0.0 83.9 1.0 C09 A:G7L401 1.4 84.0 1.0 F01 A:G7L401 2.2 83.2 1.0 F03 A:G7L401 2.2 87.0 1.0 C08 A:G7L401 2.4 81.0 1.0 H9 A:G7L401 2.6 93.7 1.0 C07 A:G7L401 2.8 77.9 1.0 HG2 A:MET49 2.8 93.4 1.0 HA A:ARG188 3.3 61.5 1.0 HB3 A:MET49 3.3 93.0 1.0 HB2 A:HIS41 3.4 52.2 1.0 N02 A:G7L401 3.6 76.7 1.0 CG A:MET49 3.7 77.7 1.0 O A:ASP187 3.7 40.5 1.0 HH A:TYR54 3.7 47.8 1.0 HB3 A:HIS41 3.7 52.2 1.0 OH A:TYR54 3.9 39.7 1.0 C A:ASP187 3.9 43.8 1.0 HB2 A:ASP187 3.9 43.6 1.0 CB A:MET49 3.9 77.4 1.0 CB A:HIS41 3.9 43.3 1.0 HA A:MET49 3.9 83.1 1.0 CA A:ARG188 4.0 51.1 1.0 N A:ARG188 4.1 48.1 1.0 CG A:HIS41 4.1 47.0 1.0 HD2 A:HIS41 4.3 46.7 1.0 CD2 A:HIS41 4.3 38.8 1.0 HG3 A:MET49 4.4 93.4 1.0 H A:GLN189 4.4 61.1 1.0 SD A:MET49 4.4 110.8 1.0 CA A:MET49 4.4 69.1 1.0 S01 A:G7L401 4.4 76.3 1.0 HE3 A:MET165 4.4 72.8 0.5 C A:ARG188 4.5 51.8 1.0 O A:MET49 4.5 58.4 1.0 HA A:ASP187 4.5 43.3 1.0 HG3 A:PRO52 4.5 65.3 1.0 N A:GLN189 4.6 50.8 1.0 HG2 A:MET165 4.6 62.1 0.5 CA A:ASP187 4.6 36.0 1.0 HE2 A:MET49 4.6 103.9 1.0 C06 A:G7L401 4.6 73.3 1.0 H A:ARG188 4.7 57.9 1.0 CB A:ASP187 4.7 36.1 1.0 HB2 A:MET49 4.7 93.0 1.0 ND1 A:HIS41 4.8 42.6 1.0 HB2 A:GLN189 4.8 69.4 1.0

Fluorine binding site 3 out of 3 in the Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Sars-Cov-2 Main Protease with 337 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:87.0 occ:1.00 F03 A:G7L401 0.0 87.0 1.0 C09 A:G7L401 1.4 84.0 1.0 F01 A:G7L401 2.2 83.2 1.0 F02 A:G7L401 2.2 83.9 1.0 C08 A:G7L401 2.4 81.0 1.0 HE3 A:MET165 2.6 72.8 0.5 N02 A:G7L401 2.9 76.7 1.0 HB2 A:GLN189 3.1 69.4 1.0 N A:GLN189 3.2 50.8 1.0 C A:ARG188 3.3 51.8 1.0 HA A:ARG188 3.3 61.5 1.0 HB3 A:MET49 3.3 93.0 1.0 HA A:GLN189 3.4 72.9 1.0 H A:GLN189 3.4 61.1 1.0 CE A:MET165 3.5 60.5 0.5 C07 A:G7L401 3.6 77.9 1.0 CA A:ARG188 3.7 51.1 1.0 CA A:GLN189 3.7 60.6 1.0 O A:ARG188 3.7 45.5 1.0 HE1 A:MET165 3.7 72.8 0.5 HG2 A:MET165 3.8 62.1 0.5 CB A:GLN189 3.8 57.6 1.0 N A:ARG188 3.9 48.1 1.0 H9 A:G7L401 3.9 93.7 1.0 HG2 A:MET49 4.1 93.4 1.0 H A:ARG188 4.1 57.9 1.0 C06 A:G7L401 4.1 73.3 1.0 O A:MET49 4.2 58.4 1.0 HE2 A:MET165 4.2 72.8 0.5 HB3 A:GLN189 4.2 69.4 1.0 CB A:MET49 4.2 77.4 1.0 SD A:MET165 4.3 57.1 0.5 C A:ASP187 4.3 43.8 1.0 CG A:MET165 4.5 51.6 0.5 HA A:ASP187 4.6 43.3 1.0 CG A:MET49 4.6 77.7 1.0 O A:ASP187 4.7 40.5 1.0 S01 A:G7L401 4.7 76.3 1.0 HB2 A:MET165 4.7 55.9 0.5 HB3 A:MET165 4.8 55.9 0.5 HB2 A:MET49 4.8 93.0 1.0 HA A:MET49 4.9 83.1 1.0 SD A:MET49 4.9 110.8 1.0 HB3 A:MET165 4.9 55.9 0.5

B.Qin, G.B.Craven, P.Hou, J.Chesti, X.Lu, E.S.Child, R.M.L.Morgan, W.Niu, L.Zhao, A.Armstrong, D.J.Mann, S.Cui. Acrylamide Fragment Inhibitors That Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and Sars-Cov-2 Main Protease. Acta Pharm Sin B V. 12 3924 2022.
ISSN: ISSN 2211-3835
PubMed: 35702321
DOI: 10.1016/J.APSB.2022.06.002