Fluorine in PDB 8jop: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A, PDB code: 8jop was solved by R.Zeng, Y.Z.Liu, F.L.Wang, S.Y.Yang, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.49 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.577, 51.656, 43.437, 90, 104.64, 90
R / Rfree (%)	19.5 / 24.8

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A (pdb code 8jop). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A, PDB code: 8jop:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:51.5 occ:1.00 F29 A:UWO401 0.0 51.5 1.0 C28 A:UWO401 1.4 56.9 1.0 F30 A:UWO401 2.1 60.6 1.0 F31 A:UWO401 2.2 53.9 1.0 C27 A:UWO401 2.4 55.2 1.0 C32 A:UWO401 2.8 54.4 1.0 C26 A:UWO401 3.7 54.5 1.0 C33 A:UWO401 4.2 48.9 1.0 C25 A:UWO401 4.8 56.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:60.6 occ:1.00 F30 A:UWO401 0.0 60.6 1.0 C28 A:UWO401 1.3 56.9 1.0 F29 A:UWO401 2.1 51.5 1.0 F31 A:UWO401 2.2 53.9 1.0 C27 A:UWO401 2.4 55.2 1.0 C26 A:UWO401 3.1 54.5 1.0 C32 A:UWO401 3.3 54.4 1.0 CB A:MET49 3.7 72.4 1.0 SD A:MET49 3.8 74.0 1.0 O A:MET49 4.0 72.9 1.0 OE1 A:GLN189 4.1 67.1 1.0 C25 A:UWO401 4.3 56.5 1.0 CG A:MET49 4.4 71.9 1.0 C33 A:UWO401 4.4 48.9 1.0 C A:MET49 4.8 68.1 1.0 CD A:GLN189 4.9 70.8 1.0 C24 A:UWO401 4.9 51.6 1.0 CA A:MET49 4.9 70.6 1.0 CG A:GLN189 5.0 64.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:53.9 occ:1.00 F31 A:UWO401 0.0 53.9 1.0 C28 A:UWO401 1.3 56.9 1.0 F30 A:UWO401 2.2 60.6 1.0 F29 A:UWO401 2.2 51.5 1.0 C27 A:UWO401 2.4 55.2 1.0 C26 A:UWO401 2.8 54.5 1.0 C32 A:UWO401 3.6 54.4 1.0 C25 A:UWO401 4.2 56.5 1.0 O A:MET49 4.6 72.9 1.0 O A:SER46 4.6 69.2 1.0 CB A:MET49 4.7 72.4 1.0 SD A:MET49 4.7 74.0 1.0 C33 A:UWO401 4.8 48.9 1.0 CB A:SER46 4.9 72.0 1.0

F.Wang, R.Zeng, J.Qiao, A.Xia, Y.Li, F.Li, Y.Wu, Y.Liu, X.Zhao, J.Lei, S.Yang. Discovery of Benzodiazepine Derivatives As A New Class of Covalent Inhibitors of Sars-Cov-2 Main Protease. Bioorg.Med.Chem.Lett. V. 92 29407 2023.
ISSN: ESSN 1464-3405
PubMed: 37437852
DOI: 10.1016/J.BMCL.2023.129407