Fluorine in PDB 9boo: Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883

All present enzymatic activity of Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883:
3.4.22.69;

The structure of Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883, PDB code: 9boo was solved by P.Chen, E.Arutyunova, M.J.Lemieux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.42 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.153, 57.4, 49.004, 90, 113, 90
R / Rfree (%)	17.5 / 19.5

The binding sites of Fluorine atom in the Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883 (pdb code 9boo). 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 Mers-Cov NSP5 in Complex with Pf-07817883, PDB code: 9boo:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883


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 Mers-Cov NSP5 in Complex with Pf-07817883 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.4 occ:1.00 F1 A:YDL401 0.0 28.4 1.0 C21 A:YDL401 1.4 25.6 1.0 F3 A:YDL401 2.2 28.8 1.0 F2 A:YDL401 2.2 28.3 1.0 C11 A:YDL401 2.4 24.6 1.0 H12 A:YDL401 2.5 30.5 1.0 H13 A:YDL401 2.7 29.6 1.0 HA A:LYS191 2.8 33.0 1.0 C10 A:YDL401 3.0 25.4 1.0 C A:LYS191 3.0 27.3 1.0 N A:GLN192 3.0 29.4 1.0 HB2 A:GLN192 3.1 36.4 1.0 CA A:LYS191 3.2 27.4 1.0 H A:GLN192 3.2 35.3 1.0 N A:LYS191 3.3 27.1 1.0 HD22 A:LEU49 3.4 40.1 1.0 HA A:GLN192 3.4 33.8 1.0 C A:ASP190 3.5 23.4 1.0 O A:LYS191 3.6 27.6 1.0 C12 A:YDL401 3.6 22.4 1.0 CA A:GLN192 3.6 28.1 1.0 H A:LYS191 3.7 32.6 1.0 HB3 A:LEU49 3.7 36.9 1.0 O A:ASP190 3.7 26.1 1.0 H11 A:YDL401 3.8 30.5 1.0 H14 A:YDL401 3.8 27.0 1.0 CB A:GLN192 3.8 30.3 1.0 N3 A:YDL401 3.9 22.7 1.0 O A:LEU49 4.0 30.1 1.0 HA A:ASP190 4.0 32.5 1.0 HE2 A:MET168 4.3 32.9 0.1 CD2 A:LEU49 4.3 33.4 1.0 C8 A:YDL401 4.3 24.7 1.0 HE3 A:MET168 4.3 30.1 0.9 CA A:ASP190 4.3 27.0 1.0 HB3 A:GLN192 4.4 36.4 1.0 H15 A:YDL401 4.4 27.0 1.0 H9 A:YDL401 4.5 29.6 1.0 HD23 A:LEU49 4.5 40.1 1.0 HB2 A:ASP190 4.5 27.5 1.0 H16 A:YDL401 4.5 30.6 1.0 HH A:TYR54 4.6 31.2 1.0 CB A:LEU49 4.6 30.7 1.0 CB A:LYS191 4.7 31.8 1.0 HD13 A:LEU49 4.8 40.2 1.0 HG3 A:GLN192 4.8 36.0 1.0 O4 A:YDL401 4.8 28.4 1.0 C A:LEU49 4.8 28.3 1.0 OE1 A:GLN192 4.8 34.5 1.0 HE1 A:MET168 4.9 30.1 0.9 CG A:GLN192 4.9 30.0 1.0 HB2 A:LYS191 4.9 38.3 1.0 C13 A:YDL401 4.9 23.7 1.0 HD21 A:LEU49 4.9 40.1 1.0 HA A:LEU49 4.9 37.6 1.0 CG A:LEU49 5.0 33.8 1.0 CB A:ASP190 5.0 22.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883


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 Mers-Cov NSP5 in Complex with Pf-07817883 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.3 occ:1.00 F2 A:YDL401 0.0 28.3 1.0 C21 A:YDL401 1.4 25.6 1.0 F1 A:YDL401 2.2 28.4 1.0 F3 A:YDL401 2.2 28.8 1.0 HE2 A:MET168 2.4 32.9 0.1 C11 A:YDL401 2.4 24.6 1.0 H9 A:YDL401 2.7 29.6 1.0 H14 A:YDL401 2.8 27.0 1.0 C12 A:YDL401 2.9 22.4 1.0 H12 A:YDL401 2.9 30.5 1.0 C10 A:YDL401 3.0 25.4 1.0 C8 A:YDL401 3.0 24.7 1.0 HB3 A:MET168 3.0 31.9 0.9 N3 A:YDL401 3.0 22.7 1.0 HB3 A:MET168 3.1 31.6 0.1 HE3 A:MET168 3.1 30.1 0.9 HA A:ASP190 3.2 32.5 1.0 CE A:MET168 3.3 27.4 0.1 H13 A:YDL401 3.4 29.6 1.0 HE1 A:MET168 3.8 32.9 0.1 HB2 A:MET168 3.8 31.6 0.1 HB2 A:ASP190 3.8 27.5 1.0 CE A:MET168 3.8 25.0 0.9 HE3 A:MET168 3.8 32.9 0.1 CB A:MET168 3.9 26.5 0.9 CB A:MET168 3.9 26.3 0.1 HB2 A:MET168 3.9 31.9 0.9 CA A:ASP190 3.9 27.0 1.0 C13 A:YDL401 3.9 23.7 1.0 C A:ASP190 3.9 23.4 1.0 H15 A:YDL401 3.9 27.0 1.0 H11 A:YDL401 4.0 30.5 1.0 N A:LYS191 4.0 27.1 1.0 SD A:MET168 4.0 27.4 0.9 HE1 A:MET168 4.1 30.1 0.9 H A:LYS191 4.1 32.6 1.0 SD A:MET168 4.2 26.8 0.1 HD2 A:HIS41 4.2 27.9 1.0 CB A:ASP190 4.3 22.9 1.0 O A:GLN167 4.4 21.6 1.0 C9 A:YDL401 4.4 23.7 1.0 O3 A:YDL401 4.4 23.5 1.0 HB3 A:ASP190 4.4 27.5 1.0 CD2 A:HIS41 4.5 23.2 1.0 O A:ASP190 4.5 26.1 1.0 C A:LYS191 4.5 27.3 1.0 HA A:LYS191 4.5 33.0 1.0 H16 A:YDL401 4.5 30.6 1.0 O A:LYS191 4.5 27.6 1.0 CG A:MET168 4.6 27.7 0.9 CA A:LYS191 4.6 27.4 1.0 CG A:MET168 4.7 26.6 0.1 HE2 A:MET168 4.7 30.1 0.9 HD22 A:LEU49 4.7 40.1 1.0 HA A:GLN192 4.7 33.8 1.0 C14 A:YDL401 4.7 25.4 1.0 HA A:MET168 4.8 25.2 0.9 HA A:MET168 4.8 25.3 0.1 HB2 A:GLN192 4.8 36.4 1.0 H10 A:YDL401 4.8 27.8 1.0 O A:MET189 4.9 25.6 1.0 NE2 A:HIS41 4.9 25.0 1.0 N A:GLN192 4.9 29.4 1.0 CA A:MET168 4.9 20.9 0.9 CA A:MET168 5.0 21.0 0.1 CG A:HIS41 5.0 24.7 1.0 O4 A:YDL401 5.0 28.4 1.0 HB3 A:HIS41 5.0 27.2 1.0 HE2 A:HIS41 5.0 30.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Mers-Cov NSP5 in Complex with Pf-07817883


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 Mers-Cov NSP5 in Complex with Pf-07817883 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.8 occ:1.00 F3 A:YDL401 0.0 28.8 1.0 C21 A:YDL401 1.4 25.6 1.0 F1 A:YDL401 2.2 28.4 1.0 F2 A:YDL401 2.2 28.3 1.0 H14 A:YDL401 2.4 27.0 1.0 C11 A:YDL401 2.4 24.6 1.0 H13 A:YDL401 2.6 29.6 1.0 C12 A:YDL401 2.9 22.4 1.0 HB2 A:ASP190 3.1 27.5 1.0 HB3 A:HIS41 3.1 27.2 1.0 HD22 A:LEU49 3.1 40.1 1.0 HB2 A:HIS41 3.2 27.2 1.0 O A:ASP190 3.4 26.1 1.0 CB A:HIS41 3.4 22.6 1.0 HD2 A:HIS41 3.4 27.9 1.0 HH A:TYR54 3.5 31.2 1.0 CG A:HIS41 3.5 24.7 1.0 C A:ASP190 3.5 23.4 1.0 CD2 A:HIS41 3.6 23.2 1.0 H15 A:YDL401 3.6 27.0 1.0 OH A:TYR54 3.7 25.9 1.0 HA A:ASP190 3.7 32.5 1.0 C10 A:YDL401 3.8 25.4 1.0 CB A:ASP190 3.9 22.9 1.0 HE2 A:MET168 3.9 32.9 0.1 H9 A:YDL401 3.9 29.6 1.0 CD2 A:LEU49 3.9 33.4 1.0 HA A:LYS191 3.9 33.0 1.0 CA A:ASP190 4.0 27.0 1.0 C8 A:YDL401 4.0 24.7 1.0 H12 A:YDL401 4.0 30.5 1.0 HD23 A:LEU49 4.1 40.1 1.0 N A:LYS191 4.1 27.1 1.0 HD21 A:LEU49 4.2 40.1 1.0 HB3 A:ASP190 4.4 27.5 1.0 ND1 A:HIS41 4.4 28.0 1.0 N3 A:YDL401 4.4 22.7 1.0 NE2 A:HIS41 4.4 25.0 1.0 CA A:LYS191 4.5 27.4 1.0 H11 A:YDL401 4.6 30.5 1.0 H A:LYS191 4.6 32.6 1.0 HB3 A:LEU49 4.7 36.9 1.0 CE A:MET168 4.8 27.4 0.1 CE1 A:HIS41 4.8 23.8 1.0 C A:LYS191 4.9 27.3 1.0 HE2 A:HIS41 4.9 30.0 1.0 HE1 A:MET168 4.9 32.9 0.1 O A:HOH532 4.9 31.1 1.0 CA A:HIS41 4.9 25.8 1.0 HB3 A:MET168 5.0 31.9 0.9 CG A:ASP190 5.0 25.4 1.0

P.Chen, T.J.Van Oers, E.Arutyunova, C.Fischer, C.Wang, T.Lamer, M.J.Van Belkum, H.S.Young, J.C.Vederas, M.J.Lemieux. A Structural Comparison of Oral Sars-Cov-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (Mpro) of Sars-Cov-2 and Mers-Cov Jacs Au 2024.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.4C00508