Fluorine in PDB 4d88: Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490

All present enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490:
3.4.23.46;

The structure of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490, PDB code: 4d88 was solved by J.M.Rondeau, E.Bourgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.29 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.876, 74.897, 104.579, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Fluorine atom in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490 (pdb code 4d88). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490, PDB code: 4d88:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490


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 Human Beta Secretase in Complex with Nvp-BXQ490 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.9 occ:1.00 F1 A:BXQ401 0.0 28.9 1.0 C2 A:BXQ401 1.4 26.2 1.0 F4 A:BXQ401 2.2 29.9 1.0 F3 A:BXQ401 2.2 29.6 1.0 C5 A:BXQ401 2.4 23.0 1.0 O7 A:BXQ401 2.8 21.5 1.0 C9 A:BXQ401 2.9 19.8 1.0 O A:GLY11 2.9 17.1 0.5 CA A:GLN12 3.0 19.4 1.0 C A:GLN12 3.1 19.3 1.0 O A:GLY11 3.2 17.3 0.5 CD1 A:ILE110 3.4 31.0 1.0 O A:GLN12 3.4 19.8 1.0 N A:GLY13 3.6 18.3 1.0 C A:GLY11 3.6 17.7 0.5 N A:GLN12 3.7 17.4 1.0 C A:GLY11 3.8 17.6 0.5 CA A:GLY13 4.3 18.2 1.0 CB A:GLN12 4.3 22.6 1.0 C12 A:BXQ401 4.4 18.5 1.0 O A:SER10 4.6 14.0 0.5 OG1 A:THR219 4.6 15.1 1.0 O A:HOH982 4.6 41.7 1.0 O A:HOH754 4.8 33.1 1.0 CG1 A:ILE110 4.9 28.9 1.0 CA A:GLY11 4.9 16.6 0.5 CG A:GLN12 4.9 27.4 1.0 CZ2 A:TRP115 5.0 16.2 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490


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 Human Beta Secretase in Complex with Nvp-BXQ490 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.6 occ:1.00 F3 A:BXQ401 0.0 29.6 1.0 C2 A:BXQ401 1.4 26.2 1.0 F4 A:BXQ401 2.2 29.9 1.0 F1 A:BXQ401 2.2 28.9 1.0 C5 A:BXQ401 2.4 23.0 1.0 C9 A:BXQ401 3.0 19.8 1.0 O A:HOH754 3.0 33.1 1.0 CA A:GLY13 3.1 18.2 1.0 N A:GLY13 3.1 18.3 1.0 C A:GLN12 3.4 19.3 1.0 O7 A:BXQ401 3.6 21.5 1.0 O A:GLN12 3.6 19.8 1.0 O A:GLY217 3.7 15.4 1.0 CD1 A:LEU30 4.1 12.3 1.0 CA A:GLN12 4.1 19.4 1.0 O A:SER10 4.2 14.0 0.5 C12 A:BXQ401 4.2 18.5 1.0 C A:GLY217 4.4 14.9 1.0 O A:GLY11 4.4 17.1 0.5 C18 A:BXQ401 4.5 16.4 1.0 CD2 A:LEU30 4.5 14.5 1.0 C A:GLY13 4.5 17.4 1.0 N A:GLN12 4.6 17.4 1.0 C A:GLY11 4.7 17.7 0.5 OG1 A:THR219 4.8 15.1 1.0 O A:GLY11 4.9 17.3 0.5 CG A:LEU30 4.9 10.7 1.0 C A:GLY11 5.0 17.6 0.5 CA A:GLY217 5.0 13.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490


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 Human Beta Secretase in Complex with Nvp-BXQ490 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.9 occ:1.00 F4 A:BXQ401 0.0 29.9 1.0 C2 A:BXQ401 1.4 26.2 1.0 F3 A:BXQ401 2.2 29.6 1.0 F1 A:BXQ401 2.2 28.9 1.0 C5 A:BXQ401 2.4 23.0 1.0 O7 A:BXQ401 2.8 21.5 1.0 OG1 A:THR219 2.9 15.1 1.0 O A:HOH982 3.0 41.7 1.0 O A:GLY11 3.3 17.1 0.5 O A:HOH754 3.3 33.1 1.0 O A:SER10 3.4 14.0 0.5 O A:GLY11 3.7 17.3 0.5 C9 A:BXQ401 3.8 19.8 1.0 C A:GLY11 3.8 17.7 0.5 N A:THR219 3.9 12.9 1.0 O A:GLY217 3.9 15.4 1.0 C A:GLY11 4.1 17.6 0.5 CB A:THR219 4.1 14.4 1.0 N A:GLY13 4.2 18.3 1.0 C A:THR218 4.3 13.6 0.5 CA A:THR218 4.4 12.8 0.5 O A:HOH941 4.4 39.9 1.0 C A:GLN12 4.4 19.3 1.0 N A:GLN12 4.4 17.4 1.0 CA A:THR219 4.4 11.5 1.0 CA A:GLN12 4.4 19.4 1.0 C A:THR218 4.4 11.6 0.5 CA A:GLY11 4.6 16.6 0.5 C A:SER10 4.6 16.1 0.5 CA A:THR218 4.6 16.0 0.5 CA A:GLY13 4.6 18.2 1.0 C A:GLY217 4.7 14.9 1.0 C12 A:BXQ401 4.9 18.5 1.0 CA A:GLY11 4.9 16.9 0.5 N A:THR218 4.9 12.5 0.5 N A:THR218 5.0 14.1 0.5

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Beta Secretase in Complex with Nvp-BXQ490 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:23.3 occ:1.00 F68 A:BXQ401 0.0 23.3 1.0 C14 A:BXQ401 1.3 20.1 1.0 C15 A:BXQ401 2.4 18.7 1.0 C13 A:BXQ401 2.4 19.4 1.0 N69 A:BXQ401 2.7 21.4 1.0 CD1 A:PHE108 3.1 13.0 1.0 O A:GLN73 3.4 26.4 1.0 CA A:PHE108 3.5 18.3 1.0 C17 A:BXQ401 3.7 14.8 1.0 C12 A:BXQ401 3.7 18.5 1.0 O A:LYS107 3.7 19.4 1.0 O A:PHE108 3.8 18.8 1.0 CE1 A:PHE108 3.8 9.8 1.0 CA A:GLY74 3.8 22.0 1.0 O A:HOH787 3.9 33.2 1.0 CG A:PHE108 3.9 13.6 1.0 CB A:PHE108 4.1 15.8 1.0 C A:PHE108 4.1 19.3 1.0 O A:HOH766 4.1 34.8 1.0 C18 A:BXQ401 4.1 16.4 1.0 CD2 A:TYR71 4.2 14.7 1.0 C A:GLY74 4.3 20.6 1.0 C A:GLN73 4.3 25.6 1.0 N A:PHE108 4.4 20.9 1.0 C A:LYS107 4.5 21.7 1.0 N A:GLY74 4.5 25.0 1.0 O A:GLY74 4.7 20.1 1.0 CE2 A:TYR71 4.7 11.8 1.0 O A:HOH774 4.7 33.4 1.0 CG A:TYR71 4.7 14.0 1.0 N A:LYS75 4.8 20.0 1.0 CB A:TYR71 4.9 14.4 1.0 C20 A:BXQ401 5.0 13.3 1.0 CZ A:PHE108 5.0 12.8 1.0

H.Rueeger, R.Lueoend, O.Rogel, J.M.Rondeau, H.Mobitz, R.Machauer, L.Jacobson, M.Staufenbiel, S.Desrayaud, U.Neumann. Discovery of Cyclic Sulfone Hydroxyethylamines As Potent and Selective Beta-Site App-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure Based Design and in Vivo Reduction of Amyloid Beta-Peptides J.Med.Chem. V. 55 3364 2012.
ISSN: ISSN 0022-2623
PubMed: 22380629
DOI: 10.1021/JM300069Y