Fluorine in PDB 6bfe: Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor

All present enzymatic activity of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor:
3.4.23.46;

The structure of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor, PDB code: 6bfe was solved by D.E.Timm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.50 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.285, 89.288, 131.177, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20

The binding sites of Fluorine atom in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor (pdb code 6bfe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor, PDB code: 6bfe:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:20.1 occ:1.00 F1 A:DJV401 0.0 20.1 1.0 C5 A:DJV401 1.4 15.9 1.0 C3 A:DJV401 2.3 15.8 1.0 C1 A:DJV401 2.3 11.9 1.0 H1 A:DJV401 2.6 11.3 1.0 H3 A:DJV401 2.6 16.5 1.0 CD1 A:PHE108 3.2 15.5 1.0 N A:GLY74 3.3 18.9 1.0 C6 A:DJV401 3.6 16.8 1.0 CA A:GLY74 3.6 16.9 1.0 C4 A:DJV401 3.6 11.3 1.0 C A:GLY74 3.8 16.1 1.0 CE1 A:PHE108 3.8 15.5 1.0 CD1 A:TYR71 3.8 14.8 1.0 CB A:GLN73 3.9 25.2 1.0 CA A:PHE108 3.9 14.2 1.0 O A:GLY74 4.0 15.8 1.0 O A:LYS107 4.0 18.9 1.0 CB A:TYR71 4.0 13.0 1.0 C2 A:DJV401 4.1 14.4 1.0 CG A:TYR71 4.1 13.2 1.0 CG A:PHE108 4.2 13.3 1.0 C A:GLN73 4.2 27.2 1.0 CB A:PHE108 4.3 13.1 1.0 O A:HOH577 4.3 30.1 1.0 O A:PHE108 4.4 18.1 1.0 O1 A:DJV401 4.4 13.8 1.0 N A:LYS75 4.5 14.2 1.0 CA A:GLN73 4.5 23.5 1.0 CG A:GLN73 4.5 35.3 1.0 CE1 A:TYR71 4.6 14.4 1.0 C A:PHE108 4.7 17.2 1.0 F2 A:DJV401 4.7 23.7 1.0 H29 A:DJV401 4.7 8.1 1.0 C A:LYS107 4.8 19.3 1.0 N A:GLN73 4.8 23.1 1.0 N A:PHE108 4.8 16.2 1.0 C19 A:DJV401 4.9 9.9 1.0 OE1 A:GLN73 5.0 46.2 1.0 C7 A:DJV401 5.0 12.6 1.0

Fluorine binding site 2 out of 4 in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:23.7 occ:1.00 F2 A:DJV401 0.0 23.7 1.0 C6 A:DJV401 1.3 16.8 1.0 H31 A:GOL404 2.3 30.3 1.0 H11 A:GOL404 2.3 33.8 1.0 C3 A:DJV401 2.3 15.8 1.0 C2 A:DJV401 2.3 14.4 1.0 H2 A:DJV401 2.6 15.8 1.0 H3 A:DJV401 2.6 16.5 1.0 HO2 A:GOL404 3.1 30.8 1.0 C3 A:GOL404 3.2 30.4 1.0 CZ2 A:TRP115 3.3 14.8 1.0 C1 A:GOL404 3.3 33.7 1.0 CD1 A:ILE110 3.5 20.2 1.0 C5 A:DJV401 3.5 15.9 1.0 C4 A:DJV401 3.6 11.3 1.0 CH2 A:TRP115 3.6 15.3 1.0 H32 A:GOL404 3.7 30.5 1.0 C2 A:GOL404 3.7 31.7 1.0 H12 A:GOL404 3.7 33.8 1.0 OE1 A:GLN73 3.7 46.2 1.0 O2 A:GOL404 3.9 30.5 1.0 C1 A:DJV401 4.1 11.9 1.0 CD2 A:LEU30 4.1 15.6 1.0 O A:HOH577 4.1 30.1 1.0 O3 A:GOL404 4.2 30.0 1.0 O A:PHE108 4.3 18.1 1.0 O1 A:GOL404 4.3 37.0 1.0 CG1 A:ILE110 4.3 20.1 1.0 HO3 A:GOL404 4.4 30.6 1.0 CE2 A:TRP115 4.5 15.4 1.0 CD A:GLN73 4.6 51.8 1.0 HO1 A:GOL404 4.6 37.3 1.0 F1 A:DJV401 4.7 20.1 1.0 O A:GLN12 4.7 16.4 1.0 H2 A:GOL404 4.8 31.7 1.0 H21 A:DJV401 4.8 12.8 1.0 H25 A:DJV401 4.8 9.4 1.0 C19 A:DJV401 4.9 9.9 1.0 CZ3 A:TRP115 5.0 14.3 1.0

Fluorine binding site 3 out of 4 in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.2 occ:1.00 F1 B:DJV401 0.0 20.2 1.0 C5 B:DJV401 1.4 14.3 1.0 C3 B:DJV401 2.3 14.1 1.0 C1 B:DJV401 2.4 11.7 1.0 H1 B:DJV401 2.6 10.7 1.0 H3 B:DJV401 2.6 14.2 1.0 CD1 B:PHE108 3.2 12.1 1.0 N B:GLY74 3.3 13.9 1.0 CA B:GLY74 3.5 14.3 1.0 C6 B:DJV401 3.6 15.6 1.0 C4 B:DJV401 3.6 10.5 1.0 C B:GLY74 3.7 12.2 1.0 O B:GLY74 3.8 11.3 1.0 CA B:PHE108 3.8 10.3 1.0 CD1 B:TYR71 3.8 13.6 1.0 CE1 B:PHE108 3.9 12.3 1.0 O B:LYS107 3.9 13.5 1.0 CB B:GLN73 4.0 19.8 1.0 CB B:TYR71 4.0 11.1 1.0 C2 B:DJV401 4.1 10.7 1.0 CG B:TYR71 4.1 10.8 1.0 C B:GLN73 4.1 20.0 1.0 CG B:PHE108 4.1 9.8 1.0 CB B:PHE108 4.3 9.2 1.0 O B:HOH534 4.3 26.9 1.0 N B:LYS75 4.4 10.4 1.0 O B:PHE108 4.4 12.7 1.0 O1 B:DJV401 4.4 11.2 1.0 CA B:GLN73 4.5 18.3 1.0 CG B:GLN73 4.5 29.1 1.0 CE1 B:TYR71 4.6 13.6 1.0 C B:PHE108 4.6 12.0 1.0 C B:LYS107 4.7 14.3 1.0 N B:PHE108 4.7 11.1 1.0 F2 B:DJV401 4.7 20.6 1.0 H29 B:DJV401 4.7 8.8 1.0 N B:GLN73 4.7 18.1 1.0 C19 B:DJV401 4.9 9.5 1.0 C7 B:DJV401 5.0 10.5 1.0 O B:GLN73 5.0 21.6 1.0

Fluorine binding site 4 out of 4 in the Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bace Crystal Structure with Hydroxy Pyrrolidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.6 occ:1.00 F2 B:DJV401 0.0 20.6 1.0 C6 B:DJV401 1.4 15.6 1.0 C3 B:DJV401 2.3 14.1 1.0 C2 B:DJV401 2.3 10.7 1.0 H2 B:DJV401 2.6 10.2 1.0 H3 B:DJV401 2.6 14.2 1.0 CZ2 B:TRP115 3.3 13.2 1.0 CD1 B:ILE110 3.5 18.7 1.0 CH2 B:TRP115 3.6 13.4 1.0 C5 B:DJV401 3.6 14.3 1.0 C4 B:DJV401 3.6 10.5 1.0 NE2 B:GLN73 3.9 29.8 1.0 O B:HOH534 4.0 26.9 1.0 CD2 B:LEU30 4.1 14.3 1.0 C1 B:DJV401 4.1 11.7 1.0 O B:PHE108 4.2 12.7 1.0 CG1 B:ILE110 4.2 17.1 1.0 CE2 B:TRP115 4.5 13.5 1.0 F1 B:DJV401 4.7 20.2 1.0 H21 B:DJV401 4.8 8.5 1.0 O B:GLN12 4.8 16.1 1.0 H25 B:DJV401 4.9 10.3 1.0 CD B:GLN73 4.9 46.2 1.0 C19 B:DJV401 4.9 9.5 1.0 CZ3 B:TRP115 4.9 13.0 1.0

A.B.Bueno, J.Agejas, H.Broughton, R.Dally, T.B.Durham, J.F.Espinosa, R.Gonzalez, P.J.Hahn, A.Marcos, R.Rodriguez, G.Sanz, J.F.Soriano, D.Timm, P.Vidal, H.C.Yang, J.R.Mccarthy. Optimization of Hydroxyethylamine Transition State Isosteres As Aspartic Protease Inhibitors By Exploiting Conformational Preferences. J. Med. Chem. V. 60 9807 2017.
ISSN: ISSN 1520-4804
PubMed: 29088532
DOI: 10.1021/ACS.JMEDCHEM.7B01304