Fluorine in PDB 6wny: Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15

All present enzymatic activity of Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15:
3.4.23.46;

The structure of Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15, PDB code: 6wny was solved by D.A.Whittington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.86
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.783, 101.783, 171.141, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 20.9

The structure of Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15 also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15 (pdb code 6wny). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15, PDB code: 6wny:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15


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 BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:19.6 occ:1.00 F2 A:U64501 0.0 19.6 1.0 C15 A:U64501 1.4 18.5 1.0 C16 A:U64501 2.3 17.4 1.0 C7 A:U64501 2.4 11.8 1.0 C20 A:U64501 2.7 15.8 1.0 HD11 A:ILE171 2.7 26.0 1.0 C2 A:U64501 2.9 17.1 1.0 C1 A:U64501 3.0 10.8 1.0 HZ2 A:TRP176 3.3 23.8 1.0 CD1 A:ILE171 3.5 21.7 1.0 HD12 A:ILE171 3.5 26.0 1.0 N4 A:U64501 3.6 12.4 1.0 HD13 A:ILE171 4.0 26.0 1.0 C19 A:U64501 4.1 17.7 1.0 CZ2 A:TRP176 4.1 19.8 1.0 C3 A:U64501 4.3 15.0 1.0 C6 A:U64501 4.3 12.6 1.0 HD13 A:LEU91 4.3 20.2 1.0 HD22 A:LEU91 4.4 26.2 1.0 O A:HOH688 4.4 23.7 1.0 O A:GLN73 4.4 20.9 1.0 HG13 A:ILE171 4.5 23.8 1.0 HH2 A:TRP176 4.5 21.0 1.0 HD11 A:LEU91 4.6 20.2 1.0 CG1 A:ILE171 4.6 19.8 1.0 C17 A:U64501 4.7 13.6 1.0 HD21 A:LEU91 4.7 26.2 1.0 CH2 A:TRP176 4.7 17.5 1.0 HA A:GLN73 4.8 19.4 1.0 HG12 A:ILE171 4.8 23.8 1.0 HE1 A:TRP176 4.9 14.2 1.0 HA3 A:GLY74 4.9 22.0 1.0 C18 A:U64501 4.9 16.5 1.0 O A:GLY291 4.9 16.2 1.0 CD1 A:LEU91 4.9 16.8 1.0 C A:GLN73 4.9 19.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15


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 BACE1 in Complex with (Z)-Fluoro-Olefin Containing Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:18.3 occ:1.00 F1 A:U64501 0.0 18.3 1.0 C4 A:U64501 1.3 18.4 1.0 C5 A:U64501 2.3 11.2 1.0 C3 A:U64501 2.4 15.0 1.0 HE1 A:PHE169 2.6 19.6 1.0 C8 A:U64501 2.9 12.9 1.0 HD1 A:PHE169 2.9 17.4 1.0 C12 A:U64501 3.0 13.0 1.0 C9 A:U64501 3.0 15.1 1.0 HE2 A:TYR132 3.1 18.9 1.0 C14 A:U64501 3.2 14.0 1.0 CE1 A:PHE169 3.2 16.3 1.0 CE2 A:TYR132 3.3 15.7 1.0 CD1 A:PHE169 3.4 14.5 1.0 HD2 A:TYR132 3.4 29.3 1.0 CD2 A:TYR132 3.5 24.4 1.0 C6 A:U64501 3.6 12.6 1.0 C2 A:U64501 3.7 17.1 1.0 HD12 A:ILE179 3.7 24.9 1.0 HD11 A:ILE179 3.9 24.9 1.0 C1 A:U64501 4.1 10.8 1.0 CZ A:TYR132 4.1 24.2 1.0 CD1 A:ILE179 4.1 20.7 1.0 HD13 A:ILE179 4.2 24.9 1.0 C10 A:U64501 4.3 18.3 1.0 N1 A:U64501 4.3 12.6 1.0 HH A:TYR132 4.4 41.5 1.0 HD1 A:TRP137 4.4 26.6 1.0 CZ A:PHE169 4.5 15.1 1.0 CG A:TYR132 4.5 21.4 1.0 HA A:PHE169 4.6 15.9 1.0 OH A:TYR132 4.7 34.5 1.0 CG A:PHE169 4.7 13.4 1.0 HZ A:PHE169 4.8 18.1 1.0 O A:HOH618 4.8 33.4 1.0 HE1 A:TRP137 4.9 26.9 1.0 CE1 A:TYR132 4.9 29.6 1.0

M.Frohn, L.Liu, A.C.Siegmund, W.Qian, A.Amegadzie, N.Chen, H.Tan, D.Hickman, S.Wood, P.H.Wen, M.D.Bartberger, D.A.Whittington, J.R.Allen, M.P.Bourbeau. The Development of A Structurally Distinct Series of BACE1 Inhibitors Via the (Z)-Fluoro-Olefin Amide Bioisosteric Replacement Bioorg.Med.Chem.Lett. 2020.
ISSN: ESSN 1464-3405
DOI: 10.1016/J.BMCL.2020.12724