4FRK

Crystal structure of BACE1 in complex with aminooxazoline xanthene 11a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure- and Property-Based Design of Aminooxazoline Xanthenes as Selective, Orally Efficacious, and CNS Penetrable BACE Inhibitors for the Treatment of Alzheimer's Disease.

Huang, H.La, D.S.Cheng, A.C.Whittington, D.A.Patel, V.F.Chen, K.Dineen, T.A.Epstein, O.Graceffa, R.Hickman, D.Kiang, Y.H.Louie, S.Luo, Y.Wahl, R.C.Wen, P.H.Wood, S.Fremeau, R.T.

(2012) J.Med.Chem. 55: 9156-9169

  • DOI: 10.1021/jm300598e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A structure- and property-based drug design approach was employed to identify aminooxazoline xanthenes as potent and selective human β-secretase inhibitors. These compounds exhibited good isolated enzyme, cell potency, and selectivity against the str ...

    A structure- and property-based drug design approach was employed to identify aminooxazoline xanthenes as potent and selective human β-secretase inhibitors. These compounds exhibited good isolated enzyme, cell potency, and selectivity against the structurally related aspartyl protease cathepsin D. Our efforts resulted in the identification of a potent, orally bioavailable CNS penetrant compound that exhibited in vivo efficacy. A single oral dose of compound 11a resulted in a significant reduction of CNS Aβ40 in naive rats.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States. hongbing.huang@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
411Homo sapiensMutation(s): 2 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DWD
Query on DWD

Download SDF File 
Download CCD File 
A
(4S)-2'-(2-methylpropoxy)-7'-(pyrimidin-5-yl)spiro[1,3-oxazole-4,9'-xanthen]-2-amine
C23 H22 N4 O3
JWSHQJYDXNPIKG-QHCPKHFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DWDIC50: 8 - 36 nM (99) BINDINGDB
DWDIC50: 8 nM BINDINGMOAD
DWDIC50: 8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.255α = 90.00
b = 102.255β = 90.00
c = 171.392γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
CrystalCleardata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references