Crystal structure of BACE1 in complex with aminooxazoline xanthene 11a

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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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: https://doi.org/10.1021/jm300598e
  • Primary Citation of Related Structures:  
    4FRI, 4FRJ, 4FRK

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1411Homo sapiensMutation(s): 2 
Gene Names: BACEBACE1KIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DWD BindingDB:  4FRK IC50: min: 8, max: 36 (nM) from 2 assay(s)
Binding MOAD:  4FRK IC50: 8 (nM) from 1 assay(s)
PDBBind:  4FRK IC50: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.255α = 90
b = 102.255β = 90
c = 171.392γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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