Crystal structure of BACE1 in complex with 2-aminooxazoline 4-fluoroxanthene inhibitor 49

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Lead Optimization and Modulation of hERG Activity in a Series of Aminooxazoline Xanthene beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors.

Epstein, O.Bryan, M.C.Cheng, A.C.Derakhchan, K.Dineen, T.A.Hickman, D.Hua, Z.Human, J.B.Kreiman, C.Marx, I.E.Weiss, M.M.Wahl, R.C.Wen, P.H.Whittington, D.A.Wood, S.Zheng, X.M.Fremeau, R.T.White, R.D.Patel, V.F.

(2014) J Med Chem 57: 9796-9810

  • DOI: https://doi.org/10.1021/jm501266w
  • Primary Citation of Related Structures:  
    4RCE, 4RCF

  • PubMed Abstract: 

    The optimization of a series of aminooxazoline xanthene inhibitors of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is described. An early lead compound showed robust Aβ lowering activity in a rat pharmacodynamic model, but advancement was precluded by a low therapeutic window to QTc prolongation in cardiovascular models consistent with in vitro activity on the hERG ion channel. While the introduction of polar groups was effective in reducing hERG binding affinity, this came at the expense of higher than desired Pgp-mediated efflux. A balance of low Pgp efflux and hERG activity was achieved by lowering the polar surface area of the P3 substituent while retaining polarity in the P2' side chain. The introduction of a fluorine in position 4 of the xanthene ring improved BACE1 potency (5-10-fold). The combination of these optimized fragments resulted in identification of compound 40, which showed robust Aβ reduction in a rat pharmacodynamic model (78% Aβ reduction in CSF at 10 mg/kg po) and also showed acceptable cardiovascular safety in vivo.

  • Organizational Affiliation

    Departments of Therapeutic Discovery, ‡Neuroscience, §Molecular Structure and Characterization, ∥Pharmacokinetics and Drug Metabolism, and ⊥Comparative Biology and Safety Sciences, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, One Amgen Center Drive, Thousand Oaks, California 91320, and 1120 Veterans Boulevard, South San Francisco, California 94080, United States.

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
3LO BindingDB:  4RCF IC50: min: 0.3, max: 4.1 (nM) from 3 assay(s)
Binding MOAD:  4RCF IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.262α = 90
b = 102.262β = 90
c = 170.306γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description