Crystal structure of BACE1 in complex with a 2-aminooxazoline 4-azaxanthene inhibitor

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Inhibitors of beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1): Identification of (S)-7-(2-Fluoropyridin-3-yl)-3-((3-methyloxetan-3-yl)ethynyl)-5'H-spiro[chromeno[2,3-b]pyridine-5,4'-oxazol]-2'-amine (AMG-8718).

Dineen, T.A.Chen, K.Cheng, A.C.Derakhchan, K.Epstein, O.Esmay, J.Hickman, D.Kreiman, C.E.Marx, I.E.Wahl, R.C.Wen, P.H.Weiss, M.M.Whittington, D.A.Wood, S.Fremeau, R.T.White, R.D.Patel, V.F.

(2014) J Med Chem 57: 9811-9831

  • DOI: https://doi.org/10.1021/jm5012676
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have previously shown that the aminooxazoline xanthene scaffold can generate potent and orally efficacious BACE1 inhibitors although certain of these compounds exhibited potential hERG liabilities. In this article, we describe 4-aza substitution on the xanthene core as a means to increase BACE1 potency while reducing hERG binding affinity. Further optimization of the P3 and P2' side chains resulted in the identification of 42 (AMG-8718), a compound with a balanced profile of BACE1 potency, hERG binding affinity, and Pgp recognition. This compound produced robust and sustained reductions of CSF and brain Aβ levels in a rat pharmacodynamic model and exhibited significantly reduced potential for QTc elongation in a cardiovascular safety model.

  • 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, and One Amgen Center Drive, Thousand Oaks, California 91320, 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
3LL BindingDB:  4RCD IC50: min: 0.7, max: 4.4 (nM) from 2 assay(s)
Binding MOAD:  4RCD IC50: 0.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.607α = 90
b = 102.607β = 90
c = 170.671γ = 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: 2015-01-21
    Type: Initial release