Crystal structure of BACE1 in complex with 2-aminooxazoline 3-azaxanthene inhibitor 28

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Development of 2-aminooxazoline 3-azaxanthenes as orally efficacious beta-secretase inhibitors for the potential treatment of Alzheimer's disease.

Chen, J.J.Liu, Q.Yuan, C.Gore, V.Lopez, P.Ma, V.Amegadzie, A.Qian, W.Judd, T.C.Minatti, A.E.Brown, J.Cheng, Y.Xue, M.Zhong, W.Dineen, T.A.Epstein, O.Human, J.Kreiman, C.Marx, I.Weiss, M.M.Hitchcock, S.A.Powers, T.S.Chen, K.Wen, P.H.Whittington, D.A.Cheng, A.C.Bartberger, M.D.Hickman, D.Werner, J.A.Vargas, H.M.Everds, N.E.Vonderfecht, S.L.Dunn, R.T.Wood, S.Fremeau, R.T.White, R.D.Patel, V.F.

(2015) Bioorg Med Chem Lett 25: 767-774

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.092
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The β-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) is one of the most hotly pursued targets for the treatment of Alzheimer's disease. We used a structure- and property-based drug design approach to identify 2-aminooxazoline 3-azaxanthenes as potent BACE1 inhibitors which significantly reduced CSF and brain Aβ levels in a rat pharmacodynamic model. Compared to the initial lead 2, compound 28 exhibited reduced potential for QTc prolongation in a non-human primate cardiovascular safety model.

  • Organizational Affiliation

    Comparative Biology and Safety Sciences, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1411Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
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
43K BindingDB:  4XKX IC50: min: 0.9, max: 21 (nM) from 2 assay(s)
Binding MOAD:  4XKX IC50: 0.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.148α = 90
b = 102.148β = 90
c = 170.894γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description