Structure of BACE Bound to (S)-4-(3'-methoxy-[1,1'-biphenyl]-3-yl)-1,4-dimethyl-6-oxotetrahydropyrimidin-2(1H)-iminium

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of beta-Secretase.

Kaller, M.R.Harried, S.S.Albrecht, B.Amarante, P.Babu-Khan, S.Bartberger, M.D.Brown, J.Brown, R.Chen, K.Cheng, Y.Citron, M.Croghan, M.D.Graceffa, R.Hickman, D.Judd, T.Kriemen, C.La, D.Li, V.Lopez, P.Luo, Y.Masse, C.Monenschein, H.Nguyen, T.Pennington, L.D.Miguel, T.S.Sickmier, E.A.Wahl, R.C.Weiss, M.M.Wen, P.H.Williamson, T.Wood, S.Xue, M.Yang, B.Zhang, J.Patel, V.Zhong, W.Hitchcock, S.

(2012) ACS Med Chem Lett 3: 886-891

  • DOI: https://doi.org/10.1021/ml3000148
  • Primary Citation of Related Structures:  
    4DUS, 4FS4

  • PubMed Abstract: 

    β-Secretase inhibitors are potentially disease-modifying treatments for Alzheimer's disease. Previous efforts in our laboratory have resulted in hydroxyethylamine-derived inhibitors such as 1 with low nanomolar potency against β-site amyloid precursor protein cleaving enzyme (BACE). When dosed intravenously, compound 1 was also shown to significantly reduce Aβ40 levels in plasma, brain, and cerebral spinal fluid. Herein, we report further optimizations that led to the discovery of inhibitor 16 as a novel, potent, and orally efficacious BACE inhibitor.

  • Organizational Affiliation

    Chemistry Research and Discovery, Department of Molecular Structure, Department of Neuroscience, Department of HTS and Molecular Pharmacology, and Department of Pharmacokinetics and Drug Metabolism, Amgen Inc. , 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 1
A, B
390Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
H24 PDBBind:  4FS4 Ki: 270 (nM) from 1 assay(s)
BindingDB:  4FS4 IC50: min: 380, max: 9.10e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.5α = 90
b = 90.364β = 90
c = 131.146γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data 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: 2012-10-10
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references