4FS4

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 3.4.23.46
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
CNXphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary