4FS4 | pdb_00004fs4

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H24Click on this verticalbar to view details

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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H24Click on this verticalbar to view details

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