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 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), 0.219 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FS4

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 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.

Macromolecule Content 

  • Total Structure Weight: 87.8 kDa 
  • Atom Count: 7,016 
  • Modeled Residue Count: 779 
  • Deposited Residue Count: 780 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
390Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, KIAA1149
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 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.192 (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 


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