Structure of BACE Bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor.

Cumming, J.N.Smith, E.M.Wang, L.Misiaszek, J.Durkin, J.Pan, J.Iserloh, U.Wu, Y.Zhu, Z.Strickland, C.Voigt, J.Chen, X.Kennedy, M.E.Kuvelkar, R.Hyde, L.A.Cox, K.Favreau, L.Czarniecki, M.F.Greenlee, W.J.McKittrick, B.A.Parker, E.M.Stamford, A.W.

(2012) Bioorg Med Chem Lett 22: 2444-2449

  • DOI: https://doi.org/10.1016/j.bmcl.2012.02.013
  • Primary Citation of Related Structures:  
    4DJU, 4DJV, 4DJW, 4DJX, 4DJY

  • PubMed Abstract: 

    From an initial lead 1, a structure-based design approach led to identification of a novel, high-affinity iminohydantoin BACE1 inhibitor that lowers CNS-derived Aβ following oral administration to rats. Herein we report SAR development in the S3 and F' subsites of BACE1 for this series, the synthetic approaches employed in this effort, and in vivo data for the optimized compound.

  • Organizational Affiliation

    Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
414Homo 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
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
0KQ Binding MOAD:  4DJX Ki: 59 (nM) from 1 assay(s)
PDBBind:  4DJX Ki: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.471α = 90
b = 89.462β = 90
c = 131.225γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata 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: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references