BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-1-methyl-5-oxo-4-(((1S,3R)-3-(3-phenylureido)cyclohexyl)methyl)imidazolidin-2-iminium

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of potent iminoheterocycle BACE1 inhibitors.

Caldwell, J.P.Mazzola, R.D.Durkin, J.Chen, J.Chen, X.Favreau, L.Kennedy, M.Kuvelkar, R.Lee, J.McHugh, N.McKittrick, B.Orth, P.Stamford, A.Strickland, C.Voigt, J.Wang, L.Zhang, L.Zhang, Q.Zhu, Z.

(2014) Bioorg Med Chem Lett 24: 5455-5459

  • DOI: https://doi.org/10.1016/j.bmcl.2014.10.006
  • Primary Citation of Related Structures:  
    4R8Y, 4R91, 4R92, 4R93, 4R95

  • PubMed Abstract: 

    The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select compounds from this subset acutely lowered Aβ40 levels upon subcutaneous and oral administration to rats.

  • Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: john.caldwell@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: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  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
779 BindingDB:  4R93 Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.49α = 90
b = 89.33β = 90
c = 130.95γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references