Design and synthesis of potent hydroxyethylamine (hea) bace-1 inhibitors

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

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Design and synthesis of potent hydroxyethylamine (HEA) BACE-1 inhibitors carrying prime side 4,5,6,7-tetrahydrobenzazole and 4,5,6,7-tetrahydropyridinoazole templates.

Sund, C.Belda, O.Borkakoti, N.Lindberg, J.Derbyshire, D.Vrang, L.Hamelink, E.Hgren, C.Woestenenk, E.Wikstrom, K.Eneroth, A.Lindstrom, E.Kalayanov, G.

(2012) Bioorg Med Chem Lett 22: 6721-6727

  • DOI: https://doi.org/10.1016/j.bmcl.2012.08.097
  • Primary Citation of Related Structures:  
    4EWO, 4EXG

  • PubMed Abstract: 

    A set of low molecular weight compounds containing a hydroxyethylamine (HEA) core structure with different prime side alkyl substituted 4,5,6,7-tetrahydrobenzazoles and one 4,5,6,7-tetrahydropyridinoazole was synthesized. Striking differences were observed on potencies in the BACE-1 enzymatic and cellular assays depending on the nature of the heteroatoms in the bicyclic ring, from the low active compound 4 to inhibitor 6, displaying BACE-1 IC(50) values of 44 nM (enzyme assay) and 65 nM (cell-based assay).

  • Organizational Affiliation

    Medivir AB, Lunastigen 7, SE-14144 Huddinge, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1386Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 996

Download Ideal Coordinates CCD File 
B [auth A]N-[(2S,3R)-4-{[(4S)-2-(2,2-dimethylpropyl)-6,6-dimethyl-4,5,6,7-tetrahydro-2H-indazol-4-yl]amino}-3-hydroxy-1-phenylbutan-2-yl]acetamide
C26 H40 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
996 PDBBind:  4EWO IC50: 44 (nM) from 1 assay(s)
Binding MOAD:  4EWO IC50: 44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.072α = 90
b = 76.429β = 90
c = 104.187γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
DNAdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release