Rational Design and Synthesis of Aminopiperazinones as Beta Secretase (BACE) Inhibitors

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Rational design and synthesis of aminopiperazinones as beta-secretase (BACE) inhibitors.

Tresadern, G.Delgado, F.Delgado, O.Gijsen, H.Macdonald, G.J.Moechars, D.Rombouts, F.Alexander, R.Spurlino, J.Van Gool, M.Vega, J.A.Trabanco, A.A.

(2011) Bioorg Med Chem Lett 21: 7255-7260

  • DOI: https://doi.org/10.1016/j.bmcl.2011.10.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aminopiperazinone inhibitors of BACE were identified by rational design. Structure based design guided idea prioritization and initial racemic hit 18a showed good activity. Modification in decoration and chiral separation resulted in the 40 nM inhibitor, (-)-37, which showed in vivo reduction of amyloid beta peptides. The crystal structure of 18a showed a binding mode driven by interaction with the catalytic aspartate dyad and distribution of the biaryl amide decoration towards S1 and S3 pockets.

  • Organizational Affiliation

    Research Informatics & Integrative Genomics, Calle Jarama 75, Poligono Industrial, Toledo 45007, Spain. gtresade@its.jnj.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
390Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 18P

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
M [auth C]
C18 H18 Cl N5 O2
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
18P BindingDB:  3U6A IC50: min: 36, max: 447 (nM) from 6 assay(s)
PDBBind:  3U6A IC50: 324 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.3α = 90
b = 104.45β = 102.66
c = 66.76γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references