Crystal Structure of Human Beta Secretase in Complex with BFG356

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors.

Rueeger, H.Rondeau, J.M.McCarthy, C.Mobitz, H.Tintelnot-Blomley, M.Neumann, U.Desrayaud, S.

(2011) Bioorg Med Chem Lett 21: 1942-1947

  • DOI: https://doi.org/10.1016/j.bmcl.2011.02.038
  • Primary Citation of Related Structures:  
    3PI5, 3QBH

  • PubMed Abstract: 

    This Letter describes the de novo design of non-peptidic hydroxyethylamine (HEA) inhibitors of BACE-1 by elimination of P-gp contributing amide attachments. The predicted binding mode of the novel cyclic sulfone HEA core template was confirmed in a X-ray co-crystal structure. Inhibitors of sub-micromolar potency with an improved property profile over historic HEA inhibitors resulting in improved brain penetration are described.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, PO Box, CH-4002 Basel, Switzerland. heinrich.rueeger@novartis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
402Homo 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
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 3P5

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
(3S,4S,5R)-3-(3-bromo-4-hydroxybenzyl)-5-[(3-cyclopropylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide
C22 H26 Br N O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
3P5 PDBBind:  3PI5 IC50: 950 (nM) from 1 assay(s)
Binding MOAD:  3PI5 IC50: 950 (nM) from 1 assay(s)
BindingDB:  3PI5 IC50: 950 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.486α = 90
b = 102.416β = 104.45
c = 100.178γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
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: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-03-01
    Changes: Other