3QBH

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

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 ...

    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.

    Related Citations: 
    • Structure-Based Design of Macrocyclic Peptidomimetic beta-Secretase (BACE-1) Inhibitors
      Machauer, R., Veenstra, S., Rondeau, J.M., Tintelnot-Blomley, M., Betschart, C., Neumann, U., Paganetti, P.
      (2009) Bioorg Med Chem Lett 19: 1361
    • Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo
      Machauer, R., Laumen, K., Veenstra, S., Rondeau, J.M., Tintelnot-Blomley, M., Betschart, C., Jaton, A.-L., Desrayaud, S., Staufenbiel, M., Rabe, S., Paganetti, P., Neumann, U.
      (2009) Bioorg Med Chem Lett 19: 1366
    • Macrocyclic BACE-1 inhibitors acutely reduce Abeta in brain after po application
      Lerchner, A., Machauer, R., Betschart, C., Veenstra, S., Rueeger, H., McCarthy, C., Tintelnot-Blomley, M., Jaton, A.-L., Rabe, S., Desrayaud, S., Enz, A., Staufenbiel, M., Paganetti, P., Rondeau, J.M., Neumann, U.
      (2010) Bioorg Med Chem Lett 20: 603
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
402Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, KIAA1149
EC: 3.4.23.46
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QBH
Query on QBH
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		(4S)-4-(2-hydroxy-5-{[(3S,4S,5R)-4-hydroxy-1,1-dioxido-5-{[3-(propan-2-yl)benzyl]amino}tetrahydro-2H-thiopyran-3-yl]methyl}benzyl)-3-propyl-1,3-oxazolidin-2-one
C29 H40 N2 O6 S
JYNDAPHZRSRSGI-KAHNYGAISA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QBH PDBBind:  3QBH IC50: 150 (nM) from 1 assay(s)
BindingDB:  3QBH IC50: 150 (nM) from 1 assay(s)
Binding MOAD:  3QBH IC50: 150 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.003α = 90
b = 103.062β = 103.98
c = 100.904γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
CNXphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description