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 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.bmcl.2011.02.038
  • Primary Citation of Related Structures:  
  • Also Cited By: 4D83, 3VG1, 3VF3, 3VEU

  • 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 ...

    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: 
    • 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
    • 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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
402Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QBH
Query on QBH

Download SDF File 
Download CCD File 
A, B, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QBHIC50: 150 nM (100) BINDINGDB
QBHIC50: 150 nM BINDINGMOAD
QBHIC50: 150 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.003α = 90.00
b = 103.062β = 103.98
c = 100.904γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
CNSrefinement
CNXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-01-13 
  • Released Date: 2011-03-23 
  • Deposition Author(s): Rondeau, J.M.

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-03-01
    Type: Other
  • Version 1.3: 2017-10-11
    Type: Data collection, Refinement description