4LXK

Crystal Structure of Human Beta Secretase in Complex with compound 11d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of cyclic sulfoxide hydroxyethylamines as potent and selective beta-site APP-cleaving enzyme 1 (BACE1) inhibitors: structure based design and in vivo reduction of amyloid beta-peptides.

Rueeger, H.Lueoend, R.Machauer, R.Veenstra, S.J.Jacobson, L.H.Staufenbiel, M.Desrayaud, S.Rondeau, J.M.Mobitz, H.Neumann, U.

(2013) Bioorg.Med.Chem.Lett. 23: 5300-5306

  • DOI: 10.1016/j.bmcl.2013.07.071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Previous structure based optimization in our laboratories led to the identification of a novel, high-affinity cyclic sulfone hydroxyethylamine-derived inhibitor such as 1 that lowers CNS-derived Aβ following oral administration to transgenic APP51/16 ...

    Previous structure based optimization in our laboratories led to the identification of a novel, high-affinity cyclic sulfone hydroxyethylamine-derived inhibitor such as 1 that lowers CNS-derived Aβ following oral administration to transgenic APP51/16 mice. Herein we report SAR development in the S3 and S2' subsites of BACE1 for cyclic sulfoxide hydroxyethyl amine inhibitors, the synthetic approaches employed in this effort, and in vivo data for optimized compound such as 11d.


    Organizational Affiliation

    Department of Global Discovery Chemistry, Institutes for BioMedical Research, Novartis Pharma AG, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1YT
Query on 1YT

Download SDF File 
Download CCD File 
A, B, C
(1R,3S,4S,5R)-3-(4-amino-3-fluoro-5-{[(2R)-1,1,1-trifluoro-3-methoxypropan-2-yl]oxy}benzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1-oxide
C27 H36 F4 N2 O4 S
FIUDDEQHPBHZBI-XPLIUGCLSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1YTIC50: 4 nM BINDINGMOAD
1YTIC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.291α = 90.00
b = 103.540β = 104.27
c = 100.428γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling
CNXrefinement
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Structure summary
  • Version 1.2: 2013-11-20
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description