3IXK

Potent beta-secretase 1 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis of potent BACE-1 inhibitors incorporating a hydroxyethylene isostere as central core.

Wangsell, F.Gustafsson, K.Kvarnstrom, I.Borkakoti, N.Edlund, M.Jansson, K.Lindberg, J.Hallberg, A.Rosenquist, A.Samuelsson, B.

(2010) Eur.J.Med.Chem. 45: 870-882

  • DOI: 10.1016/j.ejmech.2009.11.013

  • PubMed Abstract: 
  • We herein describe the design and synthesis of a series of BACE-1 inhibitors incorporating a P1-substituted hydroxylethylene transition state isostere. The synthetic route starting from commercially available carbohydrates yielded a pivotal lactone i ...

    We herein describe the design and synthesis of a series of BACE-1 inhibitors incorporating a P1-substituted hydroxylethylene transition state isostere. The synthetic route starting from commercially available carbohydrates yielded a pivotal lactone intermediate with excellent stereochemical control which subsequently could be diversified at the P1-position. The final inhibitors were optimized using three different amines to provide the residues in the P2'-P3' position and three different acids affording the residues in the P2-P3 position. In addition we report on the stereochemical preference of the P1'-methyl substituent in the synthesized inhibitors. All inhibitors were evaluated in an in vitro BACE-1 assay where the most potent inhibitor, 34-(R), exhibited a BACE-1 IC(50) value of 3.1 nM.


    Organizational Affiliation

    Department of Chemistry, Linköping University, SE-581 83 Linköping, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
405Homo 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
929
Query on 929

Download SDF File 
Download CCD File 
A, B, C
N-[(2S,3S,5R)-1-[(3,5-difluorophenyl)methoxy]-3-hydroxy-5-methyl-6-[[(2S)-3-methyl-1-oxo-1-(phenylmethylamino)butan-2-yl]amino]-6-oxo-hexan-2-yl]-5-(methyl-methylsulfonyl-amino)-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
N-[4-(1-BENZYLCARBAMOYL-2-METHYL-PROPYLCARBAMOYL)-1-(3,5-DIFLUORO-BENZYLOXYMETHYL)-2-HYDROXY-PENTYL]-5-[Methyl(METHANESULFONYL)Amino]-N'-(1-PHENYL-ETHYL)-ISOPHTHALAMIDE
C44 H53 F2 N5 O8 S
SQCCLROLILAOBD-MLLWAOEYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
929IC50: 6.6 - 4500 nM (100) BINDINGDB
929IC50: 6.6 nM BINDINGMOAD
929IC50: 6.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.838α = 90.00
b = 103.075β = 103.32
c = 100.499γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance