2YPU

human insulin degrading enzyme E111Q in complex with inhibitor compound 41367


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Imidazole-Derived 2-[N-Carbamoylmethyl-Alkylamino]Acetic Acids,Substrate-Dependent Modulators of Insulin-Degrading Enzyme in Amyloid-Beta Hydrolysis

Charton, J.Gauriot, M.Guo, Q.Hennuyer, N.Marechal, X.Dumont, J.Hamdane, M.Pottiez, V.Landry, V.Sperandio, O.Flipo, M.Buee, L.Staels, B.Leroux, F.Tang, W.-J.Deprez, B.Deprez-Poulain, R.

(2014) Eur J Med Chem 79C: 184

  • DOI: https://doi.org/10.1016/j.ejmech.2014.04.009
  • Primary Citation of Related Structures:  
    2YPU, 3QZ2, 4DTT, 4DWK, 4GS8, 4GSC

  • PubMed Abstract: 

    Insulin degrading enzyme (IDE) is a highly conserved zinc metalloprotease that is involved in the clearance of various physiologically peptides like amyloid-beta and insulin. This enzyme has been involved in the physiopathology of diabetes and Alzheimer's disease. We describe here a series of small molecules discovered by screening. Co-crystallization of the compounds with IDE revealed a binding both at the permanent exosite and at the discontinuous, conformational catalytic site. Preliminary structure-activity relationships are described. Selective inhibition of amyloid-beta degradation over insulin hydrolysis was possible. Neuroblastoma cells treated with the optimized compound display a dose-dependent increase in amyloid-beta levels.


  • Organizational Affiliation

    INSERM U761 Biostructures and Drug Discovery, Lille, France; Univ Lille Nord de France, Lille F-59000, France; Institut Pasteur de Lille, IFR 142, Lille F-59000, France; PRIM, Lille F-59000, France; CDithem Platform/IGM, Paris, France. Electronic address: benoit.deprez@univ-lille2.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN-DEGRADING ENZYME
A, B
990Homo sapiensMutation(s): 14 
EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
GTEx:  ENSG00000119912 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14735
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 262.288α = 90
b = 262.288β = 90
c = 90.63γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2014-04-30
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description