4DTT

Crystal structure of human insulin degrading enzyme (ide) in complex with compund 41367


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 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. 79: 184-193

  • DOI: 10.1016/j.ejmech.2014.04.009
  • Primary Citation of Related Structures:  2YPU, 3QZ2, 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 Alzhei ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-degrading enzyme
A, B
990Homo sapiensGene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Go to Gene View: IDE
Go to UniProtKB:  P14735
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
I41
Query on I41

Download SDF File 
Download CCD File 
A, B
2-[[2-[[(2S)-3-(3H-IMIDAZOL-4-YL)-1-METHOXY-1-OXO-PROPAN-2-YL]AMINO]-2-OXO-ETHYL]-(PHENYLMETHYL)AMINO]ETHANOIC ACID
COMPOUND 41367
C18 H22 N4 O5
VJXRDRMNYWCCEG-HNNXBMFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.175 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 263.518α = 90.00
b = 263.518β = 90.00
c = 90.401γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references
  • Version 1.2: 2014-05-28
    Type: Database references