4GSF

The structure analysis of cysteine free insulin degrading enzyme (ide) with (s)-2-{2-[carboxymethyl-(3-phenyl-propionyl)-amino]-acetylamino}-3-(3h-imidazol-4-yl)-propionic acid methyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme.

Charton, J.Gauriot, M.Totobenazara, J.Hennuyer, N.Dumont, J.Bosc, D.Marechal, X.Elbakali, J.Herledan, A.Wen, X.Ronco, C.Gras-Masse, H.Heninot, A.Pottiez, V.Landry, V.Staels, B.Liang, W.G.Leroux, F.Tang, W.J.Deprez, B.Deprez-Poulain, R.

(2015) Eur.J.Med.Chem. 90: 547-567

  • DOI: 10.1016/j.ejmech.2014.12.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Insulin degrading enzyme (IDE) is a zinc metalloprotease that degrades small amyloid peptides such as amyloid-â and insulin. So far the dearth of IDE-specific pharmacological inhibitors impacts the understanding of its role in the physiopathology of ...

    Insulin degrading enzyme (IDE) is a zinc metalloprotease that degrades small amyloid peptides such as amyloid-â and insulin. So far the dearth of IDE-specific pharmacological inhibitors impacts the understanding of its role in the physiopathology of Alzheimer's disease, amyloid-â clearance, and its validation as a potential therapeutic target. Hit 1 was previously discovered by high-throughput screening. Here we describe the structure-activity study, that required the synthesis of 48 analogues. We found that while the carboxylic acid, the imidazole and the tertiary amine were critical for activity, the methyl ester was successfully optimized to an amide or a 1,2,4-oxadiazole. Along with improving their activity, compounds were optimized for solubility, lipophilicity and stability in plasma and microsomes. The docking or co-crystallization of some compounds at the exosite or the catalytic site of IDE provided the structural basis for IDE inhibition. The pharmacokinetic properties of best compounds 44 and 46 were measured in vivo. As a result, 44 (BDM43079) and its methyl ester precursor 48 (BDM43124) are useful chemical probes for the exploration of IDE's role.


    Organizational Affiliation

    INSERM U761 Biostructures and Drug Discovery, Lille, 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 sapiensMutation(s): 14 
Gene 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
MGH
Query on MGH

Download SDF File 
Download CCD File 
A, B
methyl N-(carboxymethyl)-N-(3-phenylpropanoyl)glycyl-D-histidinate
(S)-2-{2-[Carboxymethyl-(3-phenyl-propionyl)-amino]-acetylamino}-3-(3H-imidazol-4-yl)-propionic acid methyl ester
C20 H24 N4 O6
FTBNIEVYMZAOPN-MRXNPFEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 263.179α = 90.00
b = 263.179β = 90.00
c = 90.557γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-3000data collection
HKL-3000data reduction
REFMACrefinement
HKL-3000data scaling

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: 2015-06-17
    Type: Database references