4QIA

Crystal structure of human insulin degrading enzyme (ide) in complex with inhibitor N-benzyl-N-(carboxymethyl)glycyl-L-histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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:  
    4GSF, 4QIA

  • 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 Alzheimer's disease, amyloid-â clearance, and its validation as a potential therapeutic target ...

    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. Electronic address: rebecca.deprez@univ-lille2.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-degrading enzyme AB990Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
NIH Common Fund Data Resources
PHAROS:  P14735
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
33K
Query on 33K

Download Ideal Coordinates CCD File 
A, B
N-benzyl-N-(carboxymethyl)glycyl-L-histidine
C17 H20 N4 O5
ZCJIWRBKBPEIFF-AWEZNQCLSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.505α = 90
b = 264.505β = 90
c = 90.543γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references