4RE9

Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 71290


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice.

Deprez-Poulain, R.Hennuyer, N.Bosc, D.Liang, W.G.Enee, E.Marechal, X.Charton, J.Totobenazara, J.Berte, G.Jahklal, J.Verdelet, T.Dumont, J.Dassonneville, S.Woitrain, E.Gauriot, M.Paquet, C.Duplan, I.Hermant, P.Cantrelle, F.X.Sevin, E.Culot, M.Landry, V.Herledan, A.Piveteau, C.Lippens, G.Leroux, F.Tang, W.J.van Endert, P.Staels, B.Deprez, B.

(2015) Nat Commun 6: 8250-8250

  • DOI: 10.1038/ncomms9250
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is ...

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes.


    Organizational Affiliation

    Pole de Recherche Interdisciplinaire pour le Medicament, Lille F-59000, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-degrading enzyme
A, B
990Homo sapiensMutation(s): 13 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Go to UniProtKB:  P14735
NIH Common Fund Data Resources
PHAROS  P14735
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3M9
Query on 3M9

Download CCD File 
A, B
4-fluoro-N-({1-[(2R)-4-(hydroxyamino)-1-(naphthalen-2-yl)-4-oxobutan-2-yl]-1H-1,2,3-triazol-5-yl}methyl)benzamide
C24 H22 F N5 O3
RJVYTCJRTAVEBT-OAQYLSRUSA-N
 Ligand Interaction
EPE
Query on EPE

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A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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A, B
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 262.981α = 90
b = 262.981β = 90
c = 90.508γ = 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 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references