4RE9 | pdb_00004re9

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

• PDB DOI: https://doi.org/10.2210/pdb4RE9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-22 Released: 2015-09-30 
• Deposition Author(s): Liang, W.G., Deprez, R., Deprez, B., Tang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

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

• PubMed: 26394692 
• DOI: https://doi.org/10.1038/ncomms9250
• Primary Citation Related Structures: 
  4IFH, 4NXO, 4RE9


• 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 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.

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Organizational Affiliation: 
• Institut Pasteur de Lille, Lille F-59000, France.
Université de Lille, Institut Federatif de Recherche 114, Lille F-59000, France.
Institut National de la Sante et de la Recherche Medicale, U1177 Drugs and Molecules for Living Systems, Lille F-59000, France.
Institut Federatif de Recherche 142, Molecular and Cellular Medicine, Lille F-59000, France.
Pole de Recherche Interdisciplinaire pour le Medicament, Lille F-59000, France.
Institut National de la Sante et de la Recherche Medicale, U1011 Nuclear Receptors, Cardiovascular Diseases and Diabetes, European Genomic Institute for Diabetes, Lille F-59000, France.
Ben-May Institute for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA.
Institut National de la Sante et de la Recherche Medicale, Unité 1151; Université Paris Descartes, Sorbonne Paris Cité; Centre National de la Recherche Scientifique, , Unité 8253, Paris, France.
Centre National de la Recherche Scientifique, UMR 8576, Structural and Functional Glycobiology, Université de Lille, Lille F-59000, France.
Université d'Artois, LBHE, EA2465, Lens F-62300, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 232.23 kDa 
• Atom Count: 15,851 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	990	Homo sapiens	Mutation(s): 13  Gene Names: IDE EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens) Explore P14735  Go to UniProtKB:  P14735
PHAROS:  P14735 GTEx:  ENSG00000119912

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3M9	D [auth A], N [auth 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
EPE	E [auth A], O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE	L [auth A], T [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.981	α = 90
b = 262.981	β = 90
c = 90.508	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Liang, W.G., Deprez, R., Deprez, B., Tang, W.J.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description