4DWK | pdb_00004dwk

Structure of cystein free insulin degrading enzyme with compound bdm41671 ((s)-2-{2-[carboxymethyl-(3-phenyl-propyl)-amino]-acetylamino}-3-(1h-imidazol-4-yl)-propionic acid methyl ester)

• PDB DOI: https://doi.org/10.2210/pdb4DWK/pdb

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


• Deposited: 2012-02-24 Released: 2013-04-03 
• Deposition Author(s): Guo, Q., Deprez-Poulain, R., Deprez, B., Tang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 24735644 
• DOI: https://doi.org/10.1016/j.ejmech.2014.04.009
• Primary Citation Related Structures: 
  2YPU, 3QZ2, 4DTT, 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 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.

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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.
Ben-May Institute for Cancer Research, The University of Chicago, W421 Chicago, IL, USA.
Univ Lille Nord de France, Lille F-59000, France; Institut Pasteur de Lille, IFR 142, Lille F-59000, France; INSERM U1011 Nuclear Receptors, Cardiovascular Diseases and Diabetes, Lille F-59000, France; European Genomic Institute for Diabetes (EGID), FR 3508, Lille F-59000, France.
Univ Lille Nord de France, Lille F-59000, France; INSERM U837 Neurodegenerative Diseases and Neuronal Death, Lille F-59000, France; CHRU, Lille F-59000, France.
CDithem Platform/IGM, Paris, France; Inserm UMR-S 973/MTi, University Paris Diderot, Paris, France.
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. Electronic address: [e-mail].
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. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 230.06 kDa 
• Atom Count: 15,764 
• Modeled Residue Count: 1,910 
• 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): 14  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGK	C [auth A], E [auth B]	methyl N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-L-histidinate C20 H26 N4 O5 OLFNGPVNZBLJOR-KRWDZBQOSA-N
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.227 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 261.511	α = 90
b = 261.511	β = 90
c = 91.721	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Guo, Q., Deprez-Poulain, R., Deprez, B., Tang, W.J.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Database references
• Version 1.2: 2014-05-28
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description