Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocycle Inhibitor 63

Experimental Data Snapshot

  • Resolution: 3.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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This is version 1.3 of the entry. See complete history


Substrate-selective inhibitors that reprogram the activity of insulin-degrading enzyme.

Maianti, J.P.Tan, G.A.Vetere, A.Welsh, A.J.Wagner, B.K.Seeliger, M.A.Liu, D.R.

(2019) Nat Chem Biol 15: 565-574

  • DOI: https://doi.org/10.1038/s41589-019-0271-0
  • Primary Citation of Related Structures:  
    6BYZ, 6EDS, 6MQ3

  • PubMed Abstract: 

    Enzymes that act on multiple substrates are common in biology but pose unique challenges as therapeutic targets. The metalloprotease insulin-degrading enzyme (IDE) modulates blood glucose levels by cleaving insulin, a hormone that promotes glucose clearance. However, IDE also degrades glucagon, a hormone that elevates glucose levels and opposes the effect of insulin. IDE inhibitors to treat diabetes, therefore, should prevent IDE-mediated insulin degradation, but not glucagon degradation, in contrast with traditional modes of enzyme inhibition. Using a high-throughput screen for non-active-site ligands, we discovered potent and highly specific small-molecule inhibitors that alter IDE's substrate selectivity. X-ray co-crystal structures, including an IDE-ligand-glucagon ternary complex, revealed substrate-dependent interactions that enable these inhibitors to potently block insulin binding while allowing glucagon cleavage, even at saturating inhibitor concentrations. These findings suggest a path for developing IDE-targeting therapeutics, and offer a blueprint for modulating other enzymes in a substrate-selective manner to unlock their therapeutic potential.

  • Organizational Affiliation

    Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-degrading enzyme
A, B
978Homo sapiensMutation(s): 14 
Gene Names: IDE
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
PHAROS:  P14735
GTEx:  ENSG00000119912 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14735
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on J22

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C27 H34 N4 O3 S
Query on EPE

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C8 H18 N2 O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.254α = 90
b = 263.254β = 90
c = 91.234γ = 120
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description