6BYZ

Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocyclic Inhibitor 37


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95625 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/s41589-019-0271-0
  • Primary Citation of Related Structures:  

  • 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 cl ...

    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

    Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA. drliu@fas.harvard.edu.,Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. drliu@fas.harvard.edu.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu.,Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA. markus.seeliger@stonybrook.edu.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu.,Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-degrading enzyme
A, B
1019Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Go to Gene View: IDE
Go to UniProtKB:  P14735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA
D, E
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
J18
Query on J18

Download SDF File 
Download CCD File 
A, B
[(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-{[2-(trifluoromethyl)phenyl]sulfonyl}-1,6-diazabicyclo[6.2.0]decan-10-yl]methanol
C30 H33 F3 N2 O3 S
OOPXWKPIZJCPGQ-GKRYNVPLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95625 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 264.486α = 90.00
b = 264.486β = 90.00
c = 91.094γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-05-29
    Type: Data collection, Database references