6EDS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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:  
    6MQ3, 6EDS, 6BYZ

  • 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.


    Related Citations: 
    • Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones.
      Maianti, J.P., McFedries, A., Foda, Z.H., Kleiner, R.E., Du, X.Q., Leissring, M.A., Tang, W.J., Charron, M.J., Seeliger, M.A., Saghatelian, A., Liu, D.R.
      (2014) Nature 511: 94

    Organizational Affiliation

    Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA. drliu@fas.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-degrading enzymeAB978Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
NIH Common Fund Data Resources
PHAROS  P14735
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GlucagonCD29Homo sapiensMutation(s): 0 
Gene Names: GCG
Find proteins for P01275 (Homo sapiens)
Explore P01275 
Go to UniProtKB:  P01275
NIH Common Fund Data Resources
PHAROS  P01275
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J22
Query on J22

Download CCD File 
A, B
{(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-[(1-methyl-1H-imidazol-2-yl)sulfonyl]-1,6-diazabicyclo[6.2.0]decan-10-yl}methanol
C27 H34 N4 O3 S
OJXBQVFJQWLDCX-NXCFDTQHSA-N
 Ligand Interaction
EPE
Query on EPE

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

Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download CCD File 
A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.119α = 90
b = 263.119β = 90
c = 90.322γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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