6BYZ | pdb_00006byz

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

• PDB DOI: https://doi.org/10.2210/pdb6BYZ/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-12-21 Released: 2019-04-03 
• Deposition Author(s): Tan, G.A., Seeliger, M.A., Maianti, J.P., Liu, D.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

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

• PubMed: 31086331 
• DOI: https://doi.org/10.1038/s41589-019-0271-0
• Primary Citation 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.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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.
Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA. [e-mail].
Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. [e-mail].
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. [e-mail].
Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. [e-mail].
Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 237.99 kDa 
• Atom Count: 16,150 
• Modeled Residue Count: 1,923 
• Deposited Residue Count: 2,044 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	1,019	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ALA	C [auth D], D [auth E]	3	Escherichia coli BL21(DE3)	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J18 (Subject of Investigation/LOI)	E [auth A], G [auth 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
EPE	F [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.486	α = 90
b = 264.486	β = 90
c = 91.094	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Tan, G.A., Seeliger, M.A., Maianti, J.P., Liu, D.R.

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
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description