4PL3

Crystal structure of murine IRE1 in complex with MKC9989 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of action of the hydroxy-aryl-aldehyde class of IRE1 endoribonuclease inhibitors.

Sanches, M.Duffy, N.M.Talukdar, M.Thevakumaran, N.Chiovitti, D.Canny, M.D.Lee, K.Kurinov, I.Uehling, D.Al-Awar, R.Poda, G.Prakesch, M.Wilson, B.Tam, V.Schweitzer, C.Toro, A.Lucas, J.L.Vuga, D.Lehmann, L.Durocher, D.Zeng, Q.Patterson, J.B.Sicheri, F.

(2014) Nat Commun 5: 4202-4202

  • DOI: 10.1038/ncomms5202
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Endoplasmic reticulum (ER) stress activates the unfolded protein response and its dysfunction is linked to multiple diseases. The stress transducer IRE1α is a transmembrane kinase endoribonuclease (RNase) that cleaves mRNA substrates to re-establish ...

    Endoplasmic reticulum (ER) stress activates the unfolded protein response and its dysfunction is linked to multiple diseases. The stress transducer IRE1α is a transmembrane kinase endoribonuclease (RNase) that cleaves mRNA substrates to re-establish ER homeostasis. Aromatic ring systems containing hydroxy-aldehyde moieties, termed hydroxy-aryl-aldehydes (HAA), selectively inhibit IRE1α RNase and thus represent a novel chemical series for therapeutic development. We solved crystal structures of murine IRE1α in complex with three HAA inhibitors. HAA inhibitors engage a shallow pocket at the RNase-active site through pi-stacking interactions with His910 and Phe889, an essential Schiff base with Lys907 and a hydrogen bond with Tyr892. Structure-activity studies and mutational analysis of contact residues define the optimal chemical space of inhibitors and validate the inhibitor-binding site. These studies lay the foundation for understanding both the biochemical and cellular functions of IRE1α using small molecule inhibitors and suggest new avenues for inhibitor design.


    Organizational Affiliation

    1] Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 [3] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase/endoribonuclease IRE1
A, B
435Mus musculusMutation(s): 1 
Gene Names: Ern1Ire1
EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q9EQY0 (Mus musculus)
Go to UniProtKB:  Q9EQY0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
31J
Query on 31J

Download CCD File 
A, B
7-hydroxy-6-methoxy-3-[2-(2-methoxyethoxy)ethyl]-4,8-dimethyl-2H-chromen-2-one
C17 H22 O6
CREFVEORJKJSQY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.08α = 90
b = 90.5β = 91.88
c = 72.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP 84370
Multiple Myeloma Research Foundation Biotech Investment AwardUnited States--
Canadian Cancer SocietyCanada--

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence