4PL5

Crystal structure of murine IRE1 in complex with OICR573 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 

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
  • Primary Citation of Related Structures:  

  • 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

    MannKind Corporation, 28903 North Avenue Paine, Valencia, California 91355, USA.,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].,NanoTemper Technologies, Inc., 395 Oyster Point Boulevard, Suite 135, South San Francisco, California 94080, USA.,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.,Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3.,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.,NE-CAT APS, Building 436E, Argonne National Lab, 9700 S.Cass Avenue, Argonne, Illinois 60439, USA.,1] Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5.,1] Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5 [2].,1] Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3 [2] Department of Pharmacology and Toxicology, 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
B, A, C, D
435Mus musculusMutation(s): 1 
Gene Names: Ern1 (Ire1)
Find proteins for Q9EQY0 (Mus musculus)
Go to UniProtKB:  Q9EQY0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A
3-methoxy-5-methyl-4'-(morpholin-4-yl)biphenyl-4-ol
C18 H21 N O3
LUWYUXWJRQRONA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEU
Query on PEU

Download SDF File 
Download CCD File 
A
2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
PEG 8000
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 319.220α = 90.00
b = 63.030β = 99.49
c = 140.780γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence