6URC

Crystal structure of IRE1a in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Disruption of IRE1 alpha through its kinase domain attenuates multiple myeloma.

Harnoss, J.M.Le Thomas, A.Shemorry, A.Marsters, S.A.Lawrence, D.A.Lu, M.Chen, Y.A.Qing, J.Totpal, K.Kan, D.Segal, E.Merchant, M.Reichelt, M.Ackerly Wallweber, H.Wang, W.Clark, K.Kaufman, S.Beresini, M.H.Laing, S.T.Sandoval, W.Lorenzo, M.Wu, J.Ly, J.De Bruyn, T.Heidersbach, A.Haley, B.Gogineni, A.Weimer, R.M.Lee, D.Braun, M.G.Rudolph, J.VanWyngarden, M.J.Sherbenou, D.W.Gomez-Bougie, P.Amiot, M.Acosta-Alvear, D.Walter, P.Ashkenazi, A.

(2019) Proc Natl Acad Sci U S A 116: 16420-16429

  • DOI: 10.1073/pnas.1906999116
  • Primary Citation of Related Structures:  
    6URC

  • PubMed Abstract: 
  • Multiple myeloma (MM) arises from malignant immunoglobulin (Ig)-secreting plasma cells and remains an incurable, often lethal disease despite therapeutic advances. The unfolded-protein response sensor IRE1α supports protein secretion by deploying a kinase-endoribonuclease module to activate the transcription factor XBP1s ...

    Multiple myeloma (MM) arises from malignant immunoglobulin (Ig)-secreting plasma cells and remains an incurable, often lethal disease despite therapeutic advances. The unfolded-protein response sensor IRE1α supports protein secretion by deploying a kinase-endoribonuclease module to activate the transcription factor XBP1s. MM cells may co-opt the IRE1α-XBP1s pathway; however, the validity of IRE1α as a potential MM therapeutic target is controversial. Genetic disruption of IRE1α or XBP1s, or pharmacologic IRE1α kinase inhibition, attenuated subcutaneous or orthometastatic growth of MM tumors in mice and augmented efficacy of two established frontline antimyeloma agents, bortezomib and lenalidomide. Mechanistically, IRE1α perturbation inhibited expression of key components of the endoplasmic reticulum-associated degradation machinery, as well as secretion of Ig light chains and of cytokines and chemokines known to promote MM growth. Selective IRE1α kinase inhibition reduced viability of CD138 + plasma cells while sparing CD138 - cells derived from bone marrows of newly diagnosed or posttreatment-relapsed MM patients, in both US- and European Union-based cohorts. Effective IRE1α inhibition preserved glucose-induced insulin secretion by pancreatic microislets and viability of primary hepatocytes in vitro, as well as normal tissue homeostasis in mice. These results establish a strong rationale for developing kinase-directed inhibitors of IRE1α for MM therapy.


    Organizational Affiliation

    Cancer Immunology, Genentech, Inc., South San Francisco, CA 94080; aa@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1 AB434Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for O75460 (Homo sapiens)
Explore O75460 
Go to UniProtKB:  O75460
NIH Common Fund Data Resources
PHAROS:  O75460
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QFV
Query on QFV

Download Ideal Coordinates CCD File 
A, B
2-chloro-N-(6-methyl-5-{[3-(2-{[(3S)-piperidin-3-yl]amino}pyrimidin-4-yl)pyridin-2-yl]oxy}naphthalen-1-yl)benzene-1-sulfonamide
C31 H29 Cl N6 O3 S
XMWUCMFVDXDRDE-NRFANRHFSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QFVIC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.12α = 90
b = 84.66β = 90
c = 175.51γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release