Structure of phosphorylated IRE1 in complex with G-0701

Experimental Data Snapshot

  • Resolution: 2.74 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands.

Ferri, E.Le Thomas, A.Wallweber, H.A.Day, E.S.Walters, B.T.Kaufman, S.E.Braun, M.G.Clark, K.R.Beresini, M.H.Mortara, K.Chen, Y.A.Canter, B.Phung, W.Liu, P.S.Lammens, A.Ashkenazi, A.Rudolph, J.Wang, W.

(2020) Nat Commun 11: 6387-6387

  • DOI: https://doi.org/10.1038/s41467-020-19974-5
  • Primary Citation of Related Structures:  
    6W39, 6W3A, 6W3B, 6W3C, 6W3E, 6W3K

  • PubMed Abstract: 

    Inositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.

  • Organizational Affiliation

    Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1
A, B
431Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
EC: (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75460 (Homo sapiens)
Explore O75460 
Go to UniProtKB:  O75460
PHAROS:  O75460
GTEx:  ENSG00000178607 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75460
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SJV (Subject of Investigation/LOI)
Query on SJV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl ~{N}-[6-methyl-5-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxy-naphthalen-1-yl]carbamate
C27 H28 N6 O3
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEP
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.74 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.267 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.67α = 90
b = 139.24β = 114.9
c = 63.95γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Derived calculations
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description