Crystal structure of IRE1a in complex with G-4100

Experimental Data Snapshot

  • Resolution: 2.54 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Identification of BRaf-Sparing Amino-Thienopyrimidines with Potent IRE1 alpha Inhibitory Activity.

Beveridge, R.E.Wallweber, H.A.Ashkenazi, A.Beresini, M.Clark, K.R.Gibbons, P.Ghiro, E.Kaufman, S.Larivee, A.Leblanc, M.Leclerc, J.P.Lemire, A.Ly, C.Rudolph, J.Schwarz, J.B.Srivastava, S.Wang, W.Zhao, L.Braun, M.G.

(2020) ACS Med Chem Lett 11: 2389-2396

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00344
  • Primary Citation of Related Structures:  
    6XDB, 6XDD, 6XDF

  • PubMed Abstract: 

    Amino-quinazoline BRaf kinase inhibitor 2 was identified from a library screen as a modest inhibitor of the unfolded protein response (UPR) regulating potential anticancer target IRE1α. A combination of crystallographic and conformational considerations were used to guide structure-based attenuation of BRaf activity and optimization of IRE1α potency. Quinazoline 6-position modifications were found to provide up to 100-fold improvement in IRE1α cellular potency but were ineffective at reducing BRaf activity. A salt bridge contact with Glu651 in IRE1α was then targeted to build in selectivity over BRaf which instead possesses a histidine in this position (His539). Torsional angle analysis revealed that the quinazoline hinge binder core was ill-suited to accommodate the required conformation to effectively reach Glu651, prompting a change to the thienopyrimidine hinge binder. Resulting analogues such as 25 demonstrated good IRE1α cellular potency and imparted more than 1000-fold decrease in BRaf activity.

  • Organizational Affiliation

    Paraza Pharma Inc., 2525 Ave. Marie-Curie, Montreal, QC, Canada H4S 2E1.

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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N94 (Subject of Investigation/LOI)
Query on N94

Download Ideal Coordinates CCD File 
D [auth A]4-amino-N-(6-chloro-2-fluoro-3-{[(pyrrolidin-1-yl)sulfonyl]amino}phenyl)quinazoline-8-carboxamide
C19 H18 Cl F N6 O3 S
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.54 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.919α = 90
b = 72.767β = 129.73
c = 120.054γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Advisory, Data collection, Database references