6HX1

IRE1 ALPHA IN COMPLEX WITH imidazo[1,2-b]pyridazin-8-amine compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Binding to an Unusual Inactive Kinase Conformation by Highly Selective Inhibitors of Inositol-Requiring Enzyme 1 alpha Kinase-Endoribonuclease.

Colombano, G.Caldwell, J.J.Matthews, T.P.Bhatia, C.Joshi, A.McHardy, T.Mok, N.Y.Newbatt, Y.Pickard, L.Strover, J.Hedayat, S.Walton, M.I.Myers, S.M.Jones, A.M.Saville, H.McAndrew, C.Burke, R.Eccles, S.A.Davies, F.E.Bayliss, R.Collins, I.

(2019) J Med Chem 62: 2447-2465

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01721
  • Primary Citation of Related Structures:  
    6HV0, 6HX1

  • PubMed Abstract: 

    A series of imidazo[1,2- b]pyridazin-8-amine kinase inhibitors were discovered to allosterically inhibit the endoribonuclease function of the dual kinase-endoribonuclease inositol-requiring enzyme 1α (IRE1α), a key component of the unfolded protein response in mammalian cells and a potential drug target in multiple human diseases. Inhibitor optimization gave compounds with high kinome selectivity that prevented endoplasmic reticulum stress-induced IRE1α oligomerization and phosphorylation, and inhibited endoribonuclease activity in human cells. X-ray crystallography showed the inhibitors to bind to a previously unreported and unusually disordered conformation of the IRE1α kinase domain that would be incompatible with back-to-back dimerization of the IRE1α protein and activation of the endoribonuclease function. These findings increase the repertoire of known IRE1α protein conformations and can guide the discovery of highly selective ligands for the IRE1α kinase site that allosterically inhibit the endoribonuclease.


  • Organizational Affiliation

    Department of Molecular and Cell Biology , University of Leicester , Leicester LE1 7RH , U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1403Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
EC: 2.7.11.1 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GXK (Subject of Investigation/LOI)
Query on GXK

Download Ideal Coordinates CCD File 
B [auth A]6-chloranyl-~{N}-(cyclopropylmethyl)-3-(2~{H}-indazol-5-yl)imidazo[1,2-b]pyridazin-8-amine
C17 H15 Cl N6
FLFMYUGDCXTOQI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GXK Binding MOAD:  6HX1 IC50: 1600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.408α = 90
b = 47.074β = 112.14
c = 86.369γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection
  • Version 1.3: 2019-10-30
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description