6HV0

IRE1 kinase/RNase in complex with imidazo[1,2-b]pyridazin-8-amine compound 33

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

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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 ...

    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: 

    School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1416Homo sapiensMutation(s): 0 
Gene Names: ERN1, IRE1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75460
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GUK (Subject of Investigation/LOI)
Query on GUK
Download Ideal Coordinates CCD File 
B [auth A]6-chloranyl-3-(2~{H}-indazol-5-yl)-~{N}-propan-2-yl-imidazo[1,2-b]pyridazin-8-amine
C16 H15 Cl N6
TZFOHQPMYQZELA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.04α = 90
b = 46.05β = 112.71
c = 86.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566
Cancer Research UKUnited KingdomC24461/A13231
Cancer Research UKUnited KingdomC24461/A12772

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