4U6R

Crystal structure of human IRE1 cytoplasmic domains in complex with a sulfonamide inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unfolded Protein Response in Cancer: IRE1 alpha Inhibition by Selective Kinase Ligands Does Not Impair Tumor Cell Viability.

Harrington, P.E.Biswas, K.Malwitz, D.Tasker, A.S.Mohr, C.Andrews, K.L.Dellamaggiore, K.Kendall, R.Beckmann, H.Jaeckel, P.Materna-Reichelt, S.Allen, J.R.Lipford, J.R.

(2015) Acs Med.Chem.Lett. 6: 68-72

  • DOI: 10.1021/ml500315b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The kinase/endonuclease inositol requiring enzyme 1 (IRE1α), one of the sensors of unfolded protein accumulation in the endoplasmic reticulum that triggers the unfolded protein response (UPR), has been investigated as an anticancer target. We identif ...

    The kinase/endonuclease inositol requiring enzyme 1 (IRE1α), one of the sensors of unfolded protein accumulation in the endoplasmic reticulum that triggers the unfolded protein response (UPR), has been investigated as an anticancer target. We identified potent allosteric inhibitors of IRE1α endonuclease activity that bound to the kinase site on the enzyme. Structure-activity relationship (SAR) studies led to 16 and 18, which were selective in kinase screens and were potent against recombinant IRE1α endonuclease as well as cellular IRE1α. The first X-ray crystal structure of a kinase inhibitor (16) bound to hIRE1α was obtained. Screening of native tumor cell lines (>300) against selective IRE1α inhibitors failed to demonstrate any effect on cellular viability. These results suggest that IRE1α activity is not essential for viability in most tumor cell lines, in vitro, and that interfering with the survival functions of the UPR may not be an effective strategy to block tumorigenesis.


    Organizational Affiliation

    Departments of Medicinal Chemistry, Molecular Structure, and Oncology, Amgen, Inc. , One Amgen Center Drive, Thousand Oaks, California 93012, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase/endoribonuclease IRE1
A
455Homo sapiensMutation(s): 0 
Gene Names: ERN1 (IRE1)
Find proteins for O75460 (Homo sapiens)
Go to Gene View: ERN1
Go to UniProtKB:  O75460
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
3E4
Query on 3E4

Download SDF File 
Download CCD File 
A
N-{4-[(3-{2-[(trans-4-aminocyclohexyl)amino]pyrimidin-4-yl}pyridin-2-yl)oxy]-3-methylnaphthalen-1-yl}-2-chlorobenzenesulfonamide
C32 H31 Cl N6 O3 S
VMXTWHCDROGRNY-HZCBDIJESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3E4IC50: 14 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.847α = 90.00
b = 86.433β = 90.00
c = 91.818γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-29 
  • Released Date: 2014-10-08 
  • Deposition Author(s): Mohr, C.

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references