4U6R | pdb_00004u6r

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.246 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4U6R

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/ml500315b
  • Primary Citation Related Structures: 
    4U6R, 4U79

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 53.77 kDa 
  • Atom Count: 3,429 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 455 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1455Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (UniProt)
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3E4

Query on 3E4



Download:Ideal Coordinates CCD File
B [auth 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
EPE

Query on EPE



Download:Ideal Coordinates CCD File
I [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.246 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.847α = 90
b = 86.433β = 90
c = 91.818γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary