7BMK

ATP-Competitive Partial Antagonists-'PAIR's-Rheostatically Modulate IRE1alpha's Kinase Helix-alphaC to Segregate its RNase-Mediated Biological Outputs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

ATP-competitive partial antagonists of the IRE1 alpha RNase segregate outputs of the UPR.

Feldman, H.C.Ghosh, R.Auyeung, V.C.Mueller, J.L.Kim, J.H.Potter, Z.E.Vidadala, V.N.Perera, B.G.K.Olivier, A.Backes, B.J.Zikherman, J.Papa, F.R.Maly, D.J.

(2021) Nat Chem Biol 17: 1148-1156

  • DOI: https://doi.org/10.1038/s41589-021-00852-0
  • Primary Citation of Related Structures:  
    7BMK

  • PubMed Abstract: 

    The unfolded protein response (UPR) homeostatically matches endoplasmic reticulum (ER) protein-folding capacity to cellular secretory needs. However, under high or chronic ER stress, the UPR triggers apoptosis. This cell fate dichotomy is promoted by differential activation of the ER transmembrane kinase/endoribonuclease (RNase) IRE1α. We previously found that the RNase of IRE1α can be either fully activated or inactivated by ATP-competitive kinase inhibitors. Here we developed kinase inhibitors, partial antagonists of IRE1α RNase (PAIRs), that partially antagonize the IRE1α RNase at full occupancy. Biochemical and structural studies show that PAIRs promote partial RNase antagonism by intermediately displacing the helix αC in the IRE1α kinase domain. In insulin-producing β-cells, PAIRs permit adaptive splicing of Xbp1 mRNA while quelling destructive ER mRNA endonucleolytic decay and apoptosis. By preserving Xbp1 mRNA splicing, PAIRs allow B cells to differentiate into immunoglobulin-producing plasma cells. Thus, an intermediate RNase-inhibitory 'sweet spot', achieved by PAIR-bound IRE1α, captures a desirable conformation for drugging this master UPR sensor/effector.


  • Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1
A, B
434Homo 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U4N
Query on U4N

Download Ideal Coordinates CCD File 
C [auth A],
X [auth B]
2,2,2-tris(fluoranyl)-~{N}-[4-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxynaphthalen-1-yl]ethanesulfonamide
C26 H25 F3 N6 O3 S
LVBYPSVRFGNRPW-KRWDZBQOSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
DA [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B],
CA [auth B],
FA [auth B],
W [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth B]
D [auth A]
E [auth A]
F [auth A]
I [auth A]
BA [auth B],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
K [auth A],
L [auth A],
R [auth A],
S [auth A],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth B]
G [auth A]
GA [auth B]
H [auth A]
HA [auth B]
EA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
IA [auth B],
J [auth A],
JA [auth B],
KA [auth B],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
T [auth A],
U [auth A],
V [auth A],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.903α = 90
b = 72.813β = 129.82
c = 119.239γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK100623
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesU01DK123609

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references