5CGJ

Crystal structure of murine Keap1 in complex with RA839, a non-covalent small-molecule binder to Keap1 and selective activator of Nrf2 signalling.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 

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This is version 1.2 of the entry. See complete history


Literature

Characterization of RA839, a Noncovalent Small Molecule Binder to Keap1 and Selective Activator of Nrf2 Signaling.

Winkel, A.F.Engel, C.K.Margerie, D.Kannt, A.Szillat, H.Glombik, H.Kallus, C.Ruf, S.Gussregen, S.Riedel, J.Herling, A.W.von Knethen, A.Weigert, A.Brune, B.Schmoll, D.

(2015) J Biol Chem 290: 28446-28455

  • DOI: https://doi.org/10.1074/jbc.M115.678136
  • Primary Citation of Related Structures:  
    5CGJ

  • PubMed Abstract: 

    The activation of the transcription factor NF-E2-related factor 2 (Nrf2) maintains cellular homeostasis in response to oxidative stress by the regulation of multiple cytoprotective genes. Without stressors, the activity of Nrf2 is inhibited by its interaction with the Keap1 (kelch-like ECH-associated protein 1). Here, we describe (3S)-1-[4-[(2,3,5,6-tetramethylphenyl) sulfonylamino]-1-naphthyl]pyrrolidine-3-carboxylic acid (RA839), a small molecule that binds noncovalently to the Nrf2-interacting kelch domain of Keap1 with a Kd of ∼6 μM, as demonstrated by x-ray co-crystallization and isothermal titration calorimetry. Whole genome DNA arrays showed that at 10 μM RA839 significantly regulated 105 probe sets in bone marrow-derived macrophages. Canonical pathway mapping of these probe sets revealed an activation of pathways linked with Nrf2 signaling. These pathways were also activated after the activation of Nrf2 by the silencing of Keap1 expression. RA839 regulated only two genes in Nrf2 knock-out macrophages. Similar to the activation of Nrf2 by either silencing of Keap1 expression or by the reactive compound 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid methyl ester (CDDO-Me), RA839 prevented the induction of both inducible nitric-oxide synthase expression and nitric oxide release in response to lipopolysaccharides in macrophages. In mice, RA839 acutely induced Nrf2 target gene expression in liver. RA839 is a selective inhibitor of the Keap1/Nrf2 interaction and a useful tool compound to study the biology of Nrf2.


  • Organizational Affiliation

    R&D, Sanofi, 65926 Frankfurt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1336Mus musculusMutation(s): 0 
Gene Names: Keap1Inrf2Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus)
Explore Q9Z2X8 
Go to UniProtKB:  Q9Z2X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z2X8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
51M BindingDB:  5CGJ Ki: 48 (nM) from 1 assay(s)
Kd: min: 470, max: 6000 (nM) from 3 assay(s)
IC50: min: 0.14, max: 200 (nM) from 3 assay(s)
EC50: 1.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.41α = 90
b = 103.41β = 90
c = 56.49γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references