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 

wwPDB Validation 3D Report Full Report


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: 10.1074/jbc.M115.678136

  • 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 in ...

    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

    From the R&D, Sanofi, 65926 Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kelch-like ECH-associated protein 1
A
336Mus musculusMutation(s): 0 
Gene Names: Keap1 (Inrf2, Kiaa0132)
Find proteins for Q9Z2X8 (Mus musculus)
Go to UniProtKB:  Q9Z2X8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
51M
Query on 51M

Download SDF File 
Download CCD File 
A
(3S)-1-(4-{[(2,3,5,6-tetramethylphenyl)sulfonyl]amino}naphthalen-1-yl)pyrrolidine-3-carboxylic acid
C25 H28 N2 O4 S
BVYWIQHJXAEJOD-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.137 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 103.410α = 90.00
b = 103.410β = 90.00
c = 56.490γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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