Small molecule inhibitor of the KEAP1-NRF2 protein-protein interaction

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Structure-Activity and Structure-Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein-Protein Interaction.

Heightman, T.D.Callahan, J.F.Chiarparin, E.Coyle, J.E.Griffiths-Jones, C.Lakdawala, A.S.McMenamin, R.Mortenson, P.N.Norton, D.Peakman, T.M.Rich, S.J.Richardson, C.Rumsey, W.L.Sanchez, Y.Saxty, G.Willems, H.M.G.Wolfe 3rd, L.Woolford, A.J.Wu, Z.Yan, H.Kerns, J.K.Davies, T.G.

(2019) J Med Chem 62: 4683-4702

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00279
  • Primary Citation of Related Structures:  
    6QMC, 6QMD, 6QME, 6QMJ, 6QMK

  • PubMed Abstract: 

    The KEAP1-NRF2-mediated cytoprotective response plays a key role in cellular homoeostasis. Insufficient NRF2 signaling during chronic oxidative stress may be associated with the pathophysiology of several diseases with an inflammatory component, and pathway activation through direct modulation of the KEAP1-NRF2 protein-protein interaction is being increasingly explored as a potential therapeutic strategy. Nevertheless, the physicochemical nature of the KEAP1-NRF2 interface suggests that achieving high affinity for a cell-penetrant druglike inhibitor might be challenging. We recently reported the discovery of a highly potent tool compound which was used to probe the biology associated with directly disrupting the interaction of NRF2 with the KEAP1 Kelch domain. We now present a detailed account of the medicinal chemistry campaign leading to this molecule, which included exploration and optimization of protein-ligand interactions in three energetic "hot spots" identified by fragment screening. In particular, we also discuss how consideration of ligand conformational stabilization was important to its development and present evidence for preorganization of the lead compound which may contribute to its high affinity and cellular activity.

  • Organizational Affiliation

    GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426-0989 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1321Mus musculusMutation(s): 0 
Gene Names: Keap1Inrf2Kiaa0132
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
XMS BindingDB:  6QMD Kd: 5.90e+4 (nM) from 1 assay(s)
IC50: 6.10e+4 (nM) from 1 assay(s)
J6N Binding MOAD:  6QMD IC50: 1.70e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.391α = 90
b = 103.391β = 90
c = 56.506γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2019-04-24 
  • Deposition Author(s): Davies, T.G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references