Crystal structure of cpd 16 bound to Keap1 Kelch domain

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

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This is version 1.2 of the entry. See complete history


Small molecules inhibit the interaction of Nrf2 and the Keap1 Kelch domain through a non-covalent mechanism.

Marcotte, D.Zeng, W.Hus, J.C.McKenzie, A.Hession, C.Jin, P.Bergeron, C.Lugovskoy, A.Enyedy, I.Cuervo, H.Wang, D.Atmanene, C.Roecklin, D.Vecchi, M.Vivat, V.Kraemer, J.Winkler, D.Hong, V.Chao, J.Lukashev, M.Silvian, L.

(2013) Bioorg Med Chem 21: 4011-4019

  • DOI: https://doi.org/10.1016/j.bmc.2013.04.019
  • Primary Citation of Related Structures:  
    4IN4, 4IQK

  • PubMed Abstract: 

    Keap1 binds to the Nrf2 transcription factor to promote its degradation, resulting in the loss of gene products that protect against oxidative stress. While cell-active small molecules have been identified that modify cysteines in Keap1 and effect the Nrf2 dependent pathway, few act through a non-covalent mechanism. We have identified and characterized several small molecule compounds that specifically bind to the Keap1 Kelch-DC domain as measured by NMR, native mass spectrometry and X-ray crystallography. One compound upregulates Nrf2 response genes measured by a luciferase cell reporter assay. The non-covalent inhibition strategy presents a reasonable course of action to avoid toxic side-effects due to non-specific cysteine modification.

  • Organizational Affiliation

    Biogen Idec, Drug Discovery, 12 Cambridge Center, Cambridge, MA 02142, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1299Homo sapiensMutation(s): 2 
Gene Names: INRF2KEAP1KIAA0132KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
GTEx:  ENSG00000079999 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IQK

Download Ideal Coordinates CCD File 
B [auth A]N,N'-naphthalene-1,4-diylbis(4-methoxybenzenesulfonamide)
C24 H22 N2 O6 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
IQK BindingDB:  4IQK Ki: 250 (nM) from 1 assay(s)
Kd: min: 370, max: 1700 (nM) from 4 assay(s)
IC50: min: 1600, max: 2700 (nM) from 3 assay(s)
EC50: min: 1460, max: 5800 (nM) from 2 assay(s)
Binding MOAD:  4IQK IC50: 2700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.856α = 90
b = 75.638β = 106.09
c = 48.341γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
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: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2013-07-03
    Changes: Database references