5FNU | pdb_00005fnu

Structure of the Keap1 Kelch domain in complex with a small molecule inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Mono-Acidic Inhibitors of the Kelch-Like Ech-Associated Protein 1 : Nuclear Factor Erythroid 2-Related Factor 2 (Keap1:Nrf2) Protein-Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery.

Davies, T.G.Wixted, W.E.Coyle, J.E.Griffiths-Jones, C.Hearn, K.Mcmenamin, R.L.Norton, D.Rich, S.J.Richardson, C.Saxty, G.Willems, H.M.G.Woolford, A.J.Cottom, J.E.Kou, J.Yonchuk, J.G.Feldser, H.G.Sanchez, Y.Foley, J.P.Bolognese, B.J.Logan, G.A.Podolin, P.L.Yan, H.Callahan, J.F.Heightman, T.D.Kerns, J.K.

(2016) J Med Chem 59: 3991

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00228
  • Primary Citation of Related Structures:  
    5FNQ, 5FNR, 5FNS, 5FNT, 5FNU, 5FZJ, 5FZN

  • PubMed Abstract: 

    KEAP1 is the key regulator of the NRF2-mediated cytoprotective response, and increasingly recognized as a target for diseases involving oxidative stress. Pharmacological intervention has focused on molecules that decrease NRF2-ubiquitination through covalent modification of KEAP1 cysteine residues, but such electrophilic compounds lack selectivity and may be associated with off-target toxicity. We report here the first use of a fragment-based approach to directly target the KEAP1 Kelch-NRF2 interaction. X-ray crystallographic screening identified three distinct "hot-spots" for fragment binding within the NRF2 binding pocket of KEAP1, allowing progression of a weak fragment hit to molecules with nanomolar affinity for KEAP1 while maintaining drug-like properties. This work resulted in a promising lead compound which exhibits tight and selective binding to KEAP1, and activates the NRF2 antioxidant response in cellular and in vivo models, thereby providing a high quality chemical probe to explore the therapeutic potential of disrupting the KEAP1-NRF2 interaction.


  • Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KELCH-LIKE ECH-ASSOCIATED PROTEIN 1304Mus musculusMutation(s): 0 
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
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L6I
Query on L6I

Download Ideal Coordinates CCD File 
B [auth A](3S)-3-(7-methoxy-1-methyl-1H-benzo[d][1,2,3]triazol-5-yl)-3-(4-methyl-3-(((R)-4-methyl-1,1-dioxido-3,4-dihydro-2H-benzo[b][1,4,5]oxathiazepin-2-yl)methyl)phenyl)propanoic acid
C28 H30 N4 O6 S
ZDNGJXBUEQNFBQ-GCJKJVERSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
L6I BindingDB:  5FNU Ki: 1 (nM) from 1 assay(s)
Kd: min: 1.3, max: 1.6 (nM) from 3 assay(s)
IC50: min: 8, max: 55 (nM) from 3 assay(s)
EC50: 1900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.297α = 90
b = 103.297β = 90
c = 56.434γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted L6IClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 2.0: 2018-04-04
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description