6QMK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1A321Mus musculusMutation(s): 0 
Gene Names: Keap1Inrf2Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus)
Explore Q9Z2X8 
Go to UniProtKB:  Q9Z2X8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J8H (Subject of Investigation/LOI)
Query on J8H

Download Ideal Coordinates CCD File 
C [auth A](3~{S})-3-[3-[[1,1-bis(oxidanylidene)-3,4-dihydro-5,1$l^{6},2-benzoxathiazepin-2-yl]methyl]-4-methyl-phenyl]-3-(7-methoxy-1-methyl-benzotriazol-5-yl)propanoic acid
C27 H28 N4 O6 S
RTGHTXKISWZXKJ-NRFANRHFSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
J8H BindingDB:  6QMK Kd: 35 (nM) from 1 assay(s)
IC50: min: 47, max: 55 (nM) from 2 assay(s)
Binding MOAD:  6QMK IC50: 47 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.651α = 90
b = 103.651β = 90
c = 56.359γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-02-07 
  • 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