4XMB

Crystal structure of 2,2'-(naphthalene-1,4-diylbis(((4-methoxyphenyl)sulfonyl)azanediyl))diacetamide bound to human Keap1 Kelch domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Probing the structural requirements of non-electrophilic naphthalene-based Nrf2 activators.

Jain, A.D.Potteti, H.Richardson, B.G.Kingsley, L.Luciano, J.P.Ryuzoji, A.F.Lee, H.Krunic, A.Mesecar, A.D.Reddy, S.P.Moore, T.W.

(2015) Eur J Med Chem 103: 252-268

  • DOI: https://doi.org/10.1016/j.ejmech.2015.08.049
  • Primary Citation of Related Structures:  
    4XMB

  • PubMed Abstract: 

    Activation of the transcription factor Nrf2 has been posited to be a promising therapeutic strategy in a number of inflammatory and oxidative stress diseases due to its regulation of detoxifying enzymes. In this work, we have developed a comprehensive structure-activity relationship around a known, naphthalene-based non-electrophilic activator of Nrf2, and we report highly potent non-electrophilic activators of Nrf2. Computational docking analysis of a subset of the compound series demonstrates the importance of water molecule displacement for affinity, and the X-ray structure of di-amide 12e supports the computational analysis. One of the best compounds, acid 16b, has an IC50 of 61 nM in a fluorescence anisotropy assay and a Kd of 120 nM in a surface plasmon resonance assay. Additionally, we demonstrate that the ethyl ester of 16b is an efficacious inducer of Nrf2 target genes, exhibiting ex vivo efficacy similar to the well-known electrophilic activator, sulforaphane.


  • Organizational Affiliation

    Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1289Homo sapiensMutation(s): 0 
Gene Names: KEAP1INRF2KIAA0132KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
GTEx:  ENSG00000079999 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
41P
Query on 41P

Download Ideal Coordinates CCD File 
B [auth A]2,2'-(naphthalene-1,4-diylbis(((4-methoxyphenyl)sulfonyl)azanediyl))diacetamide
C28 H28 N4 O8 S2
ZUIXHSIMKQZYPV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
41P BindingDB:  4XMB Ki: 53 (nM) from 1 assay(s)
Kd: min: 44, max: 190 (nM) from 2 assay(s)
IC50: 44 (nM) from 1 assay(s)
EC50: 1.20e+4 (nM) from 1 assay(s)
Binding MOAD:  4XMB Kd: 44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.47α = 90
b = 51.521β = 101.27
c = 67.238γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Walter Cancer Foundation - Purdue UniversityUnited StatesP30 CA023168

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description