6FFM | pdb_00006ffm

Crystal Structure of Human KEAP1 BTB Domain in Complex with isoxazoline-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.293 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.253 (Depositor) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Effects of 3-Bromo-4,5-dihydroisoxazole Derivatives on Nrf2 Activation and Heme Oxygenase-1 Expression.

Pinto, A.El Ali, Z.Moniot, S.Tamborini, L.Steegborn, C.Foresti, R.De Micheli, C.

(2018) ChemistryOpen 7: 858-864

  • DOI: https://doi.org/10.1002/open.201800185
  • Primary Citation Related Structures: 
    6FFM

  • PubMed Abstract: 

    Natural and synthetic electrophilic compounds have been shown to activate the antioxidant protective Nrf2 (nuclear factor erythroid 2-related factor 2)/heme oxygenase-1 (HO-1) axis in cells and tissues. Here, we tested the ability of different isoxazoline-based electrophiles to up-regulate Nrf2/HO-1. The potency of activation is dependent on the leaving group at the 3-position of the isoxazoline nucleus, and an additional ring on the molecule limits the Nrf2/HO-1 activating properties. Among the synthetized compounds, we identified 3-bromo-5-phenyl-4,5-dihydroisoxazole 1 as the derivative with best activating properties in THP-1 human monocytic cells. We have confirmed that the target of our compounds is the Cys151 of the BTB domain of Keap1 by using mass spectrometry analyses and X-ray crystallography. Our findings demonstrate that these compounds affect the Nrf2/HO-1 axis and highlight a positive activity that can be of relevance from a therapeutic perspective in inflammation and infection.


  • Organizational Affiliation
    • Department of Food, Environmental and Nutritional Sciences (DeFENS) University of Milan viaCeloria 2 20133 Milan Italy.

Macromolecule Content 

  • Total Structure Weight: 15.41 kDa 
  • Atom Count: 1,085 
  • Modeled Residue Count: 131 
  • Deposited Residue Count: 136 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1136Homo sapiensMutation(s): 1 
Gene Names: KEAP1INRF2KIAA0132KLHL19
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D8N
(Subject of Investigation/LOI)

Query on D8N



Download:Ideal Coordinates CCD File
B [auth A]~{N}-[4-[(5~{R})-4,5-dihydro-1,2-oxazol-5-yl]phenyl]ethanamide
C11 H12 N2 O2
NXJZQAOQHFVDJW-LLVKDONJSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.293 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.253 (Depositor) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.491α = 90
b = 42.491β = 90
c = 265.213γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary