4IQK

Crystal structure of cpd 16 bound to Keap1 Kelch domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 Nr ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1 A299Homo sapiensMutation(s): 2 
Gene Names: INRF2KEAP1KIAA0132KLHL19
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
NIH Common Fund Data Resources
PHAROS:  Q14145
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IQK
Query on IQK

Download Ideal Coordinates CCD File 
A
N,N'-naphthalene-1,4-diylbis(4-methoxybenzenesulfonamide)
C24 H22 N2 O6 S2
XLLVCULLOGKYOO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IQKIC50:  2700   nM  BindingDB
IQKEC50:  1460   nM  BindingDB
IQKIC50:  1600   nM  BindingDB
IQKIC50:  1700   nM  BindingDB
IQKKd:  1690   nM  BindingDB
IQKKd:  1700   nM  BindingDB
IQKIC50:  2700   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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