4IN4

Crystal structure of cpd 15 bound to Keap1 Kelch domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 

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:  

  • 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 th ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kelch-like ECH-associated protein 1
A, B, C
299Homo sapiensMutation(s): 0 
Gene Names: KEAP1 (INRF2, KIAA0132, KLHL19)
Find proteins for Q14145 (Homo sapiens)
Go to Gene View: KEAP1
Go to UniProtKB:  Q14145
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
4ID
Query on 4ID

Download SDF File 
Download CCD File 
A, B, C
2-({5-[(2,4-dimethylphenyl)sulfonyl]-6-oxo-1,6-dihydropyrimidin-2-yl}sulfanyl)-N-[2-(trifluoromethyl)phenyl]acetamide
C21 H18 F3 N3 O4 S2
XHKKCXMZBGDTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.604α = 90.00
b = 96.509β = 90.00
c = 142.462γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2013-07-03
    Type: Database references