8Q1Q

mouse Keap1 in complex with stapled peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction.

Iegre, J.Krajcovicova, S.Gunnarsson, A.Wissler, L.Kack, H.Luchniak, A.Tangefjord, S.Narjes, F.Spring, D.R.

(2023) Chem Sci 14: 10800-10805

  • DOI: https://doi.org/10.1039/d3sc04083f
  • Primary Citation of Related Structures:  
    8Q1Q, 8Q1R

  • PubMed Abstract: 

    The disruption of the protein-protein interaction (PPI) between Nrf2 and Keap1 is an attractive strategy to counteract the oxidative stress that characterises a variety of severe diseases. Peptides represent a complementary approach to small molecules for the inhibition of this therapeutically important PPI. However, due to their polar nature and the negative net charge required for binding to Keap1, the peptides reported to date exhibit either mid-micromolar activity or are inactive in cells. Herein, we present a two-component peptide stapling strategy to rapidly access a variety of constrained and functionalised peptides that target the Nrf2/Keap1 PPI. The most promising peptide, P8-H containing a fatty acid tag, binds to Keap1 with nanomolar affinity and is effective at inducing transcription of ARE genes in a human lung epithelial cell line at sub-micromolar concentration. Furthermore, crystallography of the peptide in complex with Keap1 yielded a high resolution X-ray structure, adding to the toolbox of structures available to develop cell-permeable peptidomimetic inhibitors.


  • Organizational Affiliation

    Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK spring@ch.cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1303Mus musculusMutation(s): 0 
Gene Names: Keap1Inrf2Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus)
Explore Q9Z2X8 
Go to UniProtKB:  Q9Z2X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z2X8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Stapled peptideB [auth D]14synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IZS (Subject of Investigation/LOI)
Query on IZS

Download Ideal Coordinates CCD File 
D
ethyl 2-[(4,6-diethylpyrimidin-2-yl)-methyl-amino]ethanoate
C13 H21 N3 O2
MVDCBXIEQXAEDI-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.44α = 90
b = 103.44β = 90
c = 55.675γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-07152
UK Research and Innovation (UKRI)United Kingdom--
Other governmentSweden2019-02496
Other governmentCzech Republic22-07138O
Other privateUnited Kingdom22.39

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary