7P5E

Pyrazole Carboxylic Acid Inhibitors of KEAP1:NRF2 interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction.

Norton, D.Bonnette, W.G.Callahan, J.F.Carr, M.G.Griffiths-Jones, C.M.Heightman, T.D.Kerns, J.K.Nie, H.Rich, S.J.Richardson, C.Rumsey, W.Sanchez, Y.Verdonk, M.L.Willems, H.M.G.Wixted, W.E.Wolfe 3rd, L.Woolford, A.J.Wu, Z.Davies, T.G.

(2021) J Med Chem 64: 15949-15972

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01351
  • Primary Citation of Related Structures:  
    7P58, 7P5E, 7P5F, 7P5I, 7P5K, 7P5N, 7P5P

  • PubMed Abstract: 

    The NRF2-mediated cytoprotective response is central to cellular homoeostasis, and there is increasing interest in developing small-molecule activators of this pathway as therapeutics for diseases involving chronic oxidative stress. The protein KEAP1, which regulates NRF2, is a key point for pharmacological intervention, and we recently described the use of fragment-based drug discovery to develop a tool compound that directly disrupts the protein-protein interaction between NRF2 and KEAP1. We now present the identification of a second, chemically distinct series of KEAP1 inhibitors, which provided an alternative chemotype for lead optimization. Pharmacophoric information from our original fragment screen was used to identify new hit matter through database searching and to evolve this into a new lead with high target affinity and cell-based activity. We highlight how knowledge obtained from fragment-based approaches can be used to focus additional screening campaigns in order to de-risk projects through the rapid identification of novel chemical series.


  • Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1321Mus 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5VX (Subject of Investigation/LOI)
Query on 5VX

Download Ideal Coordinates CCD File 
D [auth A]1-[6-[3-(dimethylcarbamoyl)phenyl]pyridin-2-yl]-5-(trifluoromethyl)pyrazole-4-carboxylic acid
C19 H15 F3 N4 O3
FRRZRAZHHYLGGZ-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.569α = 90
b = 103.569β = 90
c = 56.069γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Data collection, Database references