6ZF4

Keap1 kelch domain bound to a small molecule inhibitor of the Keap1-Nrf2 protein-protein interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds.

Pallesen, J.S.Narayanan, D.Tran, K.T.Solbak, S.M.O.Marseglia, G.Sorensen, L.M.E.Hoj, L.J.Munafo, F.Carmona, R.M.C.Garcia, A.D.Desu, H.L.Brambilla, R.Johansen, T.N.Popowicz, G.M.Sattler, M.Gajhede, M.Bach, A.

(2021) J Med Chem 64: 4623-4661

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02094
  • Primary Citation of Related Structures:  
    6ZEW, 6ZEX, 6ZEY, 6ZEZ, 6ZF0, 6ZF1, 6ZF2, 6ZF3, 6ZF4, 6ZF5, 6ZF6, 6ZF7, 6ZF8

  • PubMed Abstract: 

    Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound 8 with a 220-380-fold stronger affinity ( K i = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with K i values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.


  • Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1304Mus 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QHW (Subject of Investigation/LOI)
Query on QHW

Download Ideal Coordinates CCD File 
T [auth A]5-cyclopropyl-1-[3-[2-hydroxy-2-oxoethyl-(2,3,5,6-tetramethylphenyl)sulfonyl-amino]phenyl]pyrazole-4-carboxylic acid
C25 H27 N3 O6 S
SAPJYRTVXRKYMQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.188α = 90
b = 103.188β = 90
c = 54.936γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR190-2014-3710

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description