9ETY | pdb_00009ety

KEAP1 in complex with compound 25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.255 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Covalent Inhibitors of KEAP1 with Exquisite Selectivity.

Fejes, I.Markacz, P.Tatai, J.Rudas, M.Dunkel, P.Gyuris, M.Nyerges, M.Provost, N.Duvivier, V.Delerive, P.Martiny, V.Bristiel, A.Vidal, B.Richardson, W.Rothweiler, E.M.Tranberg-Jensen, J.Manning, C.E.Sweeney, M.N.Chalk, R.Huber, K.V.M.Bullock, A.N.Herner, A.Seedorf, K.Vinson, C.Weber, C.Kotschy, A.

(2024) J Med Chem 67: 21208-21222

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02019
  • Primary Citation of Related Structures:  
    9ETW, 9ETX, 9ETY

  • PubMed Abstract: 

    The NRF2-KEAP1 interaction is central for cytoprotection against stresses, giving it high clinical significance. Covalent modification of KEAP1 is an efficient approach, but the covalent inhibitors used in the clinic carry undesired side effects originating in their moderate selectivity. Starting with a phenotypic screen, we identified a new covalent inhibitor chemotype that was optimized to deliver a series of potent and highly selective KEAP1 binders. While the developed compounds showed both cellular and in vivo activity, upregulating antioxidant response element-dependent target genes, they showed no genotoxicity in vitro. The lead compound exhibited broad selectivity in activity-based protein profiling and showed no significant interaction with a panel of commonly studied receptors nor with a broad panel of kinases. The nature of its interaction with KEAP1 and the origin of its selectivity were revealed by X-ray crystallography.


  • Organizational Affiliation
    • Servier Research Institute of Medicinal Chemistry, Zahony u. 7., H-1031 Budapest, Hungary.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1
A, B
189Homo sapiensMutation(s): 0 
Gene Names: KEAP1INRF2KIAA0132KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
GTEx:  ENSG00000079999 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H7T (Subject of Investigation/LOI)
Query on A1H7T

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2-[[5-[(2~{R})-2,4-dimethyl-3-oxidanylidene-piperazin-1-yl]-2,3-dihydro-1,3-thiazol-4-yl]sulfonyl]benzenecarbonitrile
C16 H18 N4 O3 S2
HLDSSZGQRKEKAO-LLVKDONJSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.255 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.991α = 90
b = 60.839β = 90
c = 165.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland875510

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references