6XOO image
Entry Detail
PDB ID:
6XOO
Title:
DCN1 bound to DI-1859
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2020-07-07
Release Date:
2021-06-02
Method Details:
Experimental Method:
Resolution:
2.06 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Lysozyme, DCN1-like protein 1 chimera
Mutations:C54T,C97A,D127A,A146T,R154A
Chain IDs:A
Chain Length:386
Number of Molecules:1
Biological Source:Enterobacteria phage T4, Homo sapiens
Ligand Molecules
Primary Citation
Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity.
Nat Commun 12 2621 2621 (2021)
PMID: 33976147 DOI: 10.1038/s41467-021-22924-4

Abstact

Cullin-RING E3 ligases (CRLs) regulate the turnover of approximately 20% of mammalian cellular proteins. Neddylation of individual cullin proteins is essential for the activation of each CRL. We report herein the discovery of DI-1548 and DI-1859 as two potent, selective and covalent DCN1 inhibitors. These inhibitors selectively inhibit neddylation of cullin 3 in cells at low nanomolar concentrations and are 2-3 orders of magnitude more potent than our previously reported reversible DCN1 inhibitor. Mass spectrometric analysis and co-crystal structures reveal that these compounds employ a unique mechanism of covalent bond formation with DCN1. DI-1859 induces a robust increase of NRF2 protein, a CRL3 substrate, in mouse liver and effectively protects mice from acetaminophen-induced liver damage. Taken together, this study demonstrates the therapeutic potential of selective inhibition of cullin neddylation.

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Primary Citation of related structures