6XOP

DCN1 bound to inhibitor 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity.

Zhou, H.Lu, J.Chinnaswamy, K.Stuckey, J.A.Liu, L.McEachern, D.Yang, C.Y.Bernard, D.Shen, H.Rui, L.Sun, Y.Wang, S.

(2021) Nat Commun 12: 2621-2621

  • DOI: https://doi.org/10.1038/s41467-021-22924-4
  • Primary Citation of Related Structures:  
    6XOL, 6XOM, 6XON, 6XOO, 6XOP, 6XOQ

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme, DCN1-like protein 1 chimera386Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: eT4Tp126DCUN1D1DCN1DCUN1L1RP42SCCRO
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for D9IEF7 (Enterobacteria phage T4)
Explore D9IEF7 
Go to UniProtKB:  D9IEF7
Find proteins for Q96GG9 (Homo sapiens)
Explore Q96GG9 
Go to UniProtKB:  Q96GG9
PHAROS:  Q96GG9
GTEx:  ENSG00000043093 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ96GG9D9IEF7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H9P (Subject of Investigation/LOI)
Query on H9P

Download Ideal Coordinates CCD File 
B [auth A]N-[(1S)-1-cyclohexyl-2-{[(2S)-3-(1H-imidazol-1-yl)-2-methylpropanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide
C31 H44 N6 O3 S
SJDWTXOIFWWWBR-OUIFVKKZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.868α = 90
b = 86.702β = 90
c = 126.234γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary