6XOL | pdb_00006xol

DCN1 bound to DI-1548


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.264 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6XOL

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 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.

Macromolecule Content 

  • Total Structure Weight: 44.86 kDa 
  • Atom Count: 2,990 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
H8S
(Subject of Investigation/LOI)

Query on H8S



Download:Ideal Coordinates CCD File
B [auth A]N-{(1S)-1-cyclohexyl-2-[(2-methylpropanoyl)amino]ethyl}-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide
C28 H42 N4 O3 S
NIZDKPYPZUWWHC-XZOQPEGZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.264 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.91α = 90
b = 86.42β = 90
c = 126.02γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

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: 2024-10-16
    Changes: Structure summary