5UFI

DCN1 bound to DI-591


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation.

Zhou, H.Lu, J.Liu, L.Bernard, D.Yang, C.Y.Fernandez-Salas, E.Chinnaswamy, K.Layton, S.Stuckey, J.Yu, Q.Zhou, W.Pan, Z.Sun, Y.Wang, S.

(2017) Nat Commun 8: 1150-1150

  • DOI: 10.1038/s41467-017-01243-7

  • PubMed Abstract: 
  • The Cullin-RING E3 ubiquitin ligases (CRLs) regulate homeostasis of ~20% of cellular proteins and their activation require neddylation of their cullin subunit. Cullin neddylation is modulated by a scaffolding DCN protein through interactions with bot ...

    The Cullin-RING E3 ubiquitin ligases (CRLs) regulate homeostasis of ~20% of cellular proteins and their activation require neddylation of their cullin subunit. Cullin neddylation is modulated by a scaffolding DCN protein through interactions with both the cullin protein and an E2 enzyme such as UBC12. Here we report the development of DI-591 as a high-affinity, cell-permeable small-molecule inhibitor of the DCN1-UBC12 interaction. DI-591 binds to purified recombinant human DCN1 and DCN2 proteins with K i values of 10-12 nM, and disrupts the DCN1-UBC12 interaction in cells. Treatment with DI-591 selectively converts cellular cullin 3 into an un-neddylated inactive form with no or minimum effect on other cullin members. Our data firmly establish a previously unrecognized specific role of the DCN1-UBC12 interaction for cellular neddylation of cullin 3. DI-591 is an excellent probe compound to investigate the role of the cullin 3 CRL ligase in biological processes and human diseases.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. shaomeng@umich.edu.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA. shaomeng@umich.edu.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Oncological Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, New York, 10029, USA.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.,Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, 48109, USA. shaomeng@umich.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DCN1-like protein 1
A, B, C, D
225Homo sapiensMutation(s): 0 
Gene Names: DCUN1D1 (DCN1, DCUN1L1, RP42, SCCRO)
Find proteins for Q96GG9 (Homo sapiens)
Go to Gene View: DCUN1D1
Go to UniProtKB:  Q96GG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8B1
Query on 8B1

Download SDF File 
Download CCD File 
A, B, C, D
N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide
C31 H47 N5 O4 S
CNJKDQGPBAWNRY-IZZNHLLZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.142α = 90.00
b = 101.647β = 90.00
c = 173.521γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
HKLdata scaling
BUSTERrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
HKLdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-04 
  • Released Date: 2017-11-01 
  • Deposition Author(s): Stuckey, J.

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references