5V86

Structure of DCN1 bound to NAcM-OPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.

Scott, D.C.Hammill, J.T.Min, J.Rhee, D.Y.Connelly, M.Sviderskiy, V.O.Bhasin, D.Chen, Y.Ong, S.S.Chai, S.C.Goktug, A.N.Huang, G.Monda, J.K.Low, J.Kim, H.S.Paulo, J.A.Cannon, J.R.Shelat, A.A.Chen, T.Kelsall, I.R.Alpi, A.F.Pagala, V.Wang, X.Peng, J.Singh, B.Harper, J.W.Schulman, B.A.Guy, R.K.

(2017) Nat Chem Biol 13: 850-857

  • DOI: https://doi.org/10.1038/nchembio.2386
  • Primary Citation of Related Structures:  
    5V83, 5V86, 5V88, 5V89

  • PubMed Abstract: 

    N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions; hence, this modification may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation-dependent interaction between an E2 conjugating enzyme (UBE2M or UBC12) and DCN1 (DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl-amide-binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress anchorage-independent growth of a cell line with DCN1 amplification. Overall, our data demonstrate that N-terminal acetyl-dependent protein interactions are druggable targets and provide insights into targeting multiprotein E2-E3 ligases.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme,DCN1-like protein 1384Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: eT4Tp126DCUN1D1DCUN1L1RP42SCCRO
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
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 GroupsP00720Q96GG9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8ZA
Query on 8ZA

Download Ideal Coordinates CCD File 
B [auth A]N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea
C23 H29 Cl2 N3 O
VPHJABWIKCBGMC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8ZA BindingDB:  5V86 IC50: min: 45, max: 170 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.045α = 90
b = 96.849β = 105.83
c = 59.302γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR37GM069530

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references, Refinement description
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references