5V83

Structure of DCN1 bound to NAcM-HIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1038/nchembio.2386
  • Structures With Same Primary Citation

  • 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. S ...

    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 Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme,DCN1-like protein 1 chimera
A
384Escherichia virus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: eT4Tp126
EC: 3.2.1.17
Find proteins for D9IEF7 (Enterobacteria phage T4)
Go to UniProtKB:  D9IEF7
Find proteins for Q96GG9 (Homo sapiens)
Go to UniProtKB:  Q96GG9
NIH Common Fund Data Resources
PHAROS  Q96GG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Z7
Query on 8Z7

Download CCD File 
A
N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
C20 H22 F3 N3 O
MXZRHPHRSQJCML-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8Z7IC50:  7000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.966α = 90
b = 97.28β = 104.39
c = 58.148γ = 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



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 

  • 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