6B5Q

DCN1 bound to 38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-Affinity Peptidomimetic Inhibitors of the DCN1-UBC12 Protein-Protein Interaction.

Zhou, H.Zhou, W.Zhou, B.Liu, L.Chern, T.R.Chinnaswamy, K.Lu, J.Bernard, D.Yang, C.Y.Li, S.Wang, M.Stuckey, J.Sun, Y.Wang, S.

(2018) J Med Chem 61: 1934-1950

  • DOI: 10.1021/acs.jmedchem.7b01455
  • Primary Citation of Related Structures:  
    6B5Q

  • PubMed Abstract: 
  • The Cullin-RING ligases (CRLs) regulate the turnover of approximately 20% of the proteins in mammalian cells and are emerging therapeutic targets in human diseases. The activation of CRLs requires the neddylation of their cullin subunit, which is controlled by an activation complex consisting of Cullin-RBX1-UBC12-NEDD8-DCN1 ...

    The Cullin-RING ligases (CRLs) regulate the turnover of approximately 20% of the proteins in mammalian cells and are emerging therapeutic targets in human diseases. The activation of CRLs requires the neddylation of their cullin subunit, which is controlled by an activation complex consisting of Cullin-RBX1-UBC12-NEDD8-DCN1. Herein, we describe the design, synthesis, and evaluation of peptidomimetics targeting the DCN1-UBC12 protein-protein interaction. Starting from a 12-residue UBC12 peptide, we have successfully obtained a series of peptidomimetic compounds that bind to DCN1 protein with K D values of <10 nM. Determination of a cocrystal structure of a potent peptidomimetic inhibitor complexed with DCN1 provides the structural basis for their high-affinity interaction. Cellular investigation of one potent DCN1 inhibitor, compound 36 (DI-404), reveals that it effectively and selectively inhibits the neddylation of cullin 3 over other cullin members. Further optimization of DI-404 may yield a new class of therapeutics for the treatment of human diseases in which cullin 3 CRL plays a key role.


    Organizational Affiliation

    Institute of Translational Medicine , Zhejiang University School of Medicine , Hangzhou , Zhejiang 310029 , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DCN1-like protein 1A, B225Homo sapiensMutation(s): 0 
Gene Names: DCUN1D1DCUN1L1RP42SCCRODCN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GG9 (Homo sapiens)
Explore Q96GG9 
Go to UniProtKB:  Q96GG9
PHAROS:  Q96GG9
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidomimetic Inhibitors DI-591C [auth D], D [auth E]5synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CZS
Query on CZS
C [auth D], D [auth E]PEPTIDE LINKINGC10 H9 Cl N2 O2 SALA
MLY
Query on MLY
C [auth D], D [auth E]L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002285
Query on PRD_002285
C [auth D], D [auth E]Peptidomimetic Inhibitors, (PPI)(CZS)(2KY)(MLY)(1XY) Peptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.087α = 90
b = 90.841β = 90
c = 105.01γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-09-29 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Stuckey, J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references