6P5W | pdb_00006p5w

Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation.

Kim, H.S.Hammill, J.T.Scott, D.C.Chen, Y.Min, J.Rector, J.Singh, B.Schulman, B.A.Guy, R.K.

(2019) J Med Chem 62: 8429-8442

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00410
  • Primary Citation of Related Structures:  
    6P5V, 6P5W

  • PubMed Abstract: 

    Chemical control of cullin neddylation is attracting increased attention based largely on the successes of the NEDD8-activating enzyme (E1) inhibitor pevonedistat. Recently reported chemical probes enable selective and time-dependent inhibition of downstream members of the neddylation trienzymatic cascade including the co-E3, DCN1. In this work, we report the optimization of a novel class of small molecule inhibitors of the DCN1-UBE2M interaction. Rational X-ray co-structure enabled optimization afforded a 25-fold improvement in potency relative to the initial screening hit. The potency gains are largely attributed to additional hydrophobic interactions mimicking the N-terminal acetyl group that drives binding of UBE2M to DCN1. The compounds inhibit the protein-protein interaction, block NEDD8 transfer in biochemical assays, engage DCN1 in cells, and selectively reduce the steady-state neddylation of Cul1 and Cul3 in two squamous carcinoma cell lines harboring DCN1 amplification.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences , University of Kentucky , Lexington , Kentucky 40508 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme,DCN1-like protein 1 chimera384Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: eT4Tp126DCUN1D1DCUN1L1RP42SCCRO
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
O0A (Subject of Investigation/LOI)
Query on O0A

Download Ideal Coordinates CCD File 
B [auth A]3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]benzamide
C28 H26 N4 O2
WMAFBTHYXHDENE-DQEYMECFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O0A BindingDB:  6P5W IC50: 3709 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.71α = 90
b = 95.567β = 106.03
c = 58.989γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted O0AClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description