7KWA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Improvement of Oral Bioavailability of Pyrazolo-Pyridone Inhibitors of the Interaction of DCN1/2 and UBE2M.

Kim, H.S.Hammill, J.T.Scott, D.C.Chen, Y.Rice, A.L.Pistel, W.Singh, B.Schulman, B.A.Guy, R.K.

(2021) J Med Chem 64: 5850-5862

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00035
  • Primary Citation of Related Structures:  
    7KWA

  • PubMed Abstract: 

    The cullin-RING ubiquitin ligases (CRLs) are ubiquitin E3 enzymes that play a key role in controlling proteasomal degradation and are activated by neddylation. We previously reported inhibitors that target CRL activation by disrupting the interaction of defective in cullin neddylation 1 (DCN1), a CRL neddylation co-E3, and UBE2M, a neddylation E2. Our first-generation inhibitors possessed poor oral bioavailability and fairly rapid clearance that hindered the study of acute inhibition of DCN-controlled CRL activity in vivo. Herein, we report studies to improve the pharmacokinetic performance of the pyrazolo-pyridone inhibitors. The current best inhibitor, 40 , inhibits the interaction of DCN1 and UBE2M, blocks NEDD8 transfer in biochemical assays, thermally stabilizes cellular DCN1, and inhibits anchorage-independent growth in a DCN1 amplified squamous cell carcinoma cell line. Additionally, we demonstrate that a single oral 50 mg/kg dose sustains plasma exposures above the biochemical IC 90 for 24 h in mice.


  • 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
Endolysin,DCN1-like protein 1384Enterobacteria phage RB59Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: eRB59_126DCUN1D1DCN1DCUN1L1RP42SCCRO
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for A0A097J809 (Enterobacteria phage RB59)
Explore A0A097J809 
Go to UniProtKB:  A0A097J809
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 GroupsA0A097J809Q96GG9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YHP (Subject of Investigation/LOI)
Query on YHP

Download Ideal Coordinates CCD File 
B [auth A]N-[(4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-(trifluoromethyl)benzamide
C29 H25 F4 N5 O2
QEHZKPQZGREGTJ-ZCYQVOJMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YHP BindingDB:  7KWA IC50: 110 (nM) from 1 assay(s)
EC50: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.233α = 90
b = 97.057β = 106.11
c = 59.837γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA247365-02

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description