6BG5

Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

Starting Models: experimental
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Literature

Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation.

Hammill, J.T.Scott, D.C.Min, J.Connelly, M.C.Holbrook, G.Zhu, F.Matheny, A.Yang, L.Singh, B.Schulman, B.A.Guy, R.K.

(2018) J Med Chem 61: 2680-2693

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01277
  • Primary Citation of Related Structures:  
    6BG3, 6BG5

  • PubMed Abstract: 

    We previously discovered and validated a class of piperidinyl ureas that regulate defective in cullin neddylation 1 (DCN1)-dependent neddylation of cullins. Here, we report preliminary structure-activity relationship studies aimed at advancing our high-throughput screen hit into a tractable tool compound for dissecting the effects of acute DCN1-UBE2M inhibition on the NEDD8/cullin pathway. Structure-enabled optimization led to a 100-fold increase in biochemical potency and modestly increased solubility and permeability as compared to our initial hit. The optimized compounds inhibit the DCN1-UBE2M protein-protein interaction in our TR-FRET binding assay and inhibit cullin neddylation in our pulse-chase NEDD8 transfer assay. The optimized compounds bind to DCN1 and selectively reduce steady-state levels of neddylated CUL1 and CUL3 in a squamous cell carcinoma cell line. Ultimately, we anticipate that these studies will identify early lead compounds for clinical development for the treatment of lung squamous cell carcinomas and other cancers.


  • Organizational Affiliation

    Department of Chemical Biology and Theraputics , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin, DCN1-like protein 1 chimera384Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: EDCUN1D1DCUN1L1RP42SCCRO
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
DQD
Query on DQD

Download Ideal Coordinates CCD File 
B [auth A]N-[(2H-1,3-benzodioxol-5-yl)methyl]-N-(1-propylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
C24 H28 F3 N3 O3
PLBHVOJLFQGHAQ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DQD BindingDB:  6BG5 IC50: min: 1100, max: 3200 (nM) from 4 assay(s)
EC50: 490 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.944α = 90
b = 96.763β = 105.61
c = 59.279γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description