6BG5 image
Deposition Date 2017-10-27
Release Date 2018-09-26
Last Version Date 2023-10-04
Entry Detail
PDB ID:
6BG5
Title:
Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.10 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Endolysin, DCN1-like protein 1 chimera
Gene (Uniprot):E, DCUN1D1
Chain IDs:A
Chain Length:384
Number of Molecules:1
Biological Source:Enterobacteria phage T4, Homo sapiens
Ligand Molecules
Primary Citation
Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation.
J. Med. Chem. 61 2680 2693 (2018)
PMID: 29547696 DOI: 10.1021/acs.jmedchem.7b01277

Abstact

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.

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