8G3E image
Entry Detail
PDB ID:
8G3E
Title:
Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-02-07
Release Date:
2023-06-28
Method Details:
Experimental Method:
Resolution:
1.33 Å
R-Value Free:
0.17
R-Value Work:
0.13
R-Value Observed:
0.14
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:WD repeat-containing protein 5
Chain IDs:A, B
Chain Length:316
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Discovery and Structure-Based Design of Inhibitors of the WD Repeat-Containing Protein 5 (WDR5)-MYC Interaction.
J.Med.Chem. 66 8310 8323 (2023)
PMID: 37307526 DOI: 10.1021/acs.jmedchem.3c00787

Abstact

WDR5 is a critical chromatin cofactor of MYC. WDR5 interacts with MYC through the WBM pocket and is hypothesized to anchor MYC to chromatin through its WIN site. Blocking the interaction of WDR5 and MYC impairs the recruitment of MYC to its target genes and disrupts the oncogenic function of MYC in cancer development, thus providing a promising strategy for the treatment of MYC-dysregulated cancers. Here, we describe the discovery of novel WDR5 WBM pocket antagonists containing a 1-phenyl dihydropyridazinone 3-carboxamide core that was identified from high-throughput screening and subsequent structure-based design. The leading compounds showed sub-micromolar inhibition in the biochemical assay. Among them, compound 12 can disrupt WDR5-MYC interaction in cells and reduce MYC target gene expression. Our work provides useful probes to study WDR5-MYC interaction and its function in cancers, which can also be used as the starting point for further optimization toward drug-like small molecules.

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Primary Citation of related structures