› 8g3e

X-ray diffraction
1.33Å resolution

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)

Released:
DOI: 10.2210/pdb8g3e/pdb
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PDB entry 8g3e coloured by chain, front view.
PDB entry 8g3e coloured by chain, side view.
PDB entry 8g3e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Structure-Based Design of Inhibitors of the WD Repeat-Containing Protein 5 (WDR5)-MYC Interaction.
Ding J, Liu L, Chiang YL, Zhao M, Liu H, Yang F, Shen L, Lin Y, Deng H, Gao J, Sage DR, West L, Llamas LA, Hao X, Kawatkar S, Li E, Jain RK, Tallarico JA, Canham SM, Wang H
J Med Chem (2023)
PMID: 37307526

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158474 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
WD repeat-containing protein 5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 316 amino acids
Theoretical weight: 34.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61964 (Residues: 22-334; Coverage: 94%)
Gene names: BIG3, WDR5
Sequence domains: WD domain, G-beta repeat

Ligands and Environments

1 bound ligand:
Ligand YJR 2 x YJR
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P1
Unit cell:
a: 46.662Å b: 62.276Å c: 64.381Å
α: 114.09° β: 91.08° γ: 110.17°
R-values:
R R work R free
0.141 0.139 0.17
Expression system: Escherichia coli

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Citations

1 review citation

WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think.
Weissmiller et al. (2024)

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