› 4ia9

X-ray diffraction
1.66Å resolution

Crystal structure of human WD REPEAT DOMAIN 5 in complex with 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide

Released:
DOI: 10.2210/pdb4ia9/pdb
PDB entry 4ia9 coloured by chain, front view.
PDB entry 4ia9 coloured by chain, side view.
PDB entry 4ia9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction.
Bolshan Y, Getlik M, Kuznetsova E, Wasney GA, Hajian T, Poda G, Nguyen KT, Wu H, Dombrovski L, Dong A, Senisterra G, Schapira M, Arrowsmith CH, Brown PJ, Al-Awar R, Vedadi M, Smil D
ACS Med Chem Lett 4 353-7 (2013)
PMID: 24900672

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

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 Chain: A
Molecule details ›
Chain: A
Length: 312 amino acids
Theoretical weight: 34.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61964 (Residues: 24-334; Coverage: 93%)
Gene names: BIG3, WDR5
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand IA9 1 x IA9
Ligand EDO 2 x EDO
Ligand UNX 24 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 80.8Å b: 86.029Å c: 40.917Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

WD40 repeat domain proteins: a novel target class?
Schapira et al. (2017)
10 more

2 mentions without citation

Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia.
Grebien et al. (2015)
1 more