› 4i3l

X-ray diffraction
3.29Å resolution

Crystal structure of a metabolic reductase with 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one

Released:
DOI: 10.2210/pdb4i3l/pdb
PDB entry 4i3l coloured by chain, front view.
PDB entry 4i3l coloured by chain, side view.
PDB entry 4i3l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase.
Zheng B, Yao Y, Liu Z, Deng L, Anglin JL, Jiang H, Prasad BV, Song Y
ACS Med Chem Lett 4 542-546 (2013)
PMID: 23795241

Function and Biology Details

Reaction catalysed: 
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131150 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP] cytoplasmic Chains: A, B
Molecule details ›
Chains: A, B
Length: 414 amino acids
Theoretical weight: 46.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75874 (Residues: 1-414; Coverage: 100%)
Gene names: IDH1, PICD
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NDP 2 x NDP
2 bound ligands:
Ligand SO4 2 x SO4
Ligand 1BZ 1 x 1BZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P43212
Unit cell:
a: 80.853Å b: 80.853Å c: 304.836Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.293
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches.
Wong et al. (2017)
9 more

4 mentions without citation

Recent advances of IDH1 mutant inhibitor in cancer therapy.
Tian et al. (2022)
3 more