› 8zm2

X-ray diffraction
2.34Å resolution

Structure of human pyruvate dehydrogenase kinase 2 complexed with compound 16

Released:
DOI: 10.2210/pdb8zm2/pdb
PDB entry 8zm2 coloured by chain, front view.
PDB entry 8zm2 coloured by chain, side view.
PDB entry 8zm2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design and synthesis of novel fluorene derivatives as inhibitors of pyruvate dehydrogenase kinase.
Inoue M, Nagamori H, Morita T, Kobayashi S, Suzawa K, Kitao Y, Saito T, Kawahara I, Orita T, Akai S, Adachi T, Motomura T
Bioorg Med Chem Lett 129839 (2024)
PMID: 38844173

Function and Biology Details

Reaction catalysed: 
ATP + [pyruvate dehydrogenase (acetyl-transferring)] = ADP + [pyruvate dehydrogenase (acetyl-transferring)] phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172222 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 44.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15119 (Residues: 16-407; Coverage: 96%)
Gene names: PDHK2, PDK2
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand A1L17 1 x A1L17
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P64
Unit cell:
a: 108.886Å b: 108.886Å c: 84.421Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.199 0.22
Expression system: Escherichia coli BL21(DE3)

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