› 4mp2

X-ray diffraction
1.75Å resolution

Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA1

Released:
DOI: 10.2210/pdb4mp2/pdb
PDB entry 4mp2 coloured by chain, front view.
PDB entry 4mp2 coloured by chain, side view.
PDB entry 4mp2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-guided development of specific pyruvate dehydrogenase kinase inhibitors targeting the ATP-binding pocket.
Tso SC, Qi X, Gui WJ, Wu CY, Chuang JL, Wernstedt-Asterholm I, Morlock LK, Owens KR, Scherer PE, Williams NS, Tambar UK, Wynn RM, Chuang DT
J Biol Chem 289 4432-43 (2014)
PMID: 24356970

Function and Biology Details

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

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: 400 amino acids
Theoretical weight: 45.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15119 (Residues: 9-407; Coverage: 98%)
Gene names: PDHK2, PDK2
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PV1 1 x PV1
Ligand TLA 1 x TLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I4122
Unit cell:
a: 110.323Å b: 110.323Å c: 229.523Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.219
Expression system: Escherichia coli BL21

Quick links

Citations

14 review citations

Therapeutic Targeting of the Pyruvate Dehydrogenase Complex/Pyruvate Dehydrogenase Kinase (PDC/PDK) Axis in Cancer.
Stacpoole PW. (2017)
13 more

5 mentions without citation

Advanced Bioinformatics Tools in the Pharmacokinetic Profiles of Natural and Synthetic Compounds with Anti-Diabetic Activity.
Udrea et al. (2021)
4 more