Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS2

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Structure-guided Development of Specific Pyruvate Dehydrogenase Kinase Inhibitors Targeting the ATP-binding Pocket.

Tso, S.C.Qi, X.Gui, W.J.Wu, C.Y.Chuang, J.L.Wernstedt-Asterholm, I.Morlock, L.K.Owens, K.R.Scherer, P.E.Williams, N.S.Tambar, U.K.Wynn, R.M.Chuang, D.T.

(2014) J Biol Chem 289: 4432-4443

  • DOI: https://doi.org/10.1074/jbc.M113.533885
  • Primary Citation of Related Structures:  
    4MP2, 4MP7, 4MPC, 4MPE, 4MPN

  • PubMed Abstract: 

    Pyruvate dehydrogenase kinase isoforms (PDKs 1-4) negatively regulate activity of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation. PDK isoforms are up-regulated in obesity, diabetes, heart failure, and cancer and are potential therapeutic targets for these important human diseases. Here, we employed a structure-guided design to convert a known Hsp90 inhibitor to a series of highly specific PDK inhibitors, based on structural conservation in the ATP-binding pocket. The key step involved the substitution of a carbonyl group in the parent compound with a sulfonyl in the PDK inhibitors. The final compound of this series, 2-[(2,4-dihydroxyphenyl)sulfonyl]isoindoline-4,6-diol, designated PS10, inhibits all four PDK isoforms with IC50 = 0.8 μM for PDK2. The administration of PS10 (70 mg/kg) to diet-induced obese mice significantly augments pyruvate dehydrogenase complex activity with reduced phosphorylation in different tissues. Prolonged PS10 treatments result in improved glucose tolerance and notably lessened hepatic steatosis in the mouse model. The results support the pharmacological approach of targeting PDK to control both glucose and fat levels in obesity and type 2 diabetes.

  • Organizational Affiliation

    From the Departments of Biochemistry and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial400Homo sapiensMutation(s): 0 
Gene Names: PDK2PDHK2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15119 (Homo sapiens)
Explore Q15119 
Go to UniProtKB:  Q15119
PHAROS:  Q15119
GTEx:  ENSG00000005882 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15119
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PV2

Download Ideal Coordinates CCD File 
C [auth A]4-(isoindolin-2-ylsulfonyl)benzene-1,3-diol
C14 H13 N O4 S
Query on TLA

Download Ideal Coordinates CCD File 
C4 H6 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
PV2 Binding MOAD:  4MPC Kd: 711 (nM) from 1 assay(s)
BindingDB:  4MPC Kd: 711 (nM) from 1 assay(s)
IC50: 2110 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.628α = 90
b = 110.628β = 90
c = 228.566γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations