4MPC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrialA400Homo sapiensMutation(s): 0 
Gene Names: PDK2PDHK2
EC: 2.7.11.2
Find proteins for Q15119 (Homo sapiens)
Explore Q15119 
Go to UniProtKB:  Q15119
NIH Common Fund Data Resources
PHAROS:  Q15119
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PV2
Query on PV2

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

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PV2Kd:  711   nM  BindingDB
PV2Kd:  711   nM  Binding MOAD
PV2IC50:  2110   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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