Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.67 kDa 
• Atom Count: 3259 
• Residue Count: 363 
• Unique protein chains: 1

4MPC

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

• DOI: 10.2210/pdb4MPC/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-12 Released: 2014-01-01 
• Deposition Author(s): Gui, W.J., Tso, S.C., Chuang, J.L., Wu, C.Y., Qi, X., Tambar, U.K., Wynn, R.M., Chuang, D.T.

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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 

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

• PubMed: 24356970 
• 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. 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.

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Organizational Affiliation: 

From the Departments of Biochemistry and.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial	A	400	Homo sapiens	Mutation(s): 0  Gene Names: PDK2, PDHK2 EC: 2.7.11.2
Find proteins for Q15119 (Homo sapiens) Explore Q15119  Go to UniProtKB:  Q15119
NIH Common Fund Data Resources
PHAROS:  Q15119 GTEx:  ENSG00000005882

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PV2	A	4-(isoindolin-2-ylsulfonyl)benzene-1,3-diol C14 H13 N O4 S GBZLIDQSMMVGSH-UHFFFAOYSA-N
TLA	A	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PV2	Kd:  711   nM  BindingDB
PV2	Kd:  711   nM  Binding MOAD
PV2	IC50:  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 = 110.628	α = 90
b = 110.628	β = 90
c = 228.566	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-12 
• Released Date: 2014-01-01 
Deposition Author(s): Gui, W.J., Tso, S.C., Chuang, J.L., Wu, C.Y., Qi, X., Tambar, U.K., Wynn, R.M., Chuang, D.T.

Revision History 

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Database references