5J6A | pdb_00005j6a

Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS46

• PDB DOI: https://doi.org/10.2210/pdb5J6A/pdb

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


• Deposited: 2016-04-04 Released: 2017-01-25 
• Deposition Author(s): Gui, W.J., Tso, S.C., Chuang, J.L., Wu, C.Y., Qi, X., Wynn, R.M., Chuang, D.T.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Development of Dihydroxyphenyl Sulfonylisoindoline Derivatives as Liver-Targeting Pyruvate Dehydrogenase Kinase Inhibitors.

Tso, S.C., Lou, M., Wu, C.Y., Gui, W.J., Chuang, J.L., Morlock, L.K., Williams, N.S., Wynn, R.M., Qi, X., Chuang, D.T.

(2017) J Med Chem 60: 1142-1150

• PubMed: 28085286 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01540
• Primary Citation Related Structures: 
  5J6A, 5J71


• PubMed Abstract: 
  

  Pyruvate dehydrogenase kinases 1-4 (PDK1-4) negatively control activity of the pyruvate dehydrogenase complex (PDC) and are up-regulated in obesity, diabetes, heart failure, and cancer. We reported earlier two novel pan-PDK inhibitors PS8 [4-((5-hydroxyisoindolin-2-yl)sulfonyl)benzene-1,3-diol] (1) and PS10 [2-((2,4-dihydroxyphenyl)sulfonyl)isoindoline-4,6-diol] (2) that targeted the ATP-binding pocket in PDKs. Here, we developed a new generation of PDK inhibitors by extending the dihydroxyphenyl sulfonylisoindoline scaffold in 1 and 2 to the entrance region of the ATP-binding pocket in PDK2. The lead inhibitor (S)-3-amino-4-(4-((2-((2,4-dihydroxyphenyl)sulfonyl)isoindolin-5-yl)amino)piperidin-1-yl)-4-oxobutanamide (17) shows a ∼8-fold lower IC ₅₀ (58 nM) than 2 (456 nM). In the crystal structure, the asparagine moiety in 17 provides additional interactions with Glu-262 from PDK2. Treatment of diet-induced obese mice with 17 resulted in significant liver-specific augmentation of PDC activity, accompanied by improved glucose tolerance and drastically reduced hepatic steatosis. These findings support 17 as a potential glucose-lowering therapeutic targeting liver for obesity and type 2 diabetes.

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Organizational Affiliation: 
• Chemistry Center, National Institute of Biological Science , Beijing 102206, China.
Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences , Beijing 100730, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.73 kDa 
• Atom Count: 2,902 
• Modeled Residue Count: 337 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P46	B [auth A]	(3S)-3-amino-4-[4-({2-[(2,4-dihydroxyphenyl)sulfonyl]-2H-isoindol-5-yl}amino)piperidin-1-yl]-4-oxobutanamide C23 H27 N5 O6 S HAMJZOUVHDEUSM-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.389	α = 90
b = 109.389	β = 90
c = 84.42	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Gui, W.J., Tso, S.C., Chuang, J.L., Wu, C.Y., Qi, X., Wynn, R.M., Chuang, D.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK-62306
Welch Foundation	United States	I-1286

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-22
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description