2Q8I

Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Distinct Structural Mechanisms for Inhibition of Pyruvate Dehydrogenase Kinase Isoforms by AZD7545, Dichloroacetate, and Radicicol.

Kato, M.Li, J.Chuang, J.L.Chuang, D.T.

(2007) Structure 15: 992-1004

  • DOI: 10.1016/j.str.2007.07.001
  • Primary Citation of Related Structures:  
    2Q8I, 2Q8H, 2Q8G, 2Q8F

  • PubMed Abstract: 
  • Pyruvate dehydrogenase kinase (PDK) isoforms are molecular switches that downregulate the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation in mitochondria. We have determined structures of human PDK1 or PDK3 bound to the inhibitors AZD7 ...

    Pyruvate dehydrogenase kinase (PDK) isoforms are molecular switches that downregulate the pyruvate dehydrogenase complex (PDC) by reversible phosphorylation in mitochondria. We have determined structures of human PDK1 or PDK3 bound to the inhibitors AZD7545, dichloroacetate (DCA), and radicicol. We show that the trifluoromethylpropanamide end of AZD7545 projects into the lipoyl-binding pocket of PDK1. This interaction results in inhibition of PDK1 and PDK3 activities by aborting kinase binding to the PDC scaffold. Paradoxically, AZD7545 at saturating concentrations robustly increases scaffold-free PDK3 activity, similar to the inner lipoyl domain. Good DCA density is present in the helix bundle in the N-terminal domain of PDK1. Bound DCA promotes local conformational changes that are communicated to both nucleotide-binding and lipoyl-binding pockets of PDK1, leading to the inactivation of kinase activity. Finally, radicicol inhibits kinase activity by binding directly to the ATP-binding pocket of PDK3, similar to Hsp90 and Topo VI from the same ATPase/kinase superfamily.


    Organizational Affiliation

    Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 A419Homo sapiensMutation(s): 0 
Gene Names: PDK3PDHK3
EC: 2.7.11.2
Find proteins for Q15120 (Homo sapiens)
Explore Q15120 
Go to UniProtKB:  Q15120
NIH Common Fund Data Resources
PHAROS:  Q15120
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex B128Homo sapiensMutation(s): 0 
Gene Names: DLATDLTA
EC: 2.3.1.12
Find proteins for P10515 (Homo sapiens)
Explore P10515 
Go to UniProtKB:  P10515
NIH Common Fund Data Resources
PHAROS:  P10515
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RDC
Query on RDC

Download Ideal Coordinates CCD File 
A
RADICICOL
C18 H17 Cl O6
WYZWZEOGROVVHK-GTMNPGAYSA-N
 Ligand Interaction
RED
Query on RED

Download Ideal Coordinates CCD File 
B
DIHYDROLIPOIC ACID
C8 H16 O2 S2
IZFHEQBZOYJLPK-SSDOTTSWSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDCIC50 :  400000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.872α = 90
b = 120.872β = 90
c = 239.637γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description