Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose-lowering drug AZD7545

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1407Homo sapiensMutation(s): 0 
Gene Names: PDK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15118 (Homo sapiens)
Explore Q15118 
Go to UniProtKB:  Q15118
PHAROS:  Q15118
GTEx:  ENSG00000152256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15118
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AZX

Download Ideal Coordinates CCD File 
C19 H18 Cl F3 N2 O5 S
Query on K

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
AZX PDBBind:  2Q8G IC50: 87 (nM) from 1 assay(s)
BindingDB:  2Q8G IC50: 41 (nM) from 1 assay(s)
Binding MOAD:  2Q8G IC50: 87 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.979α = 90
b = 96.979β = 90
c = 111.352γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary