4V26

VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context-dependent cytostasis in cancer cells.

Moore, J.D.Staniszewska, A.Shaw, T.D'Alessandro, J.Davis, B.Surgenor, A.Baker, L.Matassova, N.Murray, J.Macias, A.Brough, P.Wood, M.Mahon, P.C.

(2014) Oncotarget 5: 12862-12876

  • DOI: 10.18632/oncotarget.2656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate dehydrogenase kinase (PDK) is a pivotal enzyme in cellular energy metabolism that has previously been implicated in cancer through both RNAi based studies and clinical correlations with poor prognosis in several cancer types. Here, we report ...

    Pyruvate dehydrogenase kinase (PDK) is a pivotal enzyme in cellular energy metabolism that has previously been implicated in cancer through both RNAi based studies and clinical correlations with poor prognosis in several cancer types. Here, we report the discovery of a novel and selective ATP competitive pan-isoform inhibitor of PDK, VER-246608. Consistent with a PDK mediated MOA, VER-246608 increased pyruvate dehydrogenase complex (PDC) activity, oxygen consumption and attenuated glycolytic activity. However, these effects were only observed under D-glucose-depleted conditions and required almost complete ablation of PDC E1α subunit phosphorylation. VER-246608 was weakly anti-proliferative to cancer cells in standard culture media; however, depletion of either serum or combined D-glucose/L-glutamine resulted in enhanced cellular potency. Furthermore, this condition-selective cytostatic effect correlated with reduced intracellular pyruvate levels and an attenuated compensatory response involving deamination of L-alanine. In addition, VER-246608 was found to potentiate the activity of doxorubicin. In contrast, the lipoamide site inhibitor, Nov3r, demonstrated sub-maximal inhibition of PDK activity and no evidence of cellular activity. These studies suggest that PDK inhibition may be effective under the nutrient-depleted conditions found in the tumour microenvironment and that combination treatments should be explored to reveal the full potential of this therapeutic strategy.


    Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.,Vernalis (R&D) Ltd, Granta Park, Cambridge, UK. Current address: Horizon discovery, Cambridge Research Park, Waterbeach, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
[PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE ISOZYME 2, MITOCHONDRIAL
A
407Homo sapiensMutation(s): 0 
Gene Names: PDK2 (PDHK2)
EC: 2.7.11.2
Find proteins for Q15119 (Homo sapiens)
Go to Gene View: PDK2
Go to UniProtKB:  Q15119
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7TJ
Query on 7TJ

Download SDF File 
Download CCD File 
A
N-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-2,4-DIHYDROXY-N-(4-{[(TRIFLUOROACETYL)AMINO]METHYL}BENZYL)BENZAMIDE
C28 H22 Cl F3 N4 O4
JGLCKAMQSKRYAP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TF3
Query on TF3

Download SDF File 
Download CCD File 
A
N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
C20 H25 Cl N2 O2
DFXJYVQAAFOZDP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.180 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 108.838α = 90.00
b = 108.838β = 90.00
c = 84.401γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Data collection
  • Version 1.3: 2019-10-09
    Type: Data collection, Database references, Other