6LIN

Crystal structure of human PDK2 complexed with GM10030


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

Starting Model: experimental
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Literature

Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds.

Kang, J.Pagire, H.S.Kang, D.Song, Y.H.Lee, I.K.Lee, K.T.Park, C.J.Ahn, J.H.Kim, J.

(2020) Biochem Biophys Res Commun 527: 778-784

  • DOI: https://doi.org/10.1016/j.bbrc.2020.04.102
  • Primary Citation of Related Structures:  
    6LIL, 6LIN, 6LIO

  • PubMed Abstract: 

    Pyruvate dehydrogenase kinase (PDK) controls the activity of pyruvate decarboxylase complex (PDC) by phosphorylating key serine residues on the E1 subunit, which leads to a decreased oxidative phosphorylation in mitochondria. Inhibition of PDK activity by natural/synthetic compounds has been shown to reverse the Warburg effect, a characteristic metabolism in cancer cells. PDK-PDC axis also has been associated with diabetes and heart disease. Therefore, regulation of PDK activity has been considered as a promising strategy to treat related diseases. Here we present the X-ray crystal structure of PDK2 complexed with a recently identified PDK4 inhibitor, compound 8c, which has been predicted to bind at the lipoyl-binding site and interrupt intermolecular interactions with the E2-E3bp subunits of PDC. The co-crystal structure confirmed the specific binding location of compound 8c and revealed the remote conformational change in the ATP-binding pocket. In addition, two novel 4,5-diarylisoxazole derivatives, GM10030 and GM67520, were synthesized and used for structural studies, which target the ATP-binding site of PDK2. These compounds bind to PDK2 with a sub-100nM affinity as determined by isothermal titration calorimetry experiments. Notably, the crystal structure of the PDK2-GM10030 complex displays unprecedented asymmetric conformation of human PDK2 dimer, especially in the ATP-lids and C-terminal tails.


  • Organizational Affiliation

    Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
A, B, C, D
411Homo sapiensMutation(s): 0 
Gene Names: PDK2PDHK2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15119
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EH0 (Subject of Investigation/LOI)
Query on EH0

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
L [auth D]
4-[[[4-[3,5-bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid
C28 H21 Cl F2 N2 O9
SZFDJLAHDKEQBS-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.42α = 90
b = 156.186β = 103.97
c = 102.012γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2016R1D1A1B03930716

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description