8ZM1

Structure of human pyruvate dehydrogenase kinase 2 complexed with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Design and synthesis of novel fluorene derivatives as inhibitors of pyruvate dehydrogenase kinase.

Inoue, M.Nagamori, H.Morita, T.Kobayashi, S.Suzawa, K.Kitao, Y.Saito, T.Kawahara, I.Orita, T.Akai, S.Adachi, T.Motomura, T.

(2024) Bioorg Med Chem Lett 109: 129839-129839

  • DOI: https://doi.org/10.1016/j.bmcl.2024.129839
  • Primary Citation of Related Structures:  
    8ZM1, 8ZM2

  • PubMed Abstract: 

    Activation of pyruvate dehydrogenase (PDH) by inhibition of pyruvate dehydrogenase kinase (PDHK) has the potential for the treatment of diabetes mellitus and its complications, caused by the malfunction of the glycolytic system and glucose oxidation. In this paper, we describe the identification of novel PDHK inhibitors with a fluorene structure. High-throughput screening using our in-house library provided compound 6 as a weak inhibitor that occupied the allosteric lipoyl group binding site in PDHK2. Structure-based drug design (SBDD) while addressing physicochemical properties succeeded in boosting inhibitory activity approximately 700-fold. Thus obtained compound 32 showed favorable pharmacokinetics profiles supported by high membrane permeability and metabolic stability, and exhibited activation of PDH in rat livers and a glucose lowering effect in Zucker fatty rats.


  • Organizational Affiliation

    Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan. Electronic address: masafumi.inoue@jt.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial394Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L16 (Subject of Investigation/LOI)
Query on A1L16

Download Ideal Coordinates CCD File 
B [auth A](5~{R})-5-propan-2-ylindeno[1,2-b]pyridin-5-ol
C15 H15 N O
VQGAKSMYTWYVAJ-OAHLLOKOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.304α = 90
b = 109.304β = 90
c = 84.495γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references