9M3O | pdb_00009m3o

Crystal structure of human pyruvate dehydrogenase kinase isoform 1 in complex with ATP competitive inhibitor 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Literature

Discovery of ATP competitive PDHK1/2 dual inhibitors.

Xu, H.Ding, D.Han, X.Miao, K.Liang, C.Yun, H.Zhu, W.Dey, F.Zhao, D.Wu, Y.Reutlinger, M.Yang, J.Zhai, G.Lin, Z.Li, C.Wu, W.Xu, B.Han, L.Chen, S.Huang, X.Casagrande, F.Hilbert, M.Strebel, Q.Wichert, M.Westwood, P.Schafer, R.Roth, D.Heer, D.Tian, X.Ma, T.Zhang, T.Zhao, J.Urich, E.Xia, G.Lassen, K.Shen, H.C.Zou, G.

(2025) Bioorg Med Chem Lett 122: 130190-130190

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130190
  • Primary Citation of Related Structures:  
    9M3O, 9M3P, 9M3R, 9M3T, 9M3U

  • PubMed Abstract: 

    Multiple screening approaches were carried out to identify novel chemistry starting for Pyruvate Dehydrogenase Kinases (PDHKs) inhibitors. Through hit triaging efforts and structure-based optimization, two series of ATP competitive inhibitors with single digit nanomolar enzymatic potency for PDHK1/2 and around 10-100-fold selectivity over PDHK4/3 were discovered. Approach of covalent inhibitor was explored to successfully improve the cellular target engagement to single digit micromolar range.


  • Organizational Affiliation

    China Innovation Center of Roche, No. 371 Lishizhen Road, Shanghai, 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial383Homo sapiensMutation(s): 0 
Gene Names: PDK1PDHK1
EC: 2.7.11.2
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.88α = 90
b = 98.88β = 90
c = 110.339γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2025-04-02
    Type: Initial release