9M3U | pdb_00009m3u

Crystal structure of human pyruvate dehydrogenase kinase isoform 2 in complex with ATP competitive inhibitor 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.213 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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 2, mitochondrial362Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EQJ (Subject of Investigation/LOI)
Query on A1EQJ

Download Ideal Coordinates CCD File 
G [auth A]2-cyano-N-[(3R)-1-[(3S)-3-ethyl-7-(ethylamino)-5-fluoranyl-2-oxidanylidene-1H-indol-3-yl]piperidin-3-yl]-2-azaspiro[3.3]heptane-6-carboxamide
C25 H33 F N6 O2
SXYDOCWKRRIRAC-CJAUYULYSA-N
TF3
Query on TF3

Download Ideal Coordinates CCD File 
E [auth A]N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
C20 H25 Cl N2 O2
DFXJYVQAAFOZDP-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.63α = 90
b = 110.63β = 90
c = 84γ = 120
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: 2025-06-25
    Type: Initial release