9M3O | pdb_00009m3o

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

• PDB DOI: https://doi.org/10.2210/pdb9M3O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-03 Released: 2025-04-02 
• Deposition Author(s): Xu, Z.H., Chen, S.
• Funding Organization(s): Not funded

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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

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

• PubMed: 40107630 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.45 kDa 
• Atom Count: 3,337 
• Modeled Residue Count: 372 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial	A	383	Homo sapiens	Mutation(s): 0  Gene Names: PDK1, PDHK1 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EMR (Subject of Investigation/LOI)	C [auth A]	6-fluoranyl-8-(methylamino)-N-(pyrimidin-5-ylmethyl)-9H-pyrido[2,3-b]indole-3-carboxamide C18 H15 F N6 O UUTSYXMIEHJQPN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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 = 98.88	α = 90
b = 98.88	β = 90
c = 110.339	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Xu, Z.H., Chen, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release