9M3T | pdb_00009m3t

Crystal structure of human pyruvate dehydrogenase kinase isoform 2 in complex with ATP competitive inhibitor 22

• PDB DOI: https://doi.org/10.2210/pdb9M3T/pdb

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


• Deposited: 2025-03-03 Released: 2025-06-11 
• 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: 2.08 Å
• R-Value Free: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

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 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.
Pharmaceutical Research and Early Development, F. Hoffmann-La Roche AG, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland.
China Innovation Center of Roche, No. 371 Lishizhen Road, Shanghai, 201203, China. Electronic address: [e-mail].

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: 42.7 kDa 
• Atom Count: 3,122 
• Modeled Residue Count: 352 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	A	367	Homo sapiens	Mutation(s): 0  Gene Names: PDK2, PDHK2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EQI (Subject of Investigation/LOI)	C [auth A]	2-chloranyl-4-[[(3R)-1-[(3S)-7-(ethylamino)-5-fluoranyl-3-methyl-2-oxidanylidene-1H-indol-3-yl]piperidin-3-yl]amino]benzoic acid C23 H26 Cl F N4 O3 IVLYNRUVQRISEI-CMJOXMDJSA-N
TF3	B [auth A]	N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE C20 H25 Cl N2 O2 DFXJYVQAAFOZDP-UHFFFAOYSA-N
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.57	α = 90
b = 106.57	β = 90
c = 85.66	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Xu, Z.H., Chen, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release