ISDA

Deposition Date 2025-03-03

Release Date 2025-06-25

Last Version Date 2025-06-25

Entry Detail

PDB ID:

9M3U

Keywords:

TRANSFERASE

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.92 Å

R-Value Free:

0.21

R-Value Work:

0.17

R-Value Observed:

0.18

Space Group:

P 64

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Gene (Uniprot):PDK2
Chain IDs:A
Chain Length:362
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15119 Pfam ID:PF10436, PF02518 EC:2.7.11.2

Ligand Molecules

A1EQJ

EDO

GOL

TF3

Primary Citation

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.Show

Bioorg.Med.Chem.Lett. 122 130190 130190 (2025)

PMID: 40107630 DOI: 10.1016/j.bmcl.2025.130190

Abstact

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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Primary Citation of related structures