8ZM1 image
Entry Detail
PDB ID:
8ZM1
Keywords:
TRANSFERASE
Title:
Structure of human pyruvate dehydrogenase kinase 2 complexed with compound 6
Biological Source:
Source Organism:
Homo sapiens
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2024-05-22
Release Date:
2024-06-19
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.35 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 64
8ZM1 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Chain IDs:A
Chain Length:394
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15119 Pfam ID:PF10436, PF02518 EC:2.7.11.2
Ligand Molecules
A1L16
Primary Citation
Design and synthesis of novel fluorene derivatives as inhibitors of pyruvate dehydrogenase kinase.
Bioorg.Med.Chem.Lett. 109 129839 129839 (2024)
PMID: 38844173 DOI: 10.1016/j.bmcl.2024.129839

Abstact

Activation of pyruvate dehydrogenase (PDH) by inhibition of pyruvate dehydrogenase kinase (PDHK) has the potential for the treatment of diabetes mellitus and its complications, caused by the malfunction of the glycolytic system and glucose oxidation. In this paper, we describe the identification of novel PDHK inhibitors with a fluorene structure. High-throughput screening using our in-house library provided compound 6 as a weak inhibitor that occupied the allosteric lipoyl group binding site in PDHK2. Structure-based drug design (SBDD) while addressing physicochemical properties succeeded in boosting inhibitory activity approximately 700-fold. Thus obtained compound 32 showed favorable pharmacokinetics profiles supported by high membrane permeability and metabolic stability, and exhibited activation of PDH in rat livers and a glucose lowering effect in Zucker fatty rats.

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Primary Citation of related structures
8ZM1