9VDD image
Deposition Date 2025-06-08
Release Date 2026-05-06
Last Version Date 2026-05-06
Entry Detail
PDB ID:
9VDD
Keywords:
Title:
The crystal structure of PDE4D with inhibitor LH17
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:3',5'-cyclic-AMP phosphodiest
Gene (Uniprot):PDE4D
Chain IDs:A, B
Chain Length:327
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Discovery of kaempferol derivatives as novel PDE4 inhibitors for treatment of idiopathic pulmonary fibrosis.
Eur.J.Med.Chem. 304 118505 118505 (2026)
PMID: 41443085 DOI: 10.1016/j.ejmech.2025.118505

Abstact

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with a rapidly rising global incidence. Despite its growing prevalence, effective therapeutic options for IPF remain limited. Phosphodiesterase 4 (PDE4) inhibitors have recently emerged as promising anti-fibrotic candidates. In this study, the natural product kaempferol was identified as a weak PDE4 inhibitor with half maximal inhibitory concentration (IC(50)) of 22 muM and structure-based optimization by targeting M-pocket was performed, yielding a lead compound LH17 with dramatically improved potency (IC(50) of 73 nM). Crystallographic analysis revealed that this kaempferol-derived compound LH17 displayed distinct interactions with PDE4 M-pocket. Notably, lead LH17 demonstrated remarkable anti-fibrotic efficacy in both in vitro and in vivo models, underscoring its potential as a novel therapeutic agent for IPF treatment. This study also could establish a rational strategy for optimizing weakly bioactive natural PDE4 inhibitors into potent therapeutics.

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Chemical

Disease

Primary Citation of related structures
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