5K32 image
Deposition Date 2016-05-19
Release Date 2017-03-29
Last Version Date 2024-01-10
Entry Detail
PDB ID:
5K32
Keywords:
Title:
PDE4D crystal structure in complex with small molecule inhibitor
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.99 Å
R-Value Free:
0.28
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Gene (Uniprot):PDE4D
Chain IDs:A, B
Chain Length:325
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
4-Amino-7,8-dihydro-1,6-naphthyridin-5(6 H)-ones as Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships.
J. Med. Chem. 61 2472 2489 (2018)
PMID: 29502405 DOI: 10.1021/acs.jmedchem.7b01751

Abstact

Rational design of a novel template of naphthyridinones rapidly led to PDE4 inhibitors with subnanomolar enzymatic potencies. X-ray crystallography confirmed the binding mode of this novel template. We achieved compounds with double-digit picomolar enzymatic potencies through further structure-based design by targeting both the PDE4 enzyme metal-binding pocket and occupying the solvent-filled pocket. A strategy for lung retention and long duration of action based on low aqueous solubility was followed. In vivo efficacies were measured in a rat lung neutrophilia model by suspension microspray and dry powder administration. Suspension microspray of potent compounds showed in vivo efficacy with a clear dose-response. Despite sustained lung levels, dry powder administration performed much less well and without proper dose-response, highlighting clear differences between the two formulations. This indicates a deficiency in the low aqueous solubility strategy for long duration lung efficacy.

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Primary Citation of related structures
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