PhosphoDiEsterase Structure and ligand Interaction Annotated database (PDEStrIAn), developed at the Division of Medicinal Chemistry - VU University Amsterdam, is a database that revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. Based on the underlying systematic and consistent protocol all PED structures and the binding mode of PDE ligands can be directly compared to each other. Moreover, because of the classification of an all-encompassing binding site of 57 residues it is possible to compare the interaction patterns of PDE-inhibitors to each other to, for example, identify crucial interactions determining PDE-inhibitor selectivity.

This work is described in a perspective in the Journal of Medicinal Chemistry article and is available here. The structure-based PDE-ligand interaction data described, including the processed PDB collection, PDE binding pocket sequence alignment, structurally aligned binding site mol2 files, and the PDE-ligand IFPs, are available from the ZENODO repository (DOI:10.5281/zenodo.45774).

Contents
Species: 5
PDE types: 16
PDB entries: 271
Monomers: 856
Unique ligands: 198

Latest additions:
PDBSpeciesPDE typeLigand
HumanPDE5-4-Chimera1-(5-chloro-6-methoxypyridin-3-yl)-3-methyl-N-(methylsulfonyl)-1H-indazole-5-carboxamide
HumanPDE4D4-[(3-methoxyphenyl)amino]-2-phenyl-7,8-dihydro-1,6-naphthyridin-5(6H)-one
HumanPDE4B6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]oxy]-5-chloranyl-2-(4-oxidanylidenepentoxy)pyridine-3-carbonitrile
HumanPDE4DN-[(2R)-2,3-dihydroxy-2-methylpropyl]-8-(methylamino)-6-[(2,3,5,6-tetrafluorophenyl)amino]imidazo[1,2-b]pyridazine-3-carboxamide
HumanPDE2A2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one
HumanPDE2A4-[3-(4-methoxyphenoxy)azetidin-1-yl]-1-methyl-3-(2-methylpropyl)-1H-pyrazolo[3,4-d]pyrimidine
HumanPDE2A5-[2-(2-methoxyphenyl)ethoxy]-3-(2-methylpropyl)[1,2,4]triazolo[4,3-a]pyrazine
HumanPDE2A3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-5-propoxy[1,2,4]triazolo[4,3-a]pyrazine
HumanPDE2A(3R)-1-{3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl}-N,N-dimethylpyrrolidin-3-amine
HumanPDE1B6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
HumanPDE1B6-[(4-chlorophenyl)methyl]-8,9,10,11-tetrahydro[1]benzothieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
HumanPDE109-[(1S)-2,2-difluorocyclopropane-1-carbonyl]-6-[(4-methoxyphenyl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one