ArticleJournal of computer-aided molecular design
Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling.
Article in Journal of computer-aided molecular design. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The microglial P2YTranslational neurodegeneration · 2024Review
- Demystifying P2YJournal of chemical information and modeling · 2017Article
- Probing GPCR structure: adenosine and P2Y nucleotide receptors.Methods in enzymology · 2013Article
- Molecular Structure of P2Y Receptors: Mutagenesis, Modeling, and Chemical Probes.Wiley interdisciplinary reviews. Membrane transport and signaling · 2012Article
- P2Y receptors in the mammalian nervous system: pharmacology, ligands and therapeutic potential.CNS & neurological disorders drug targets · 2012Review
- Virtual screening leads to the discovery of novel non-nucleotide P2Y₁ receptor antagonists.Bioorganic & medicinal chemistry · 2012Article
- Farnesyl pyrophosphate is an endogenous antagonist to ADP-stimulated P2Y₁₂ receptor-mediated platelet aggregation.Thrombosis and haemostasis · 2012Article
- Pharmacochemistry of the platelet purinergic receptors.Purinergic signalling · 2011Article
- ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.BMC bioinformatics · 2011Article
- P2Y nucleotide receptors: promise of therapeutic applications.Drug discovery today · 2010Review
- Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach.BMC structural biology · 2010Article
- Basal release of ATP: an autocrine-paracrine mechanism for cell regulation.Science signaling · 2010Review
- Toward the three-dimensional structure and lysophosphatidic acid binding characteristics of the LPA(4)/p2y(9)/GPR23 receptor: a homology modeling study.Journal of molecular graphics & modelling · 2009Article
- Molecular recognition in the P2Y(14) receptor: Probing the structurally permissive terminal sugar moiety of uridine-5'-diphosphoglucose.Bioorganic & medicinal chemistry · 2009Article
- Synthesis and P2Y receptor activity of nucleoside 5'-phosphonate derivatives.Bioorganic & medicinal chemistry letters · 2009Article
- Development of selective agonists and antagonists of P2Y receptors.Purinergic signalling · 2009Article
- Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors.PloS one · 2009Article
- GPR17: molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors.BMC bioinformatics · 2008Article
- On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor.Journal of medicinal chemistry · 2008Article
- Probing the binding site of the A1 adenosine receptor reengineered for orthogonal recognition by tailored nucleosides.Biochemistry · 2007Article
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Authors and funding
3 authors.
Funding
Abstract
Ongoing efforts to model P2Y receptors for extracellular nucleotides, i.e., endogenous ADP, ATP, UDP, UTP, and UDP-glucose, were summarized and correlated for the eight known subtypes. The rhodopsin-based homology modeling of the P2Y receptors is supported by a growing body of site-directed mutagenesis data, mainly for P2Y(1) receptors. By comparing molecular models of the P2Y receptors, it was concluded that nucleotide binding could occur in the upper part of the helical bundle, with the ribose moiety accommodated between transmembrane domain (TM) 3 and TM7. The nucleobase was oriented towards TM1, TM2, and TM7, in the direction of the extracellular side of the receptor. The phosphate chain was oriented towards TM6, in the direction of the extracellular loops (ELs), and was coordinated by three critical cationic residues. In particular, in the P2Y(1), P2Y(2), P2Y(4), and P2Y(6) receptors the nucleotide ligands had very similar positions. ADP in the P2Y(12) receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y(14) receptor was located even deeper and shifted toward TM7. In general, these findings are in agreement with the proposed binding site of small molecules to other class A GPCRs.
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