We are analyzing https://link.springer.com/article/10.1007/s10822-006-9054-2.

Title:
Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling | Journal of Computer-Aided Molecular Design
Description:
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 P2Y1 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 P2Y1, P2Y2, P2Y4, and P2Y6 receptors the nucleotide ligands had very similar positions. ADP in the P2Y12 receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y14 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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Keywords {🔍}

article, receptors, jacobson, google, scholar, receptor, molecular, modeling, cas, human, recognition, chem, harden, med, costanzi, nucleotide, binding, moro, analogues, national, privacy, cookies, content, journal, homology, ivanov, extracellular, access, ligand, kim, data, information, publish, research, search, design, kenneth, structure, proteincoupled, boyer, purinergic, maddileti, protein, author, analysis, log, sites, rhodopsinbased, mutagenesis, transmembrane,

Topics {✒️}

l-α-threofuranosyl ring systems protein-coupled nucleotide receptors rhodopsin-based homology modeling month download article/chapter protein-coupled receptor structures substrate binding mode protein-coupled receptors suramin-derived compound library p2y nucleotide receptors nucleotide binding sites antagonist recognition sites human platelet p2y12-receptor model p2y receptors comparative protein modeling site-directed mutagenesis data proposed binding site structural comparison based privacy choices/manage cookies protein structure alignments full article pdf intramural research program homology modeling adenosine bisphosphate antagonists molecular modeling analyses molecular modeling leads base-modified udp ligand–receptor interactions nucleotide binding extracellular nucleotides related subjects investigate molecular recognition molecular modeling study author information authors comparative protein modelling uridine 5′-diphosphate analogues van galen pjm comprehensive computational study ligand recognition structure-activity relationships structure activity relationship p2y receptors european economic area comparing molecular models critical cationic residues ectonucleotide phosphodiesterase/pyrophosphatase-3 gonzalez-moa mj unique conformational preference molecular dynamics simulation site-directed mutagenesis human p2y1 receptor

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         headline:Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
         description: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 P2Y1 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 P2Y1, P2Y2, P2Y4, and P2Y6 receptors the nucleotide ligands had very similar positions. ADP in the P2Y12 receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y14 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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      headline:Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
      description: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 P2Y1 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 P2Y1, P2Y2, P2Y4, and P2Y6 receptors the nucleotide ligands had very similar positions. ADP in the P2Y12 receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y14 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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