title: Two disparate ligand-binding sites in the human P2Y1 receptor.
abstract: In response to adenosine 5'-diphosphate, the P2Y1 receptor (P2Y1R) facilitates platelet aggregation, and thus serves as an important antithrombotic drug target. Here we report the crystal structures of the human P2Y1R in complex with a nucleotide antagonist MRS2500 at 2.7 Å resolution, and with a non-nucleotide antagonist BPTU at 2.2 Å resolution. The structures reveal two distinct ligand-binding sites, providing atomic details of P2Y1R's unique ligand-binding modes. MRS2500 recognizes a binding site within the seven transmembrane bundle of P2Y1R, which is different in shape and location from the nucleotide binding site in the previously determined structure of P2Y12R, representative of another P2YR subfamily. BPTU binds to an allosteric pocket on the external receptor interface with the lipid bilayer, making it the first structurally characterized selective G-protein-coupled receptor (GPCR) ligand located entirely outside of the helical bundle. These high-resolution insights into P2Y1R should enable discovery of new orthosteric and allosteric antithrombotic drugs with reduced adverse effects.
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Zhan-Guo
authors.initials: ZG
authors.lastname: Gao
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Kaihua
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Evgeny
authors.initials: E
authors.lastname: Kiselev
authors.affiliation: Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Crane
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Wang
authors.affiliation: Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Silvia
authors.initials: S
authors.lastname: Paoletta
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Cuiying
authors.initials: C
authors.lastname: Yi
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Limin
authors.initials: L
authors.lastname: Ma
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Wenru
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Gye Won
authors.initials: GW
authors.lastname: Han
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Liu
authors.affiliation: Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Vadim
authors.initials: V
authors.lastname: Cherezov
authors.affiliation: Bridge Institute, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.
authors.forename: Vsevolod
authors.initials: V
authors.lastname: Katritch
authors.affiliation: Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
authors.affiliation: 1] Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA [2] Bridge Institute, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA [3] iHuman Institute, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China.
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Stevens
authors.affiliation: Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Jacobson
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.
authors.forename: Beili
authors.initials: B
authors.lastname: Wu
mesh_terms: D000244:Adenosine Diphosphate / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D003838:Deoxyadenine Nucleotides / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D058921:Purinergic P2Y Receptor Antagonists / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D058472:Receptors, Purinergic P2Y1 / Q000737:chemistry* / Q000378:metabolism*; D013873:Thionucleotides / Q000737:chemistry / Q000378:metabolism; D014498:Uracil / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology
chemical_list: C094217:1-benzyloxymethyl-5-ethyl-6-(alpha-pyridylthio)uracil; C495475:2-iodo-N(6)-methyl-(N)-methanocarba-2'-deoxyadenosine-3',5'-bisphosphate; D003838:Deoxyadenine Nucleotides; D008024:Ligands; D058921:Purinergic P2Y Receptor Antagonists; D058472:Receptors, Purinergic P2Y1; D013873:Thionucleotides; C002480:methylthio-ADP; D014498:Uracil; D000244:Adenosine Diphosphate
references.citation: J Med Chem. 2003 Nov 6;46(23):4974-87
references.pmid: 14584948
references.citation: PLoS One. 2009;4(2):e4382
references.pmid: 19194506
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references.pmid: 20383002
references.citation: J Neurosci. 2003 Mar 15;23(6):2348-56
references.pmid: 12657694
references.citation: Circulation. 2011 May 31;123(21):2404-13
references.pmid: 21576651
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Nature. 2008 Jul 10;454(7201):183-7
references.pmid: 18563085
references.citation: Nature. 2012 Dec 20;492(7429):387-92
references.pmid: 23222541
references.citation: Nature. 2014 May 1;509(7498):115-8
references.pmid: 24670650
references.citation: J Med Chem. 2004 Oct 21;47(22):5393-404
references.pmid: 15481977
references.citation: Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8070-4
references.pmid: 9653141
references.citation: J Med Chem. 2013 Feb 28;56(4):1704-14
references.pmid: 23368907
references.citation: Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80
references.pmid: 22505257
references.citation: J Neurosci. 2000 Apr 15;20(8):2800-8
references.pmid: 10751431
references.citation: Structure. 2012 Jun 6;20(6):967-76
references.pmid: 22681902
references.citation: Science. 2010 Nov 19;330(6007):1066-71
references.pmid: 20929726
references.citation: Pharmacol Rev. 2006 Sep;58(3):281-341
references.pmid: 16968944
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references.pmid: 15299926
references.citation: Science. 2011 Apr 15;332(6027):322-7
references.pmid: 21393508
references.citation: Nature. 2014 May 1;509(7498):119-22
references.pmid: 24784220
references.citation: Thromb Haemost. 2008 Mar;99(3):466-72
references.pmid: 18327393
references.citation: Nat Protoc. 2009;4(5):706-31
references.pmid: 19390528
references.citation: Nature. 2012 Oct 25;490(7421):508-13
references.pmid: 23051748
references.citation: J Pharmacol Exp Ther. 2006 Feb;316(2):556-63
references.pmid: 16236815
references.citation: Nature. 2014 Sep 4;513(7516):124-7
references.pmid: 25043059
references.citation: J Med Chem. 2014 Jul 24;57(14):6150-64
references.pmid: 24931384
references.citation: Bioinformatics. 2006 Mar 1;22(5):623-5
references.pmid: 16397007
references.citation: Drug Dev Res. 2002 Dec 1;57(4):173-181
references.pmid: 23105165
references.citation: Science. 2012 Feb 17;335(6070):851-5
references.pmid: 22344443
references.citation: Science. 2013 Sep 20;341(6152):1387-90
references.pmid: 24030490
references.citation: Purinergic Signal. 2011 Sep;7(3):305-24
references.pmid: 21484092
references.citation: Nature. 2011 Jan 13;469(7329):175-80
references.pmid: 21228869
references.citation: J Med Chem. 1998 Apr 23;41(9):1456-66
references.pmid: 9554879
references.citation: Nature. 2012 May 17;485(7398):327-32
references.pmid: 22437504
references.citation: J Med Chem. 2013 Nov 27;56(22):9275-95
references.pmid: 24164581
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references.pmid: 20124692
references.citation: Bioorg Med Chem Lett. 2013 Jun 1;23(11):3239-43
references.pmid: 23602442