4NTJ

Structure of the human P2Y12 receptor in complex with an antithrombotic drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of the human P2Y12 receptor in complex with an antithrombotic drug

Zhang, K.Zhang, J.Gao, Z.-G.Zhang, D.Zhu, L.Han, G.W.Moss, S.M.Paoletta, S.Kiselev, E.Lu, W.Fenalti, G.Zhang, W.Muller, C.E.Yang, H.Jiang, H.Cherezov, V.Katritch, V.Jacobson, K.A.Stevens, R.C.Wu, B.Zhao, Q.

(2014) Nature 509: 115-118

  • DOI: 10.1038/nature13083
  • Primary Citation of Related Structures:  
    4NTJ

  • PubMed Abstract: 
  • P2Y receptors (P2YRs), a family of purinergic G-protein-coupled receptors (GPCRs), are activated by extracellular nucleotides. There are a total of eight distinct functional P2YRs expressed in human, which are subdivided into P2Y1-like receptors and P2Y12-like receptors ...

    P2Y receptors (P2YRs), a family of purinergic G-protein-coupled receptors (GPCRs), are activated by extracellular nucleotides. There are a total of eight distinct functional P2YRs expressed in human, which are subdivided into P2Y1-like receptors and P2Y12-like receptors. Their ligands are generally charged molecules with relatively low bioavailability and stability in vivo, which limits our understanding of this receptor family. P2Y12R regulates platelet activation and thrombus formation, and several antithrombotic drugs targeting P2Y12R--including the prodrugs clopidogrel (Plavix) and prasugrel (Effient) that are metabolized and bind covalently, and the nucleoside analogue ticagrelor (Brilinta) that acts directly on the receptor--have been approved for the prevention of stroke and myocardial infarction. However, limitations of these drugs (for example, a very long half-life of clopidogrel action and a characteristic adverse effect profile of ticagrelor) suggest that there is an unfulfilled medical need for developing a new generation of P2Y12R inhibitors. Here we report the 2.6 Å resolution crystal structure of human P2Y12R in complex with a non-nucleotide reversible antagonist, AZD1283. The structure reveals a distinct straight conformation of helix V, which sets P2Y12R apart from all other known class A GPCR structures. With AZD1283 bound, the highly conserved disulphide bridge in GPCRs between helix III and extracellular loop 2 is not observed and appears to be dynamic. Along with the details of the AZD1283-binding site, analysis of the extracellular interface reveals an adjacent ligand-binding region and suggests that both pockets could be required for dinucleotide binding. The structure provides essential insights for the development of improved P2Y12R ligands and allosteric modulators as drug candidates.


    Organizational Affiliation

    CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12A466Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: P2RY12HORK3cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9H244 (Homo sapiens)
Explore Q9H244 
Go to UniProtKB:  Q9H244
PHAROS:  Q9H244
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZJ (Subject of Investigation/LOI)
Query on AZJ

Download Ideal Coordinates CCD File 
B [auth A]ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin-1-yl}-5-cyano-2-methylpyridine-3-carboxylate
C23 H26 N4 O5 S
NEMHKCNXXRQYRF-UHFFFAOYSA-N
 Ligand Interaction
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A], F [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AZJ BindingDB:  4NTJ IC50: min: 9, max: 3200 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.65α = 90
b = 156.43β = 111.08
c = 47.77γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 1.2: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description