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 

wwPDB Validation 3D Report Full Report


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 ...

    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: P2RY12HORK3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
P2Y12 receptor in complex with an antithrombotic drug
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9H244 (Homo sapiens)
Explore Q9H244 
Go to UniProtKB:  Q9H244
NIH Common Fund Data Resources
PHAROS  Q9H244
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZJ
Query on AZJ

Download CCD File 
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
Query on CLR

Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZJIC50:  14   nM  BindingDB
AZJIC50:  25   nM  BindingDB
AZJIC50:  3200   nM  BindingDB
AZJIC50:  11   nM  BindingDB
AZJIC50:  22   nM  BindingDB
AZJIC50:  44   nM  BindingDB
AZJIC50:  9   nM  BindingDB
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

View Full Validation Report



Entry History 

Revision History 

  • 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