Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.92 kDa 
• Atom Count: 3114 
• Modelled Residue Count: 340 
• Deposited Residue Count: 421 
• Unique protein chains: 1

4XNV

The human P2Y1 receptor in complex with BPTU

• PDB DOI: 10.2210/pdb4XNV/pdb

• Classification: TRANSPORT PROTEIN/INHIBITOR
• Organism(s): Homo sapiens, Clostridium pasteurianum
• Expression System: Spodoptera
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-01-16 Released: 2015-04-01 
• Deposition Author(s): Zhang, D., Gao, Z., Jacobson, K., Han, G.W., Stevens, R., Zhao, Q., Wu, B., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.230 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Two disparate ligand-binding sites in the human P2Y1 receptor

Zhang, D., Gao, Z.G., Zhang, K., Kiselev, E., Crane, S., Wang, J., Paoletta, S., Yi, C., Ma, L., Zhang, W., Han, G.W., Liu, H., Cherezov, V., Katritch, V., Jiang, H., Stevens, R.C., Jacobson, K.A., Zhao, Q., Wu, B.

(2015) Nature 520: 317-321

• PubMed: 25822790 
• DOI: 10.1038/nature14287
• Primary Citation of Related Structures:  
  4XNV, 4XNW


• PubMed 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1	A	421	Homo sapiens, Clostridium pasteurianum	Mutation(s): 1  Gene Names: P2RY1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00268 (Clostridium pasteurianum) Explore P00268  Go to UniProtKB:  P00268
Find proteins for P47900 (Homo sapiens) Explore P47900  Go to UniProtKB:  P47900
PHAROS:  P47900
UniProt Groups	P00268P47900

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01	D [auth A], E [auth A], F [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
BUR	B [auth A]	1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea C23 H22 F3 N3 O3 AHFLGPTXSIRAQK-UHFFFAOYSA-N
CLR	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
1PE	O [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ZN	P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BUR	Binding MOAD:  4XNV	Ki: 161 (nM) from 1 assay(s)
	BindingDB:  4XNV	Ki: 6 (nM) from 1 assay(s)
		IC50: min: 29, max: 2100 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.230 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.27	α = 90
b = 66.27	β = 90
c = 239.07	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-16 
• Released Date: 2015-04-01 
Deposition Author(s): Zhang, D., Gao, Z., Jacobson, K., Han, G.W., Stevens, R., Zhao, Q., Wu, B., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Structure summary
• Version 1.3: 2020-02-05
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary