5YVE

Crystal structure of human P2X3 receptor in complex with the AF-219 negative allosteric modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

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This is version 1.2 of the entry. See complete history


Literature

Druggable negative allosteric site of P2X3 receptors.

Wang, J.Wang, Y.Cui, W.W.Huang, Y.Yang, Y.Liu, Y.Zhao, W.S.Cheng, X.Y.Sun, W.S.Cao, P.Zhu, M.X.Wang, R.Hattori, M.Yu, Y.

(2018) Proc Natl Acad Sci U S A 115: 4939-4944

  • DOI: https://doi.org/10.1073/pnas.1800907115
  • Primary Citation of Related Structures:  
    5YVE

  • PubMed Abstract: 

    Allosteric modulation provides exciting opportunities for drug discovery of enzymes, ion channels, and G protein-coupled receptors. As cation channels gated by extracellular ATP, P2X receptors have attracted wide attention as new drug targets. Although small molecules targeting P2X receptors have entered into clinical trials for rheumatoid arthritis, cough, and pain, negative allosteric modulation of these receptors remains largely unexplored. Here, combining X-ray crystallography, computational modeling, and functional studies of channel mutants, we identified a negative allosteric site on P2X3 receptors, fostered by the left flipper (LF), lower body (LB), and dorsal fin (DF) domains. Using two structurally analogous subtype-specific allosteric inhibitors of P2X3, AF-353 and AF-219, the latter being a drug candidate under phase II clinical trials for refractory chronic cough and idiopathic pulmonary fibrosis, we defined the molecular interactions between the drugs and receptors and the mechanism by which allosteric changes in the LF, DF, and LB domains modulate ATP activation of P2X3. Our detailed characterization of this druggable allosteric site should inspire new strategies to develop P2X3-specific allosteric modulators for clinical use.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200438 Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2X purinoceptor 3363Homo sapiensMutation(s): 3 
Gene Names: P2RX3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56373 (Homo sapiens)
Explore P56373 
Go to UniProtKB:  P56373
PHAROS:  P56373
GTEx:  ENSG00000109991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56373
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.613α = 90
b = 119.613β = 90
c = 235.691γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary