6IIV

Crystal structure of the human thromboxane A2 receptor bound to daltroban


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for ligand recognition of the human thromboxane A2receptor.

Fan, H.Chen, S.Yuan, X.Han, S.Zhang, H.Xia, W.Xu, Y.Zhao, Q.Wu, B.

(2019) Nat. Chem. Biol. 15: 27-33

  • DOI: 10.1038/s41589-018-0170-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Stimulated by thromboxane A <sub>2 </sub>, an endogenous arachidonic acid metabolite, the thromboxane A <sub>2 </sub> receptor (TP) plays a pivotal role in cardiovascular homeostasis, and thus is considered as an important drug target for cardiovascu ...

    Stimulated by thromboxane A 2 , an endogenous arachidonic acid metabolite, the thromboxane A 2 receptor (TP) plays a pivotal role in cardiovascular homeostasis, and thus is considered as an important drug target for cardiovascular disease. Here, we report crystal structures of the human TP bound to two nonprostanoid antagonists, ramatroban and daltroban, at 2.5 Å and 3.0 Å resolution, respectively. The TP structures reveal a ligand-binding pocket capped by two layers of extracellular loops that are stabilized by two disulfide bonds, limiting ligand access from the extracellular milieu. These structures provide details of interactions between the receptor and antagonists, which help to integrate previous mutagenesis and SAR data. Molecular docking of prostanoid-like ligands, combined with mutagenesis, ligand-binding and functional assays, suggests a prostanoid binding mode that may also be adopted by other prostanoid receptors. These insights into TP deepen our understanding about ligand recognition and selectivity mechanisms of this physiologically important receptor.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. beiliwu@simm.ac.cn.,University of Chinese Academy of Sciences, Beijing, China. zhaoq@simm.ac.cn.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. zhaoq@simm.ac.cn.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. beiliwu@simm.ac.cn.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. zhaoq@simm.ac.cn.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. zhaoq@simm.ac.cn.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China. beiliwu@simm.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor
A
484Escherichia coliHomo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 4 
Gene Names: cybC, TBXA2R,
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P21731 (Homo sapiens)
Go to Gene View: TBXA2R
Go to UniProtKB:  P21731
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
A90
Query on A90

Download SDF File 
Download CCD File 
A
2-[4-[2-[(4-chlorophenyl)sulfonylamino]ethyl]phenyl]ethanoic acid
Daltroban
C16 H16 Cl N O4 S
IULOBWFWYDMECP-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.530α = 90.00
b = 152.170β = 90.00
c = 125.220γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-07 
  • Released Date: 2018-12-19 
  • Deposition Author(s): Fan, H., Zhao, Q., Wu, B.

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDB-SSW-SMC024

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references