5XPR

Human endothelin receptor type-B in complex with antagonist bosentan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog

Shihoya, W.Nishizawa, T.Yamashita, K.Inoue, A.Hirata, K.Kadji, F.M.N.Okuta, A.Tani, K.Aoki, J.Fujiyoshi, Y.Doi, T.Nureki, O.

(2017) Nat Struct Mol Biol 24: 758-764

  • DOI: 10.1038/nsmb.3450
  • Primary Citation of Related Structures:  
    5X93, 5XPR

  • PubMed Abstract: 
  • Endothelin receptors (ETRs) have crucial roles in vascular control and are targets for drugs designed to treat circulatory-system diseases and cancer progression. The nonpeptide dual-ETR antagonist bosentan is the first oral drug approved to treat pulmonary arterial hypertension ...

    Endothelin receptors (ETRs) have crucial roles in vascular control and are targets for drugs designed to treat circulatory-system diseases and cancer progression. The nonpeptide dual-ETR antagonist bosentan is the first oral drug approved to treat pulmonary arterial hypertension. Here we report crystal structures of human endothelin ET B receptor bound to bosentan and to the ET B -selective analog K-8794, at 3.6-Å and 2.2-Å resolution, respectively. The K-8794-bound structure reveals the detailed water-mediated hydrogen-bonding network at the transmembrane core, which could account for the weak negative allosteric modulation of ET B by Na + ions. The bosentan-bound structure reveals detailed interactions with ET B , which are probably conserved in the ET A receptor. A comparison of the two structures shows unexpected similarity between antagonist and agonist binding. Despite this similarity, bosentan sterically prevents the inward movement of transmembrane helix 6 (TM6), and thus exerts its antagonistic activity. These structural insights will facilitate the rational design of new ETR-targeting drugs.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelin B receptor,Endolysin,Endothelin B receptorA464Homo sapiensEscherichia virus T4Mutation(s): 9 
Gene Names: EDNRBETRBE
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P24530 (Homo sapiens)
Explore P24530 
Go to UniProtKB:  P24530
PHAROS:  P24530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP24530P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K86
Query on K86

Download Ideal Coordinates CCD File 
B [auth A]4-tert-butyl-N-[6-(2-hydroxyethyloxy)-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]benzenesulfonamide
C27 H29 N5 O6 S
GJPICJJJRGTNOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
K86 BindingDB:  5XPR Ki: min: 80, max: 340 (nM) from 4 assay(s)
IC50: min: 95, max: 1000 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.253 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.72α = 90
b = 74.72β = 90
c = 218.87γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
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: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Structure summary