6K1Q

Human endothelin receptor type-B in complex with inverse agonist IRL2500


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of human endothelin ETBreceptor in complex with peptide inverse agonist IRL2500.

Nagiri, C.Shihoya, W.Inoue, A.Kadji, F.M.N.Aoki, J.Nureki, O.

(2019) Commun Biol 2: 236-236

  • DOI: 10.1038/s42003-019-0482-7

  • PubMed Abstract: 
  • Endothelin receptors (ET <sub>A </sub> and ET <sub>B </sub>) are G-protein-coupled receptors activated by endothelin-1 and are involved in blood pressure regulation. IRL2500 is a peptide-mimetic of the C-terminal tripeptide of endothelin-1, and has b ...

    Endothelin receptors (ET A and ET B ) are G-protein-coupled receptors activated by endothelin-1 and are involved in blood pressure regulation. IRL2500 is a peptide-mimetic of the C-terminal tripeptide of endothelin-1, and has been characterized as a potent ET B -selective antagonist, which has preventive effects against brain edema. Here, we report the crystal structure of the human ET B receptor in complex with IRL2500 at 2.7 Å-resolution. The structure revealed the different binding modes between IRL2500 and endothelin-1, and provides structural insights into its ET B -selectivity. Notably, the biphenyl group of IRL2500 penetrates into the transmembrane core proximal to D 2.50 , thus stabilizing the inactive conformation. Using the newly-established constitutively active mutant, we clearly demonstrate that IRL2500 functions as an inverse agonist for the ET B receptor. The current findings will expand the chemical space of ETR antagonists and facilitate the design of inverse agonists for other class A GPCRs.


    Organizational Affiliation

    2Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578 Miyagi Japan.,1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelin B receptor,Endolysin,Endothelin B receptor
A
464Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 9 
Gene Names: EDNRB (ETRB), E
EC: 3.2.1.17
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
endothelin ETB receptor with bound endothelin-1
Find proteins for P24530 (Homo sapiens)
Go to Gene View: EDNRB
Go to UniProtKB:  P24530
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
D2U
Query on D2U

Download SDF File 
Download CCD File 
A
(2~{S})-2-[[(2~{R})-2-[(3,5-dimethylphenyl)carbonyl-methyl-amino]-3-(4-phenylphenyl)propanoyl]amino]-3-(1~{H}-indol-3-yl)propanoic acid
C36 H35 N3 O4
UZDORQWMYRRLQV-JHOUSYSJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 109.910α = 90.00
b = 109.910β = 90.00
c = 291.590γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H06294

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release