4EJ4

Structure of the delta opioid receptor bound to naltrindole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the delta opioid receptor bound to naltrindole

Granier, S.Manglik, A.Kruse, A.C.Kobilka, T.S.Thian, F.S.Weis, W.I.Kobilka, B.K.

(2012) Nature 485: 400-404

  • DOI: 10.1038/nature11111

  • PubMed Abstract: 
  • The opioid receptor family comprises three members, the µ-, δ- and κ-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coup ...

    The opioid receptor family comprises three members, the µ-, δ- and κ-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The δ-opioid receptor (δ-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the µ-OR and κ-OR have recently been solved. Here we report the crystal structure of the mouse δ-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the µ-OR and κ-OR, the δ-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the δ-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.


    Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA. granier@stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Delta-type opioid receptor, Lysozyme chimera
A
461Enterobacteria phage T4Mus musculus
This entity is chimeric
Gene Names: E, Oprd1
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
δ-opioid receptor in complex with naltrindol
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Find proteins for P32300 (Mus musculus)
Go to UniProtKB:  P32300
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EJ4
Query on EJ4

Download SDF File 
Download CCD File 
A
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
Naltrindole
C26 H26 N2 O3
WIYUZYBFCWCCQJ-IFKAHUTRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EJ4Ki: 0 - 2.6 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.278α = 90.00
b = 73.278β = 90.00
c = 266.653γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
Blu-Icedata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Refinement description, Source and taxonomy