4EJ4

Structure of the delta opioid receptor bound to naltrindole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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
  • Primary Citation of Related Structures:  
    4EJ4

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Delta-type opioid receptor, Lysozyme chimeraA461Mus musculusEscherichia virus T4Mutation(s): 3 
Gene Names: Oprd1E
EC: 3.2.1.17
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
δ-opioid receptor in complex with naltrindol
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P32300 (Mus musculus)
Explore P32300 
Go to UniProtKB:  P32300
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EJ4
Query on EJ4

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
C26 H26 N2 O3
WIYUZYBFCWCCQJ-IFKAHUTRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EJ4Ki:  0.3100000023841858   nM  BindingDB
EJ4Ki:  0.46000000834465027   nM  BindingDB
EJ4Ki:  0.2199999988079071   nM  BindingDB
EJ4Ki:  0.20000000298023224   nM  BindingDB
EJ4Ki:  0.30000001192092896   nM  BindingDB
EJ4Ki:  0.8999999761581421   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.278α = 90
b = 73.278β = 90
c = 266.653γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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