Crystal structure of the active delta opioid receptor in complex with the small molecule agonist DPI-287

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

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Elucidating the active delta-opioid receptor crystal structure with peptide and small-molecule agonists.

Claff, T.Yu, J.Blais, V.Patel, N.Martin, C.Wu, L.Han, G.W.Holleran, B.J.Van der Poorten, O.White, K.L.Hanson, M.A.Sarret, P.Gendron, L.Cherezov, V.Katritch, V.Ballet, S.Liu, Z.J.Muller, C.E.Stevens, R.C.

(2019) Sci Adv 5: eaax9115-eaax9115

  • DOI: https://doi.org/10.1126/sciadv.aax9115
  • Primary Citation of Related Structures:  
    6PT2, 6PT3

  • PubMed Abstract: 

    Selective activation of the δ-opioid receptor (DOP) has great potential for the treatment of chronic pain, benefitting from ancillary anxiolytic and antidepressant-like effects. Moreover, DOP agonists show reduced adverse effects as compared to μ-opioid receptor (MOP) agonists that are in the spotlight of the current "opioid crisis." Here, we report the first crystal structures of the DOP in an activated state, in complex with two relevant and structurally diverse agonists: the potent opioid agonist peptide KGCHM07 and the small-molecule agonist DPI-287 at 2.8 and 3.3 Å resolution, respectively. Our study identifies key determinants for agonist recognition, receptor activation, and DOP selectivity, revealing crucial differences between both agonist scaffolds. Our findings provide the first investigation into atomic-scale agonist binding at the DOP, supported by site-directed mutagenesis and pharmacological characterization. These structures will underpin the future structure-based development of DOP agonists for an improved pain treatment with fewer adverse effects.

  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Rd, Pudong, Shanghai 201210, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta opioid receptor
A, B
454Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
PHAROS:  P41143
GTEx:  ENSG00000116329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41143
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OWY (Subject of Investigation/LOI)
Query on OWY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C31 H39 N3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.084α = 90
b = 142.101β = 90
c = 157.491γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description