Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.09 kDa 
• Atom Count: 5,718 
• Modelled Residue Count: 753 
• Deposited Residue Count: 908 
• Unique protein chains: 1

 6PT3

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

• PDB DOI: 10.2210/pdb6PT3/pdb

• Classification: MEMBRANE PROTEIN/AGONIST
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2019-07-14 Released: 2019-12-11 
• Deposition Author(s): Claff, T., Yu, J., Blais, V., Patel, N., Martin, C., Wu, L., Han, G.W., Holleran, B.J., Van der Poorten, O., Hanson, M.A., Sarret, P., Gendron, L., Cherezov, V., Katritch, V., Ballet, S., Liu, Z., Muller, C.E., Stevens, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 

Literature

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

• PubMed: 31807708 
• DOI: 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.

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Organizational Affiliation: 

Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta opioid receptor	A, B	454	Homo sapiens	Mutation(s): 0  Gene Names: OPRD1, OPRD Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens) Explore P41143  Go to UniProtKB:  P41143
PHAROS:  P41143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OWY (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-[(R)-[(2S,5R)-4-benzyl-2,5-dimethylpiperazin-1-yl](3-hydroxyphenyl)methyl]-N,N-diethylbenzamide C31 H39 N3 O2 PQMGDEIHRXQPCQ-FSGGQHMVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 49.084	α = 90
b = 142.101	β = 90
c = 157.491	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Claff, T., Yu, J., Blais, V., Patel, N., Martin, C., Wu, L., Han, G.W., Holleran, B.J., Van der Poorten, O., Hanson, M.A., Sarret, P., Gendron, L., Cherezov, V., Katritch, V., Ballet, S., Liu, Z., Muller, C.E., Stevens, R.C.

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references