6PT2

Crystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1126/sciadv.aax9115
  • Primary Citation of Related Structures:  

  • 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-opi ...

    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

    School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.,PharmaCenter Bonn, University of Bonn, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.,Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.,iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Rd, Pudong, Shanghai 201210, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.,Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Centre de Recherche du CHUS, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada.,GPCR Consortium, San Marcos, CA 92078, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Delta opioid receptor
A, B
454N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide agonist KGCHM07
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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

Download SDF File 
Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
SAR
Query on SAR
C, D
PEPTIDE LINKINGC3 H7 N O2GLY
DI7
Query on DI7
C, D
L-peptide linkingC11 H15 N O3TYR
OXJ
Query on OXJ
C, D
NON-POLYMERC10 H9 F6 N

--

DAR
Query on DAR
C, D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.960α = 90.00
b = 140.880β = 90.00
c = 158.640γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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