9YDP | pdb_00009ydp

Human delta opioid receptor complex with mini-Gi and agonist DADLE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-guided allosteric modulation of the delta opioid receptor.

Mobbs, J.I.Nguyen, M.D.Deo, O.Bartuzi, D.Venugopal, H.Alvi, S.Pham, V.Barnes, N.Christopoulos, A.Poole, D.P.Carbone, S.E.Jorg, M.Capuano, B.Carlsson, J.Gondin, A.B.Scammells, P.J.Valant, C.Thal, D.M.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.10.16.682975
  • Primary Citation of Related Structures:  
    9YDP, 9YDQ, 9YDR

  • PubMed Abstract: 

    Opioid analgesics remain essential for pain management but are associated with significant adverse effects, including respiratory depression, tolerance, and dependence. The δ-opioid receptor (δOR) represents a promising therapeutic target for developing safer opioid analgesics with reduced adverse effects compared to conventional μ-opioid receptor-targeting drugs. Positive allosteric modulators (PAMs) offer advantages over direct agonists by enhancing endogenous opioid signaling while preserving natural spatiotemporal activation patterns, potentially avoiding tolerance and dependence issues. Here, we present high-resolution cryo-EM structures of δOR complexed with the peptide agonist DADLE and the PAM MIPS3614, revealing a novel lipid-facing allosteric binding site formed by transmembrane helices 2, 3, and 4. MIPS3614 stabilizes the active receptor conformation through a critical hydrogen bond with residue N131 3.35 in the conserved sodium binding site, a key regulatory region controlling GPCR activation. Comprehensive mutagenesis, molecular dynamics simulations, and structure-activity relationships validate this proposed mechanism. Structure-guided optimization yielded MIPS3983 with enhanced binding affinity and retained cooperativity. Our findings establish the first molecular framework for δOR allosteric modulation and provide a structural foundation for the rational design of safer opioid therapeutics.


  • Organizational Affiliation
    • Monash Institute of Pharmaceutical Sciences, Parkville, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas245Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1
EC: 3.6.5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1350Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 35D [auth N]156Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-type opioid receptorE [auth R]387Homo sapiensMutation(s): 0 
Gene Names: OPRD1OPRD
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Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
PHAROS:  P41143
GTEx:  ENSG00000116329 
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UniProt GroupP41143
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  • Reference Sequence

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DADLEF [auth P]5Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia2021675
National Health and Medical Research Council (NHMRC, Australia)Australia1196951

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release