8Y71 | pdb_00008y71

positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Y71

This is version 1.1 of the entry. See complete history

Literature

Structure-based design of an opioid receptor modulator for enhanced morphine analgesia.

Wang, Y.Luo, P.Xu, H.Zhan, L.Sakamoto, K.Li, M.Wang, J.Huang, X.P.Zhou, J.Liu, T.Suo, Y.Fan, W.He, X.Xu, Y.Cai, Y.Wang, C.Zhao, Y.Dai, A.Lai, Y.Yuan, Q.Hu, W.Wu, K.Yang, D.Cheng, X.Lu, X.Krumm, B.Kenakin, T.Zhang, J.Roth, B.L.Gao, Z.Xu, H.E.Zhuang, Y.

(2026) Sci Adv 12: eaea9832-eaea9832

  • DOI: https://doi.org/10.1126/sciadv.aea9832
  • Primary Citation Related Structures: 
    8Y71, 8Y72, 8Y73, 9L60

  • PubMed Abstract: 

    The alarming rates of deaths due to opioid overdose present an urgent need for safer opioid analgesics. Positive allosteric modulators (PAMs) of opioid receptors (ORs) offer a promising approach to enhance opioid efficacy while reducing risks of overdose. In this study, we unveil the selective mechanism of PAM modulation of the OR family through structure elucidation of the δ-opioid receptor and μ-opioid receptor (μOR) bound to orthosteric agonists and PAMs BMS986187 (BMS187) and BMS986122 (BMS122). In addition, we uncovered an unexpected but conserved allosteric site across the transmembrane helices TM2 to TM4 of ORs, occupied by BMS187 but not BMS122. Leveraging these structural insights, we designed 9-(5-(4-chlorophenyl)furan-2-yl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1 H -xanthene-1,8(2 H )-dione (MPAM-15), whose αβ cooperativity factor is 33-fold higher than BMS122 and threefold higher than BMS187, indicating markedly stronger positive allosterism. Animal studies demonstrate that MPAM-15 shows excellent brain penetration and enhances morphine-induced antinociception without exacerbating respiratory depression or constipation. Molecular dynamics simulations revealed that MPAM-15 promotes and stabilizes the conformational equilibrium of μOR toward the canonical active state, providing a mechanistic basis for its enhanced allosteric potency. These discoveries substantially advance our understanding of OR allosteric mechanism and pave the way for the structure-based development of allosteric opioid analgesics.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecule Content 

  • Total Structure Weight: 173.05 kDa 
  • Atom Count: 8,933 
  • Modeled Residue Count: 1,136 
  • Deposited Residue Count: 1,564 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 2 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
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UniProt GroupP63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1371Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
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UniProt GroupP54311
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-268Bos taurusMutation(s): 0 
Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus)
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Go to UniProtKB:  P63212
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UniProt GroupP63212
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16D [auth E]248synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Delta-type opioid receptorE [auth R]523Homo sapiensMutation(s): 0 
Gene Names: OPRD1OPRD
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
PHAROS:  P41143
GTEx:  ENSG00000116329 
Entity Groups
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UniProt GroupP41143
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D6B
(Subject of Investigation/LOI)

Query on A1D6B



Download:Ideal Coordinates CCD File
F [auth R]3,3,6,6-tetramethyl-9-[4-[(2-methylphenyl)methoxy]phenyl]-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione
C31 H34 O4
UEKIYVKPQNKSDI-UHFFFAOYSA-N
A1D6F
(Subject of Investigation/LOI)

Query on A1D6F



Download:Ideal Coordinates CCD File
G [auth R]4-[(~{S})-[(2~{R},5~{S})-2,5-dimethyl-4-prop-2-enyl-piperazin-1-yl]-(3-methoxyphenyl)methyl]-~{N},~{N}-diethyl-benzamide
C28 H39 N3 O2
KQWVAUSXZDRQPZ-XXAUWVGASA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32130022
National Natural Science Foundation of China (NSFC)China82121005

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Data collection, Database references