9XDQ | pdb_00009xdq

Cryo-EM structure of BMS986187 bound DOR-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XDQ

This is version 1.0 of the entry. See complete history

Literature

Molecular mechanism of allosteric modulation of opioid receptors.

Wang, H.Miao, Z.Zhao, C.Fu, H.Tian, X.Liu, X.Wang, L.Liu, Y.Liu, X.Yong, X.Su, L.Yan, W.Cheng, L.Chai, R.Shao, Z.Ke, B.

(2026) Signal Transduct Target Ther 11

  • DOI: https://doi.org/10.1038/s41392-026-02759-5
  • Primary Citation Related Structures: 
    9XC6, 9XDQ, 9XDR, 9XF4

  • PubMed Abstract: 

    Opioid analgesics provide potent pain relief but are limited by severe adverse effects, tolerance, and interindividual genetic variability in response. Poly-pharmacology and allosteric modulation of opioid receptors offer promising strategies to enhance analgesic efficacy while mitigating these limitations. Pan-positive allosteric modulators (pan-PAMs), which simultaneously potentiate multiple opioid receptor subtypes, integrate the advantages of both approaches and represent an emerging therapeutic paradigm for pain management. However, the molecular mechanisms underlying pan-PAM activity at opioid receptors remain poorly understood. Here, we characterize BMS-986187 as a pan-PAM of opioid receptors and report the cryo-electron microscopy (cryo-EM) structures of multiple opioid receptor subtypes bound to this modulator, revealing a previously unidentified allosteric pocket. Structural and functional analyses revealed a conserved binding motif that mediates PAM recognition across the opioid receptor family and revealed the essential contributions of key opioid receptor residues to allosteric modulation by BMS-986187. Functionally, BMS-986187 enhances analgesic efficacy through an opioid-sparing effect, allowing lower opioid doses and reducing side effects, while restoring activity in loss-of-function (LOF) μ-opioid receptor variants. These findings define a previously unrecognized allosteric site in opioid receptors and establish a structural framework for the rational design of safer and more effective opioid therapeutics through allosteric modulation.


  • Organizational Affiliation
    • Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, Division of Nephrology and Kidney Research Institute, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 157.01 kDa 
  • Atom Count: 7,094 
  • Modeled Residue Count: 906 
  • Deposited Residue Count: 1,405 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Delta-type opioid receptor,Soluble cytochrome b562,Delta-type opioid receptor,Oplophorus-luciferin 2-monooxygenase catalytic subunit595Escherichia coliHomo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCOPRD1OPRD
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
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 GroupsP0ABE7P41143
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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-1384Homo 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 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2355Homo sapiensMutation(s): 0 
Gene Names: GNAI2GNAI2B
EC: 3.6.5
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Find proteins for P04899 (Homo sapiens)
Explore P04899 
Go to UniProtKB:  P04899
PHAROS:  P04899
GTEx:  ENSG00000114353 
Entity Groups
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UniProt GroupP04899
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D6B
(Subject of Investigation/LOI)

Query on A1D6B



Download:Ideal Coordinates CCD File
E [auth A]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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371288
National Natural Science Foundation of China (NSFC)China323B2038

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release