9BJK

Inactive mu opioid receptor bound to Nb6, naloxone and NAM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A mu-opioid receptor modulator that works cooperatively with naloxone.

O'Brien, E.S.Rangari, V.A.El Daibani, A.Eans, S.O.Hammond, H.R.White, E.Wang, H.Shiimura, Y.Krishna Kumar, K.Jiang, Q.Appourchaux, K.Huang, W.Zhang, C.Kennedy, B.J.Mathiesen, J.M.Che, T.McLaughlin, J.P.Majumdar, S.Kobilka, B.K.

(2024) Nature 631: 686-693

  • DOI: https://doi.org/10.1038/s41586-024-07587-7
  • Primary Citation of Related Structures:  
    9BJK

  • PubMed Abstract: 

    The µ-opioid receptor (µOR) is a well-established target for analgesia 1 , yet conventional opioid receptor agonists cause serious adverse effects, notably addiction and respiratory depression. These factors have contributed to the current opioid overdose epidemic driven by fentanyl 2 , a highly potent synthetic opioid. µOR negative allosteric modulators (NAMs) may serve as useful tools in preventing opioid overdose deaths, but promising chemical scaffolds remain elusive. Here we screened a large DNA-encoded chemical library against inactive µOR, counter-screening with active, G-protein and agonist-bound receptor to 'steer' hits towards conformationally selective modulators. We discovered a NAM compound with high and selective enrichment to inactive µOR that enhances the affinity of the key opioid overdose reversal molecule, naloxone. The NAM works cooperatively with naloxone to potently block opioid agonist signalling. Using cryogenic electron microscopy, we demonstrate that the NAM accomplishes this effect by binding a site on the extracellular vestibule in direct contact with naloxone while stabilizing a distinct inactive conformation of the extracellular portions of the second and seventh transmembrane helices. The NAM alters orthosteric ligand kinetics in therapeutically desirable ways and works cooperatively with low doses of naloxone to effectively inhibit various morphine-induced and fentanyl-induced behavioural effects in vivo while minimizing withdrawal behaviours. Our results provide detailed structural insights into the mechanism of negative allosteric modulation of the µOR and demonstrate how this can be exploited in vivo.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
kappa opioid receptor Nanobody 6A [auth N]133Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mu-type opioid receptorB [auth R]426Mus musculusMutation(s): 2 
Gene Names: Oprm1MorOprm
Membrane Entity: Yes 
UniProt
Find proteins for P42866 (Mus musculus)
Explore P42866 
Go to UniProtKB:  P42866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42866
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1APU (Subject of Investigation/LOI)
Query on A1APU

Download Ideal Coordinates CCD File 
D [auth R]Nalpha-[({(1M)-1-[5-(benzyloxy)pyridin-3-yl]naphthalen-2-yl}sulfanyl)acetyl]-3-methoxy-N,4-dimethyl-L-phenylalaninamide
C36 H35 N3 O4 S
IBQRWMDLUKSOJL-HKBQPEDESA-N
A1APV (Subject of Investigation/LOI)
Query on A1APV

Download Ideal Coordinates CCD File 
C [auth R]Naloxone
C19 H21 N O4
UZHSEJADLWPNLE-GRGSLBFTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chan Zuckerberg InitiativeUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-14
    Changes: Data collection