9L60 | pdb_00009l60

Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15

PDB DOI: https://doi.org/10.2210/pdb9L60/pdb
EM Map EMD-62849: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-12-23 Released: 2025-12-31
Deposition Author(s): Zhuang, Y., Wang, Y., Xu, Y., Luo, P., Xu, H.E.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

PubMed: 41671375 Search on PubMed Search on PubMed Central
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: 134.94 kDa
Atom Count: 7,260
Modeled Residue Count: 910
Deposited Residue Count: 1,188
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	353	Rattus norvegicus	Mutation(s): 0 Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311 Go to UniProtKB: P54311
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Bos taurus	Mutation(s): 0 Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa-type opioid receptor	D	397	Homo sapiens	Mutation(s): 0 Gene Names: OPRK1, OPRK
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens) Explore P41145 Go to UniProtKB: P41145
PHAROS: P41145 GTEx: ENSG00000082556
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41145
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynorphin A(1-13)	E [auth P]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01213 (Homo sapiens) Explore P01213 Go to UniProtKB: P01213
PHAROS: P01213 GTEx: ENSG00000101327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01213
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D6C (Subject of Investigation/LOI) Query on A1D6C Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione C₂₇ H₂₇ Cl O₄ ZEPFMYCUUQVNAO-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth D] MOL2 format, chain G [auth D] MOL2 format, chain F [auth D] mmCIF format, chain G [auth D] mmCIF format, chain F [auth D]	F [auth D], G [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain F [auth D] Focus chain G [auth D] Interactions & Density Focus chain F [auth D] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32130022 and 82121005
Ministry of Science and Technology (MoST, China)	China	2019YFA0904200, 2022YFC2703105 and 2022YFA1302900
Chinese Academy of Sciences	China	XDB37030103