9MQL: Kappa-Opioid Receptor

Locally-Refined Inactive Kappa-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound #020_E1. Determined by electron microscopy at 2.96 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.96 Å
Organism: Mus musculus
Chains: 1
Atoms: 2,303
Mol. weight: 44.02 kDa
Ligands: A1BNM
Released: 12 Feb 2025

Explore 9MQL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MQL contains 15 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	60-68	9
α-helix	69-73	5
α-helix	74-86	13
α-helix	93-110	18
α-helix	112-115	4
α-helix	117-120	4
α-helix	128-161	34
α-helix	163-169	7
α-helix	172-196	25
β-strand	197-201	5	1
β-strand	208-212	5	1
α-helix	221-231	11
α-helix	232-236	5
α-helix	237-257	21
α-helix	263-299	37
α-helix	308-333	26
α-helix	335-345	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kappa-Opioid Receptor	A	protein	388	Mus musculus	P41145 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MQL_1 Kappa-Opioid Receptor (chains A)
DYKDDDDAMESPIQIFRGDPGPTCSPSACLLPNSSSWFPNWAESDSNGSVGSEDQQLESA
HISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTTM
PFQSAVYLMNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTP
LKAKIINICIWLLASSVGISAIVLGGTKVREDVDVIECSLQFPDDEYSWWDLFMKICVFV
FAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITKLVLVVVAVFIICWTPIHI
FILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPVLYAFLDENFKRCFRDFCFPIKMRM
ERQSTNRVRNTVQDPASMRDVGGMNKPV

Ligands and cofactors

ID	Name	Formula	Copies
A1BNM	methyl (1S,3R,4S,6S,8M)-2-[(1-ethyl-1H-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)…	C23 H29 N3 O3	1

Primary citation

Docking 14 million virtual isoquinuclidines against the mu and kappa opioid receptors reveals dual antagonists-inverse agonists with reduced withdrawal effects. Vigneron, S.F., Ohno, S., Braz, J. et al. bioRxiv (2025). DOI 10.1101/2025.01.09.632033 · PubMed

Other PDB entries of the same protein (UniProt P41145 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UL2 2.4 Å, CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
7T10 2.5 Å, CryoEM structure of somatostatin receptor 2 in complex with somatostatin-14 and Gi3
9PA4 2.5 Å, (S)-ketamine bound kappa-opioid receptor in complex with Gi1
8FEG 2.54 Å, CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1
9XDR 2.58 Å, Cryo-EM structure of asimadoline-BMS-986187-bound KOR-Gi1 complex
9ZZO 2.6 Å, MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
8DZR 2.61 Å, GR89,696 bound Kappa Opioid Receptor in complex with gustducin
9PA1 2.63 Å, PCP bound kappa-opioid receptor in complex with Gi1
8DZS 2.65 Å, GR89,696 bound Kappa Opioid Receptor in complex with Gz
7T11 2.7 Å, CryoEM structure of somatostatin receptor 2 in complex with Octreotide and Gi3.
8DZP 2.71 Å, momSalB bound Kappa Opioid Receptor in complex with Gi1

Browse structure collections

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