Structure of the human kappa opioid receptor in complex with JDTic

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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tructure of the human kappa-opioid receptor in complex with JDTic

Wu, H.Wacker, D.Mileni, M.Katritch, V.Han, G.W.Vardy, E.Liu, W.Thompson, A.A.Huang, X.P.Carroll, F.I.Mascarella, S.W.Westkaemper, R.B.Mosier, P.D.Roth, B.L.Cherezov, V.Stevens, R.C.

(2012) Nature 485: 327-332

  • DOI: https://doi.org/10.1038/nature10939
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Opioid receptors mediate the actions of endogenous and exogenous opioids on many physiological processes, including the regulation of pain, respiratory drive, mood, and--in the case of κ-opioid receptor (κ-OR)--dysphoria and psychotomimesis. Here we report the crystal structure of the human κ-OR in complex with the selective antagonist JDTic, arranged in parallel dimers, at 2.9 Å resolution. The structure reveals important features of the ligand-binding pocket that contribute to the high affinity and subtype selectivity of JDTic for the human κ-OR. Modelling of other important κ-OR-selective ligands, including the morphinan-derived antagonists norbinaltorphimine and 5'-guanidinonaltrindole, and the diterpene agonist salvinorin A analogue RB-64, reveals both common and distinct features for binding these diverse chemotypes. Analysis of site-directed mutagenesis and ligand structure-activity relationships confirms the interactions observed in the crystal structure, thereby providing a molecular explanation for κ-OR subtype selectivity, and essential insights for the design of compounds with new pharmacological properties targeting the human κ-OR.

  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa-type opioid receptor, Lysozyme
A, B
480Homo sapiensTequatrovirus T4Mutation(s): 3 
Gene Names: OPRKOPRK1e
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens)
Explore P41145 
Go to UniProtKB:  P41145
PHAROS:  P41145
GTEx:  ENSG00000082556 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41145P00720
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JDC

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C28 H39 N3 O3
Query on OLC

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on CIT

Download Ideal Coordinates CCD File 
C6 H8 O7
Query on PEG

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
C4 H10 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
JDC BindingDB:  4DJH Ki: min: 1.00e-2, max: 0.41 (nM) from 7 assay(s)
EC50: 6 (nM) from 1 assay(s)
PDBBind:  4DJH Ki: 0.32 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.896α = 90
b = 147.297β = 90
c = 205.288γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references
  • Version 1.2: 2012-08-08
    Changes: Database references, Structure summary
  • Version 1.3: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description