Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.63 kDa 
• Atom Count: 7089 
• Modelled Residue Count: 895 
• Deposited Residue Count: 960 
• Unique protein chains: 1

4DJH

Structure of the human kappa opioid receptor in complex with JDTic

• DOI: 10.2210/pdb4DJH/pdb

• Classification: Hormone receptor/antagonist
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2012-02-01 Released: 2012-03-21 
• Deposition Author(s): Wu, H., Wacker, D., Katritch, V., Mileni, M., 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., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.265 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

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

• PubMed: 22437504 
• DOI: 10.1038/nature10939
• Primary Citation of Related Structures:  
  4DJH


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa-type opioid receptor, Lysozyme	A, B	480	Homo sapiens, Escherichia virus T4	Mutation(s): 3  Gene Names: OPRK, OPRK1, E EC: 3.2.1.17 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JDC	C [auth A], E [auth B]	(3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C28 H39 N3 O3 ZLVXBBHTMQJRSX-VMGNSXQWSA-N
OLC	F [auth B], G [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG	H [auth B], I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JDC	Ki:  0.3199999928474426   nM  BindingDB
JDC	Ki:  0.009999999776482582   nM  BindingDB
JDC	Ki:  0.019999999552965164   nM  BindingDB
JDC	Ki:  0.3199999928474426   nM  BindingDB
JDC	EC50:  6   nM  BindingDB
JDC	Ki:  0.4099999964237213   nM  BindingDB
JDC	Ki :  0.3199999928474426   nM  PDBBind
JDC	Ki:  0.029999999329447746   nM  BindingDB
JDC	Ki:  0.05999999865889549   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 54.896	α = 90
b = 147.297	β = 90
c = 205.288	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-01 
• Released Date: 2012-03-21 
Deposition Author(s): Wu, H., Wacker, D., Katritch, V., Mileni, M., 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., GPCR Network (GPCR)

Revision History  

• 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