4DJH

Structure of the human kappa opioid receptor in complex with JDTic

Structural Biology Knowledgebase: 4DJH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.227

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DJH

Classification: Hormone receptor / antagonist

Total Structure Weight: 110630.74

Macromolecule Entities
Molecule Chains Length Organism Details
Kappa-type opioid receptor, Lysozyme A, B 480 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358
Mutation: I135L, C1054T, C1097A
Gene Name(s): E OPRK1 Gene View OPRK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: κ-opioid receptor in complex with JDTic


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
JDC
Query on JDC

A, 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
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

B (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CIT
Query on CIT

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
JDC EC50: 6 nM (98) BindingDB
Ki: 0.02 - 0.41 nM (94 - 98) BindingDB

N/A in BindingMoad
Ki: 0.32 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.227
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.90 α = 90.00
b = 147.30 β = 90.00
c = 205.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2012-08-08
    Type: Function and keywords | Details: --
  • 2012-08-08
    Type: Citation | Details: Citation update
  • 2012-05-30
    Type: Citation | Details: Citation update