5DHG

The crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (PSI Community Target)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor.

Miller, R.L.Thompson, A.A.Trapella, C.Guerrini, R.Malfacini, D.Patel, N.Han, G.W.Cherezov, V.Calo, G.Katritch, V.Stevens, R.C.

(2015) Structure 23: 2291-2299

  • DOI: 10.1016/j.str.2015.07.024
  • Primary Citation of Related Structures:  
    5DHH, 5DHG

  • PubMed Abstract: 
  • Understanding the mechanism by which ligands affect receptor conformational equilibria is key in accelerating membrane protein structural biology. In the case of G protein-coupled receptors (GPCRs), we currently pursue a brute-force approach for identifying ligands that stabilize receptors and facilitate crystallogenesis ...

    Understanding the mechanism by which ligands affect receptor conformational equilibria is key in accelerating membrane protein structural biology. In the case of G protein-coupled receptors (GPCRs), we currently pursue a brute-force approach for identifying ligands that stabilize receptors and facilitate crystallogenesis. The nociceptin/orphanin FQ peptide receptor (NOP) is a member of the opioid receptor subfamily of GPCRs for which many structurally diverse ligands are available for screening. We observed that antagonist potency is correlated with a ligand's ability to induce receptor stability (Tm) and crystallogenesis. Using this screening strategy, we solved two structures of NOP in complex with top candidate ligands SB-612111 and C-35. Docking studies indicate that while potent, stabilizing antagonists strongly favor a single binding orientation, less potent ligands can adopt multiple binding modes, contributing to their low Tm values. These results suggest a mechanism for ligand-aided crystallogenesis whereby potent antagonists stabilize a single ligand-receptor conformational pair.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: stevens@usc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562,Nociceptin receptorA, B424Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybCOPRL1OORORL1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41146 (Homo sapiens)
Explore P41146 
Go to UniProtKB:  P41146
PHAROS:  P41146
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGV (Subject of Investigation/LOI)
Query on DGV

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide
C26 H33 Cl2 N3 O
UWHDLFOAIARROU-XMMPIXPASA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
H [auth B](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA (Subject of Investigation/LOI)
Query on OLA

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DGV BindingDB:  5DHG Ki: 0.72 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.079α = 90
b = 171.696β = 103.25
c = 66.491γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2016-03-02
    Changes: Database references
  • Version 1.4: 2017-05-31
    Changes: Source and taxonomy
  • Version 1.5: 2017-07-05
    Changes: Database references