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

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


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

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Nociceptin receptor
A, B
424Escherichia 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
GTEx:  ENSG00000125510 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41146P0ABE7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DGV

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C26 H33 Cl2 N3 O
Query on OLC

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

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

Experimental Data

  • 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
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

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
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description