4EA3

Structure of the N/OFQ Opioid Receptor in Complex with a Peptide Mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic.

Thompson, A.A.Liu, W.Chun, E.Katritch, V.Wu, H.Vardy, E.Huang, X.P.Trapella, C.Guerrini, R.Calo, G.Roth, B.L.Cherezov, V.Stevens, R.C.

(2012) Nature 485: 395-399

  • DOI: https://doi.org/10.1038/nature11085
  • Primary Citation of Related Structures:  
    4EA3

  • PubMed Abstract: 

    Members of the opioid receptor family of G-protein-coupled receptors (GPCRs) are found throughout the peripheral and central nervous system, where they have key roles in nociception and analgesia. Unlike the 'classical' opioid receptors, δ, κ and μ (δ-OR, κ-OR and μ-OR), which were delineated by pharmacological criteria in the 1970s and 1980s, the nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP, also known as ORL-1) was discovered relatively recently by molecular cloning and characterization of an orphan GPCR. Although it shares high sequence similarity with classical opioid GPCR subtypes (∼60%), NOP has a markedly distinct pharmacology, featuring activation by the endogenous peptide N/OFQ, and unique selectivity for exogenous ligands. Here we report the crystal structure of human NOP, solved in complex with the peptide mimetic antagonist compound-24 (C-24) (ref. 4), revealing atomic details of ligand-receptor recognition and selectivity. Compound-24 mimics the first four amino-terminal residues of the NOP-selective peptide antagonist UFP-101, a close derivative of N/OFQ, and provides important clues to the binding of these peptides. The X-ray structure also shows substantial conformational differences in the pocket regions between NOP and the classical opioid receptors κ (ref. 5) and μ (ref. 6), and these are probably due to a small number of residues that vary between these receptors. The NOP-compound-24 structure explains the divergent selectivity profile of NOP and provides a new structural template for the design of NOP ligands.


  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Nociceptin receptor and cytochrome b562
A, B
434Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: OOROPRL1ORL1cybC
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0NN
Query on 0NN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
1-benzyl-N-[3-(1'H,3H-spiro[2-benzofuran-1,4'-piperidin]-1'-yl)propyl]-D-prolinamide
C27 H35 N3 O2
MAKMQGKJURAJEN-RUZDIDTESA-N
OLC
Query on OLC

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

Download Ideal Coordinates CCD File 
D [auth A](2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
E [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0NN BindingDB:  4EA3 Ki: 0.24 (nM) from 1 assay(s)
IC50: min: 0.15, max: 0.27 (nM) from 2 assay(s)
EC50: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.106α = 90
b = 170.939β = 103.14
c = 65.353γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0NNClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view detailsBest fitted OLBClick on this verticalbar to view detailsBest fitted OLAClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary