4EA3 | pdb_00004ea3

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), 0.300 (DCC) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 98.02 kDa 
  • Atom Count: 5,130 
  • Modeled Residue Count: 654 
  • Deposited Residue Count: 868 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P41146 (Homo sapiens)
Explore P41146 
Go to UniProtKB:  P41146
PHAROS:  P41146
GTEx:  ENSG00000125510 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41146P0ABE7
Sequence Annotations
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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), 0.300 (DCC) 
  • R-Value Work:  0.248 (Depositor) 
  • 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

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Ligand Structure Quality Assessment 


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