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 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 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 ( ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein of Nociceptin receptor and cytochrome b562AB434Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: OOROPRL1ORL1cybC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
Nociceptin/orphanin FQ (N/OFQ) receptor with bound peptide
Find proteins for P41146 (Homo sapiens)
Explore P41146 
Go to UniProtKB:  P41146
NIH Common Fund Data Resources
PHAROS  P41146
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0NN
Query on 0NN

Download CCD File 
A, 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
 Ligand Interaction
OLB
Query on OLB

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A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0NNIC50 :  0.27000001072883606   nM  PDBBind
0NNIC50:  0.15000000596046448   nM  BindingDB
0NNKi:  0.23999999463558197   nM  BindingDB
0NNEC50:  1000   nM  BindingDB
0NNIC50:  0.27000001072883606   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • 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



Entry History 

Deposition Data

Revision History 

  • 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