4ZJC | pdb_00004zjc

Structures of the human OX1 orexin receptor bound to selective and dual antagonists


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.262 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors.

Yin, J.Babaoglu, K.Brautigam, C.A.Clark, L.Shao, Z.Scheuermann, T.H.Harrell, C.M.Gotter, A.L.Roecker, A.J.Winrow, C.J.Renger, J.J.Coleman, P.J.Rosenbaum, D.M.

(2016) Nat Struct Mol Biol 23: 293-299

  • DOI: https://doi.org/10.1038/nsmb.3183
  • Primary Citation Related Structures: 
    4ZJ8, 4ZJC

  • PubMed Abstract: 

    The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) regulate sleep and other behavioral functions in mammals, and are therapeutic targets for sleep and wake disorders. The human receptors hOX1R and hOX2R, which are 64% identical in sequence, have overlapping but distinct physiological functions and potential therapeutic profiles. We determined structures of hOX1R bound to the OX1R-selective antagonist SB-674042 and the dual antagonist suvorexant at 2.8-Å and 2.75-Å resolution, respectively, and used molecular modeling to illuminate mechanisms of antagonist subtype selectivity between hOX1R and hOX2R. The hOX1R structures also reveal a conserved amphipathic α-helix, in the extracellular N-terminal region, that interacts with orexin-A and is essential for high-potency neuropeptide activation at both receptors. The orexin-receptor crystal structures are valuable tools for the design and development of selective orexin-receptor antagonists and agonists.


  • Organizational Affiliation
    • Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 63.7 kDa 
  • Atom Count: 4,076 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 553 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
human OX1R fusion protein to P.abysii glycogen synthase553Homo sapiensPyrococcus abyssi GE5Mutation(s): 1 
Gene Names: HCRTR1PAB2292PYRAB00770
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43613 (Homo sapiens)
Explore O43613 
Go to UniProtKB:  O43613
PHAROS:  O43613
GTEx:  ENSG00000121764 
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8O43613
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4OT

Query on 4OT



Download:Ideal Coordinates CCD File
B [auth A][5-(2-fluorophenyl)-2-methyl-1,3-thiazol-4-yl]{(2S)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyrrolidin-1-yl}methanone
C24 H21 F N4 O2 S
HYBZWVLPALMACV-KRWDZBQOSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.262 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.431α = 90
b = 66.466β = 90
c = 182.129γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary