Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.82 kDa 
• Atom Count: 3878 
• Residue Count: 478 
• Unique protein chains: 1

4S0V

Crystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant

• DOI: 10.2210/pdb4S0V/pdb
• Entry: 4S0V supersedes: 4RNB

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Pyrococcus abyssi GE5
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-01-06 Released: 2015-01-14 
• Deposition Author(s): Yin, J., Kolb, P., Mobarec, J.C., Rosenbaum, D.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant.

Yin, J., Mobarec, J.C., Kolb, P., Rosenbaum, D.M.

(2015) Nature 519: 247-250

• PubMed: 25533960 
• DOI: 10.1038/nature14035
• Primary Citation of Related Structures:  
  4S0V


• PubMed Abstract: 
  

The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) respond to orexin neuropeptides in the central nervous system to regulate sleep and other behavioural functions in humans. Defects in orexin signalling are responsible for the human diseases of narcolepsy and cataplexy; inhibition of orexin receptors is an effective therapy for insomnia. The human OX2 receptor (OX2R) belongs to the β branch of the rhodopsin family of GPCRs, and can bind to diverse compounds including the native agonist peptides orexin-A and orexin-B and the potent therapeutic inhibitor suvorexant. Here, using lipid-mediated crystallization and protein engineering with a novel fusion chimaera, we solved the structure of the human OX2R bound to suvorexant at 2.5 Å resolution. The structure reveals how suvorexant adopts a π-stacked horseshoe-like conformation and binds to the receptor deep in the orthosteric pocket, stabilizing a network of extracellular salt bridges and blocking transmembrane helix motions necessary for activation. Computational docking suggests how other classes of synthetic antagonists may interact with the receptor at a similar position in an analogous π-stacked fashion. Elucidation of the molecular architecture of the human OX2R expands our understanding of peptidergic GPCR ligand recognition and will aid further efforts to modulate orexin signalling for therapeutic ends.

---

Organizational Affiliation: 

Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Orexin receptor type 2 fusion protein to P. abysii Glycogen Synthase	A	559	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: HCRTR2, PAB2292, PYRAB00770
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  OX2 orexin receptor with bound suvorexant
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8  Go to UniProtKB:  Q9V2J8
Find proteins for O43614 (Homo sapiens) Explore O43614  Go to UniProtKB:  O43614
NIH Common Fund Data Resources
PHAROS  O43614 GTEx  ENSG00000137252

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SUV	A	[(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone C23 H23 Cl N6 O2 JYTNQNCOQXFQPK-MRXNPFEDSA-N
OLA	A	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SUV	IC50:  56   nM  BindingDB
SUV	Ki:  0.3499999940395355   nM  BindingDB
SUV	Ki:  8.699999809265137   nM  BindingDB
SUV	Ki:  12   nM  BindingDB
SUV	IC50:  0.4000000059604645   nM  BindingDB
SUV	Ki:  0.4000000059604645   nM  BindingDB
SUV	IC50:  138   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.358	α = 90
b = 75.819	β = 111.71
c = 96.335	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-06 
• Released Date: 2015-01-14 
Deposition Author(s): Yin, J., Kolb, P., Mobarec, J.C., Rosenbaum, D.M.
• This entry supersedes: 4RNB

Revision History 

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2015-03-25
  Changes: Database references
• Version 1.3: 2017-08-23
  Changes: Refinement description, Source and taxonomy