6TPJ

Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6TPJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Pyrococcus abyssi GE5
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-12-13 Released: 2020-01-01 
• Deposition Author(s): Rappas, M., Ali, A., Bennett, K.A., Brown, J.D., Bucknell, S.J., Congreve, M., Cooke, R.M., Cseke, G., de Graaf, C., Dore, A.S., Errey, J.C., Jazayeri, A., Marshall, F.H., Mason, J.S., Mould, R., Patel, J.C., Tehan, B.G., Weir, M., Christopher, J.A.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.254 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis.

Rappas, M., Ali, A.A.E., Bennett, K.A., Brown, J.D., Bucknell, S.J., Congreve, M., Cooke, R.M., Cseke, G., de Graaf, C., Dore, A.S., Errey, J.C., Jazayeri, A., Marshall, F.H., Mason, J.S., Mould, R., Patel, J.C., Tehan, B.G., Weir, M., Christopher, J.A.

(2020) J Med Chem 63: 1528-1543

• PubMed: 31860301 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b01787
• Primary Citation of Related Structures:  
  6TO7, 6TOD, 6TOS, 6TOT, 6TP3, 6TP4, 6TP6, 6TPG, 6TPJ, 6TPN, 6TQ4, 6TQ6, 6TQ7, 6TQ9


• PubMed Abstract: 
  

  The orexin system, which consists of the two G protein-coupled receptors OX ₁ and OX ₂ , activated by the neuropeptides OX-A and OX-B, is firmly established as a key regulator of behavioral arousal, sleep, and wakefulness and has been an area of intense research effort over the past two decades. X-ray structures of the receptors in complex with 10 new antagonist ligands from diverse chemotypes are presented, which complement the existing structural information for the system and highlight the critical importance of lipophilic hotspots and water molecules for these peptidergic GPCR targets. Learnings from the structural information regarding the utility of pharmacophore models and how selectivity between OX ₁ and OX ₂ can be achieved are discussed.

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Organizational Affiliation: 

Sosei Heptares , Steinmetz Building, Granta Park , Cambridge CB21 6DG , U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 140.02 kDa 
• Atom Count: 8,578 
• Modelled Residue Count: 1,000 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orexin receptor type 2,GlgA glycogen synthase,Hypocretin receptor-2	A, B	564	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 20  Gene Names: HCRTR2, PAB2292 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
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
PHAROS:  O43614 GTEx:  ENSG00000137252
UniProt Groups	Q9V2J8O43614

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SUV (Subject of Investigation/LOI)	D [auth A], T [auth B]	[(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	AA [auth B], BA [auth B], C [auth A], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], X [auth B], Y [auth B], Z [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PG4	S [auth A], SA [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
NH4	E [auth A], H [auth A], U [auth B], V [auth B], W [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A, B	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
SUV	BindingDB:  6TPJ	Ki: min: 0.35, max: 12 (nM) from 5 assay(s)
		IC50: min: 0.4, max: 138 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.254 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.325	α = 89.99
b = 76.247	β = 85.25
c = 82.737	γ = 89.97

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Rappas, M., Ali, A., Bennett, K.A., Brown, J.D., Bucknell, S.J., Congreve, M., Cooke, R.M., Cseke, G., de Graaf, C., Dore, A.S., Errey, J.C., Jazayeri, A., Marshall, F.H., Mason, J.S., Mould, R., Patel, J.C., Tehan, B.G., Weir, M., Christopher, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R01DA039553

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2020-03-11
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description