6TQ9

Crystal structure of the Orexin-1 receptor in complex with SB-408124

• PDB DOI: https://doi.org/10.2210/pdb6TQ9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-12-16 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: 2.65 Å
• R-Value Free: 0.269 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

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: 82.21 kDa 
• Atom Count: 5,233 
• Modelled Residue Count: 606 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orexin receptor type 1	A, B	336	Homo sapiens	Mutation(s): 11  Gene Names: HCRTR1 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGW	L [auth A], M [auth A]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C40 H77 O10 P PAZGBAOHGQRCBP-HGWHEPCSSA-N
NVN (Subject of Investigation/LOI)	C [auth A], D [auth A], N [auth B]	1-[6,8-bis(fluoranyl)-2-methyl-quinolin-4-yl]-3-[4-(dimethylamino)phenyl]urea C19 H18 F2 N4 O JTARFZSNUAGHRB-UHFFFAOYSA-N
SOG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N
SO4	J [auth A], K [auth A], T [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
NVN	BindingDB:  6TQ9	Ki: min: 19, max: 25 (nM) from 3 assay(s)
		Kd: 27 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.269 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.365	α = 90
b = 147.067	β = 111.09
c = 72.536	γ = 90

Software Package:

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

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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary