Crystal structure of the Orexin-1 receptor in complex with filorexant

Experimental Data Snapshot

  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orexin receptor type 1
A, B
368Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43613
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PGW

Download Ideal Coordinates CCD File 
M [auth A],
V [auth B]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
NT5 (Subject of Investigation/LOI)
Query on NT5

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C [auth A],
N [auth B]
C24 H25 F N4 O2
Query on SOG

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
octyl 1-thio-beta-D-glucopyranoside
C14 H28 O5 S
Query on PG4

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D [auth A],
O [auth B]
C8 H18 O5
Query on SO4

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E [auth A],
F [auth A],
P [auth B],
Q [auth B]
O4 S
Query on CL

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Binding Affinity Annotations 
IDSourceBinding Affinity
NT5 BindingDB:  6TP6 Ki: min: 0.63, max: 2.9 (nM) from 5 assay(s)
IC50: min: 11, max: 16 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.892α = 90
b = 146.202β = 111.12
c = 72.328γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01DA039553

Revision History  (Full details and data files)

  • 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