6TO7

Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1021/acs.jmedchem.9b01787
  • Primary Citation of Related Structures:  
    6TOD, 6TO7, 6TPJ, 6TPN, 6TPG, 6TP3, 6TOT, 6TOS, 6TP4, 6TP6

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orexin receptor type 1A, B336Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW

Download Ideal Coordinates CCD File 
BA [auth A], CB [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
PAZGBAOHGQRCBP-HGWHEPCSSA-N
 Ligand Interaction
SUV
Query on SUV

Download Ideal Coordinates CCD File 
C [auth A], DA [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
 Ligand Interaction
SOG
Query on SOG

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth B] , BB [auth B] , F [auth A] , G [auth A] , H [auth A] , HA [auth B] , I [auth A] , 
AA [auth A],  AB [auth B],  BB [auth B],  F [auth A],  G [auth A],  H [auth A],  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],  S [auth A],  SA [auth B],  T [auth A],  TA [auth B],  U [auth A],  UA [auth B],  V [auth A],  VA [auth B],  W [auth A],  WA [auth B],  X [auth A],  XA [auth B],  Y [auth A],  YA [auth B],  Z [auth A],  ZA [auth B]
octyl 1-thio-beta-D-glucopyranoside
C14 H28 O5 S
CGVLVOOFCGWBCS-RGDJUOJXSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A], EA [auth B], FA [auth B], GA [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth A], DB [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SUVIC50:  50   nM  BindingDB
SUVIC50:  199   nM  BindingDB
SUVKi:  0.6000000238418579   nM  BindingDB
SUVKi:  0.550000011920929   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 158.47β = 95.31
c = 183.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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