6TPJ

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 2,GlgA glycogen synthase,Hypocretin receptor-2A, B564Homo sapiensPyrococcus abyssi GE5Mutation(s): 20 
Gene Names: HCRTR2PAB2292
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUV
Query on SUV

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
OLA
Query on OLA

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , C [auth A] , CA [auth B] , DA [auth B] , EA [auth B] , F [auth A] , FA [auth B] , 
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
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
S [auth A], SA [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
E [auth A], H [auth A], U [auth B], V [auth B], W [auth B]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A, BL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SUVKi:  8.699999809265137   nM  BindingDB
SUVIC50:  138   nM  BindingDB
SUVIC50:  56   nM  BindingDB
SUVKi:  0.4000000059604645   nM  BindingDB
SUVKi:  0.3499999940395355   nM  BindingDB
SUVKi:  12   nM  BindingDB
SUVIC50:  0.4000000059604645   nM  BindingDB
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 = 55.325α = 89.99
b = 76.247β = 85.25
c = 82.737γ = 89.97
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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