6TPG

Crystal structure of the Orexin-2 receptor in complex with EMPA at 2.74 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.741 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.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.Weir, M.Christopher, J.A.

(2019) J.Med.Chem. --: --

  • DOI: 10.1021/acs.jmedchem.9b01787
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The orexin system, which consists of the two G protein-coupled receptors OX <sub>1 </sub> and OX <sub>2 </sub>, activated by the neuropeptides OX-A and OX-B, is firmly established as a key regulator of behavioural arousal, sleep and wakefulness, and ...

    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 behavioural 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 ten 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orexin receptor type 2,GlgA glycogen synthase,Hypocretin receptor-2
A
564Pyrococcus abyssi (strain GE5 / Orsay)Homo sapiens
This entity is chimeric
Mutation(s): 20 
Gene Names: HCRTR2, HCRTR2
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for O43614 (Homo sapiens)
Go to Gene View: HCRTR2
Go to UniProtKB:  O43614
Find proteins for Q548Y0 (Homo sapiens)
Go to Gene View: HCRTR2
Go to UniProtKB:  Q548Y0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
7MA
Query on 7MA

Download SDF File 
Download CCD File 
A
N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide
C23 H26 N4 O4 S
KJPHTXTWFHVJIG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.741 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.097α = 90.00
b = 172.914β = 90.00
c = 77.810γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release