6TOD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 

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 1
A, B
336Homo sapiensMutation(s): 12 
Gene Names: HCRTR1
Find proteins for O43613 (Homo sapiens)
Go to Gene View: HCRTR1
Go to UniProtKB:  O43613
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SOG
Query on SOG

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A, B
2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
1-S-OCTYL-BETA-D-THIOGLUCOSIDE
C14 H28 O5 S
CGVLVOOFCGWBCS-RGDJUOJXSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGW
Query on PGW

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A, B
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)]; PHOSPHATIDYLGLYCEROL
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
 Ligand Interaction
7MA
Query on 7MA

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A, B
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.907α = 90.00
b = 158.891β = 95.77
c = 182.354γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
STARANISOdata scaling
BUSTERrefinement
XDSdata reduction

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