7L1V

Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation.

Hong, C.Byrne, N.J.Zamlynny, B.Tummala, S.Xiao, L.Shipman, J.M.Partridge, A.T.Minnick, C.Breslin, M.J.Rudd, M.T.Stachel, S.J.Rada, V.L.Kern, J.C.Armacost, K.A.Hollingsworth, S.A.O'Brien, J.A.Hall, D.L.McDonald, T.P.Strickland, C.Brooun, A.Soisson, S.M.Hollenstein, K.

(2021) Nat Commun 12: 815-815

  • DOI: 10.1038/s41467-021-21087-6
  • Primary Citation of Related Structures:  
    7L1U, 7L1V

  • PubMed Abstract: 
  • Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OX 2 R) have shown promise as novel therapeutics that directly target the pathophysiology of the disease ...

    Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OX 2 R) have shown promise as novel therapeutics that directly target the pathophysiology of the disease. However, identification of drug-like OX 2 R agonists has proven difficult. Here we report cryo-electron microscopy structures of active-state OX 2 R bound to an endogenous peptide agonist and a small-molecule agonist. The extended carboxy-terminal segment of the peptide reaches into the core of OX 2 R to stabilize an active conformation, while the small-molecule agonist binds deep inside the orthosteric pocket, making similar key interactions. Comparison with antagonist-bound OX 2 R suggests a molecular mechanism that rationalizes both receptor activation and inhibition. Our results enable structure-based discovery of therapeutic orexin agonists for the treatment of NT1 and other hypersomnia disorders.


    Organizational Affiliation

    Computational & Structural Chemistry, MRL, Merck & Co., Inc, West Point, PA, USA. kaspar.hollenstein@merck.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Engineered Guanine nucleotide-binding protein subunit alphaA244Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B349Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
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UniProt GroupP62873
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C71Homo sapiensMutation(s): 1 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
single-chain antibody Fv fragment (svFv16)D [auth H]250Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Hypocretin receptor type 2E [auth R]374Homo sapiensMutation(s): 0 
Gene Names: HCRTR2
Membrane Entity: Yes 
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Find proteins for O43614 (Homo sapiens)
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PHAROS:  O43614
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Synthetic nanobody 51 (Sb51)F [auth S]118Lama glamaMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XGD (Subject of Investigation/LOI)
Query on XGD

Download Ideal Coordinates CCD File 
G [auth R]4'-methoxy-N,N-dimethyl-3'-{[3-(2-{[2-(2H-1,2,3-triazol-2-yl)benzene-1-carbonyl]amino}ethyl)phenyl]sulfamoyl}[1,1'-biphenyl]-3-carboxamide
C33 H32 N6 O5 S
AMTAVIZAVFJXIJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references