7LD3

Cryo-EM structure of the human adenosine A1 receptor-Gi2-protein complex bound to its endogenous agonist and an allosteric ligand


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Positive allosteric mechanisms of adenosine A 1 receptor-mediated analgesia.

Draper-Joyce, C.J.Bhola, R.Wang, J.Bhattarai, A.Nguyen, A.T.N.Cowie-Kent, I.O'Sullivan, K.Chia, L.Y.Venugopal, H.Valant, C.Thal, D.M.Wootten, D.Panel, N.Carlsson, J.Christie, M.J.White, P.J.Scammells, P.May, L.T.Sexton, P.M.Danev, R.Miao, Y.Glukhova, A.Imlach, W.L.Christopoulos, A.

(2021) Nature 597: 571-576

  • DOI: https://doi.org/10.1038/s41586-021-03897-2
  • Primary Citation of Related Structures:  
    7LD3, 7LD4

  • PubMed Abstract: 

    The adenosine A 1 receptor (A 1 R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain 1,2 . However, development of analgesic orthosteric A 1 R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects 3 . Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521), a positive allosteric modulator of the A 1 R, exhibits analgesic efficacy in rats in vivo through modulation of the increased levels of endogenous adenosine that occur in the spinal cord of rats with neuropathic pain. We also report the structure of the A 1 R co-bound to adenosine, MIPS521 and a G i2 heterotrimer, revealing an extrahelical lipid-detergent-facing allosteric binding pocket that involves transmembrane helixes 1, 6 and 7. Molecular dynamics simulations and ligand kinetic binding experiments support a mechanism whereby MIPS521 stabilizes the adenosine-receptor-G protein complex. This study provides proof of concept for structure-based allosteric drug design of non-opioid analgesic agents that are specific to disease contexts.


  • Organizational Affiliation

    Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2355Homo sapiensMutation(s): 0 
Gene Names: GNAI2GNAI2B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04899 (Homo sapiens)
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Go to UniProtKB:  P04899
PHAROS:  P04899
GTEx:  ENSG00000114353 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04899
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera protein of Muscarinic acetylcholine receptor M4 and Adenosine receptor A1B [auth R]387Homo sapiensMutation(s): 0 
Gene Names: CHRM4ADORA1
Membrane Entity: Yes 
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Find proteins for P08173 (Homo sapiens)
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Go to UniProtKB:  P08173
PHAROS:  P08173
GTEx:  ENSG00000180720 
Find proteins for P30542 (Homo sapiens)
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Go to UniProtKB:  P30542
PHAROS:  P30542
GTEx:  ENSG00000163485 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP30542P08173
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]350Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XTD (Subject of Investigation/LOI)
Query on XTD

Download Ideal Coordinates CCD File 
F [auth R]{2-amino-4-[3,5-bis(trifluoromethyl)phenyl]thiophen-3-yl}(4-chlorophenyl)methanone
C19 H10 Cl F6 N O S
IVHJBJJHYFIUOA-UHFFFAOYSA-N
ADN
Query on ADN

Download Ideal Coordinates CCD File 
E [auth R]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references