8GNG

Crystal structure of human adenosine A2A receptor in complex with istradefylline.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

In Vitro Pharmacological Profile of KW-6356, a Novel Adenosine A 2A Receptor Antagonist/Inverse Agonist.

Ohno, Y.Suzuki, M.Asada, H.Kanda, T.Saki, M.Miyagi, H.Yasunaga, M.Suno, C.Iwata, S.Saito, J.I.Uchida, S.

(2023) Mol Pharmacol 103: 311-324

  • DOI: https://doi.org/10.1124/molpharm.122.000633
  • Primary Citation of Related Structures:  
    8GNE, 8GNG

  • PubMed Abstract: 

    KW-6356 is a novel adenosine A 2A (A 2A ) receptor antagonist/inverse agonist, and its efficacy as monotherapy in Parkinson's disease (PD) patients has been reported. Istradefylline is a first-generation A 2A receptor antagonist approved for use as adjunct treatment to levodopa/decarboxylase inhibitor in adult PD patients experiencing "OFF" episodes. In this study, we investigated the in vitro pharmacological profile of KW-6356 as an A 2A receptor antagonist/inverse agonist and the mode of antagonism and compared them with istradefylline. In addition, we determined cocrystal structures of A 2A receptor in complex with KW-6356 and istradefylline to explore the structural basis of the antagonistic properties of KW-6356. Pharmacological studies have shown that KW-6356 is a potent and selective ligand for the A 2A receptor (the -log of inhibition constant = 9.93 ± 0.01 for human receptor) with a very low dissociation rate from the receptor (the dissociation kinetic rate constant = 0.016 ± 0.006 minute -1 for human receptor). In particular, in vitro functional studies indicated that KW-6356 exhibits insurmountable antagonism and inverse agonism, whereas istradefylline exhibits surmountable antagonism. Crystallography of KW-6356- and istradefylline-bound A 2A receptor have indicated that interactions with His250 6.52 and Trp246 6.48 are essential for the inverse agonism, whereas the interactions at both deep inside the orthosteric pocket and the pocket lid stabilizing the extracellular loop conformation may contribute to the insurmountable antagonism of KW-6356. These profiles may reflect important differences in vivo and help predict better clinical performance. SIGNIFICANCE STATEMENT: KW-6356 is a potent and selective adenosine A 2A receptor antagonist/inverse agonist and exhibits insurmountable antagonism, whereas istradefylline, a first-generation adenosine A 2A receptor antagonist, exhibits surmountable antagonism. Structural studies of adenosine A 2A receptor in complex with KW-6356 and istradefylline explain the characteristic differences in the pharmacological properties of KW-6356 and istradefylline.


  • Organizational Affiliation

    Biomedical Science Research Laboratories 1 (Y.O., S.U.) and Molecular Analysis Center (Mi.S., H.M., J.S.), Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Shizuoka, Japan; Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.A., S.I.); R&D Planning Department, R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan (T.K.); Medical Affairs Department, Kyowa Kirin Co., Ltd., Tokyo, Japan (Ma.S.); CMC R&D Center, Production Division, Kyowa Kirin Co., Ltd., Shizuoka, Japan (M.Y.); and Department of Medical Chemistry, Kansai Medical University, Osaka, Japan (C.S.).


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine receptor A2aA,
D [auth X]
333Homo sapiensMutation(s): 5 
Gene Names: ADORA2AADORA2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29274
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody fab fragment light chainB [auth L],
E [auth Y]
214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
antibody fab fragment heavy chainC [auth H],
F [auth Z]
226Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JQ9 (Subject of Investigation/LOI)
Query on JQ9

Download Ideal Coordinates CCD File 
G [auth A],
Q [auth X]
8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione
C20 H24 N4 O4
IQVRBWUUXZMOPW-PKNBQFBNSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
M [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth A],
P [auth X],
R [auth X],
S [auth X],
T [auth X]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
K
Query on K

Download Ideal Coordinates CCD File 
O [auth L],
V [auth Y]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A],
U [auth X]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
JQ9 BindingDB:  8GNG Ki: min: 2, max: 200 (nM) from 17 assay(s)
IC50: min: 228, max: 5250 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.59α = 97.72
b = 134.84β = 91.44
c = 42.15γ = 89.38
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description