Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 174.8 kDa 
• Atom Count: 11,322 
• Modelled Residue Count: 1,440 
• Deposited Residue Count: 1,546 
• Unique protein chains: 3

 8GNG

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

• PDB DOI:  https://doi.org/10.2210/pdb8GNG/pdb

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2022-08-23 Released: 2023-03-22 
• Deposition Author(s): Suzuki, M., Saito, J., Miyagi, H., Yasunaga, M.
• Funding Organization(s): Not funded

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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 

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

• PubMed: 36894319 
• 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 receptor (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 co-crystal 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 {plus minus} 0.01 for human receptor) with a very low dissociation rate from the receptor (the dissociation kinetic rate constant = 0.016 {plus minus} 0.006 min ^-1 for human receptor). In particular, in vitro functional studies indicated that KW-6356 exhibits insurmountable antagonism and inverse agonism, while 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, while 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 difference 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, while 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.

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Organizational Affiliation: 

Biomedical Science Research Laboratories 1, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Japan [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a	A, D [auth X]	333	Homo sapiens	Mutation(s): 5  Gene Names: ADORA2A, ADORA2
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens) Explore P29274  Go to UniProtKB:  P29274
PHAROS:  P29274

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody fab fragment light chain	B [auth L], E [auth Y]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody fab fragment heavy chain	C [auth H], F [auth Z]	226	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQ9 (Subject of Investigation/LOI)	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	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	O [auth L], V [auth Y]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	L [auth A], U [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 74.59	α = 97.72
b = 134.84	β = 91.44
c = 42.15	γ = 89.38

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Suzuki, M., Saito, J., Miyagi, H., Yasunaga, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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