6ZDV | pdb_00006zdv

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 5d

• PDB DOI: https://doi.org/10.2210/pdb6ZDV/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Trichoplusia ni
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2020-06-15 Released: 2020-09-16 
• Deposition Author(s): Verdon, G., Jespers, W., Azuaje, J., Majellaro, M., Keranen, H., Garcia-mera, X., Congreve, M., Deflorian, F., de Graaf, C., Zhukov, A., Dore, A., Mason, J., Aqvist, J., Cooke, R., Sotelo, E., Gutierrez-de-Teran, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists.

Jespers, W., Verdon, G., Azuaje, J., Majellaro, M., Keranen, H., Garcia-Mera, X., Congreve, M., Deflorian, F., de Graaf, C., Zhukov, A., Dore, A.S., Mason, J.S., Aqvist, J., Cooke, R.M., Sotelo, E., Gutierrez-de-Teran, H.

(2020) Angew Chem Int Ed Engl 59: 16536-16543

• PubMed: 32542862 
• DOI: https://doi.org/10.1002/anie.202003788
• Primary Citation Related Structures: 
  6ZDR, 6ZDV


• PubMed Abstract: 
  

  We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A _2A adenosine receptor (AR). Eight A _2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A _2A AR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A _2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A _2A AR, an emerging target in immuno-oncology.

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Organizational Affiliation: 
• Department of Cell and Molecular Biology, Uppsala University, BMC, Biomedical Center, Box 596, Uppsala, Sweden.
Sosei Heptares, Steinmetz Granta Park, Great Abington, Cambridge, CB21 6DG, UK.
Departament of Organic Chemistry, Faculty of Farmacy, Universidade de Santiago de Compostela, Spain.
Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Spain.
Present address: H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.2 kDa 
• Atom Count: 3,331 
• Modeled Residue Count: 382 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a	A	433	Homo sapiens, Escherichia coli	Mutation(s): 0  Gene Names: ADORA2A, ADORA2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens) Explore P29274  Go to UniProtKB:  P29274
PHAROS:  P29274 GTEx:  ENSG00000128271
UniProt Groups	P0ABE7P29274

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	D [auth A], E [auth A], F [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
QGW (Subject of Investigation/LOI)	B [auth A]	[2-methyl-3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl] ethanoate C19 H19 N O4 S NVGMNXGIQPMJSN-UHFFFAOYSA-N
OLB	G [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLC	V [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.414	α = 90
b = 179.833	β = 90
c = 140.085	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Verdon, G., Jespers, W., Azuaje, J., Majellaro, M., Keranen, H., Garcia-mera, X., Congreve, M., Deflorian, F., de Graaf, C., Zhukov, A., Dore, A., Mason, J., Aqvist, J., Cooke, R., Sotelo, E., Gutierrez-de-Teran, H.

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-12-16
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary