8DU3 | pdb_00008du3

Crystal structure of A2AAR-StaR2-bRIL in complex with compound 21a

PDB DOI: https://doi.org/10.2210/pdb8DU3/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM

Deposited: 2022-07-26 Released: 2022-08-10
Deposition Author(s): Shiriaeva, A., Stauch, B., Han, G.W., Cherezov, V.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.189 (Depositor), 0.196 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

High ligand efficiency quinazoline compounds as novel A 2A adenosine receptor antagonists.

Bolteau, R., Duroux, R., Laversin, A., Vreulz, B., Shiriaeva, A., Stauch, B., Han, G.W., Cherezov, V., Renault, N., Barczyk, A., Ravez, S., Coevoet, M., Melnyk, P., Liberelle, M., Yous, S.

(2022) Eur J Med Chem 241: 114620-114620

PubMed: 35933788 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2022.114620
Primary Citation Related Structures:
8DU3

PubMed Abstract:
The past fifty years have been marked by the surge of neurodegenerative diseases. Unfortunately, current treatments are only symptomatic. Hence, the search for new and innovative therapeutic targets for curative treatments becomes a major challenge. Among these targets, the adenosine A _2A receptor (A _2AAR) has been the subject of much research in recent years. In this paper, we report the design, synthesis and pharmacological analysis of quinazoline derivatives as A _2AAR antagonists with high ligand efficiency. This class of molecules has been discovered by a virtual screening and bears no structural semblance with reference antagonist ZM-241385. More precisely, we identified a series of 2-aminoquinazoline as promising A _2AAR antagonists. Among them, one compound showed a high affinity towards A _2AAR (21a, K _i = 20 nM). We crystallized this ligand in complex with A _2AAR, confirming one of our predicted docking poses and opening up possibilities for further optimization to derive selective ligands for specific adenosine receptor subtypes.

Organizational Affiliation

Univ. Lille, Inserm, CHU Lille, U1172, LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France.

Macromolecule Content

Total Structure Weight: 57.35 kDa
Atom Count: 3,466
Modeled Residue Count: 390
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a, soluble cytochrome b562 chimera,Soluble cytochrome b562,Adenosine receptor A2a	A	447	Homo sapiens	Mutation(s): 12 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0ABE7 P29274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
TKO (Subject of Investigation/LOI) Query on TKO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4M)-6-bromo-4-(furan-2-yl)quinazolin-2-amine C₁₂ H₈ Br N₃ O XDIROSBRBKJBMH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain S [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain S [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain S [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [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], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]