9H37: Adenosine receptor A2a,Soluble cytochrome b562

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 9, a novel nanomolar A2A receptor antagonist from modern hit-finding with structure-guided de novo design. Determined by X-ray diffraction at 1.72 Å resolution. Released 18 Jun 2025.

Method: X-ray diffraction
Resolution: 1.72 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 1
Atoms: 3,585
Mol. weight: 55.39 kDa
Ligands: CLR, OLA, A1IR0
Released: 18 Jun 2025

Explore 9H37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H37 contains 23 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-33	32
α-helix	35-37	3
α-helix	40-54	15
α-helix	55-59	5
α-helix	60-67	8
β-strand	71-73	3	1
α-helix	74-107	34
α-helix	109-115	7
α-helix	118-136	19
α-helix	138-141	4
α-helix	151-156	6
β-strand	163-165	3	1
α-helix	168-171	4
α-helix	174-175	2
α-helix	176-187	12
α-helix	188-1018	39
α-helix	1023-1040	18
α-helix	1061-1080	20
α-helix	1084-1092	9
α-helix	1094-1097	4
α-helix	1098-1102	5
α-helix	1103-258	44
α-helix	263-266	4
α-helix	267-291	25
α-helix	293-304	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenosine receptor A2a,Soluble cytochrome b562	A	protein	433	Homo sapiens, Escherichia coli	P29274 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9H37_1 Adenosine receptor A2a,Soluble cytochrome b562 (chains A)
DYKDDDDGAPPIMGSSVYITVELAIAVLAILGNVLVCWAVWLNSNLQNVTNYFVVSLAAA
DILVGVLAIPFAITISTGFCAACHGCLFIACFVLVLAQSSIFSLLAIAIDRYIAIAIPLR
YNGLVTGTRAAGIIAICWVLSFAIGLTPMLGWNNCGQPKEGKAHSQGCGEGQVACLFEDV
VPMNYMVYFNFFACVLVPLLLMLGVYLRIFAAARRQLADLEDNWETLNDNLKVIEKADNA
AQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGK
VKEAQAAAEQLKTTRNAYIQKYLERARSTLQKEVHAAKSAAIIAGLFALCWLPLHIINCF
TFFCPDCSHAPLWLMYLAIVLAHTNSVVNPFIYAYRIREFRQTFRKIIRSHVLRQQEPFK
AAAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	3
OLA	Oleic acid	C18 H34 O2	21
A1IR0	2-(furan-2-yl)-7-pyridin-4-yl-pyrrolo[2,3-d]pyrimidin-4-amine	C15 H11 N5 O	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Identification of nanomolar adenosine A 2A receptor ligands using reinforcement learning and structure-based drug design. Thomas, M., Matricon, P.G., Gillespie, R.J. et al. Nat Commun (2025) 16:5485-5485. DOI 10.1038/s41467-025-60629-0 · PubMed

Other PDB entries of the same protein (UniProt P29274 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NM4 1.7 Å, A2A Adenosine receptor room-temperature structure determined by serial femtosecond…
5IU4 1.72 Å, Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with…
9H2X 1.75 Å, Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with…
4EIY 1.8 Å, Crystal structure of the chimeric protein of A2aAR-BRIL in complex with ZM241385 at 1.8A…
6LPJ 1.8 Å, A2AR crystallized in EROCOC17+4, LCP-SFX at 277 K
6LPK 1.8 Å, A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K
7IO5 1.84 Å, Crystal structure of A2A in complex with FU12-45
7IPE 1.84 Å, Crystal structure of A2A in complex with FU428-8
6PS7 1.85 Å, XFEL A2aR structure by ligand exchange from LUF5843 to ZM241385.
5OLG 1.87 Å, Structure of the A2A-StaR2-bRIL562-ZM241385 complex at 1.86A obtained from in meso…
7IPC 1.87 Å, Crystal structure of A2A in complex with FU336-61
7IOZ 1.88 Å, Crystal structure of A2A in complex with FU223-7

Browse structure collections

About this viewer

MolViewer shows 9H37 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.