SMTL ID : 8cu6.1

Crystal structure of A2AAR-StaR2-S277-bRIL in complex with a novel A2a antagonist, LJ-4517

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

16 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.1: 8 residues within 4Å: Chain A: V.82, P.86, I.89, T.90, T.93 Ligands: OLA.20, OLA.23, OLA.24 Ligand excluded by PLIP OLA.2: 8 residues within 4Å: Chain A: L.121, I.125, I.160, F.205, A.209, C.210, P.214, L.217 Ligand excluded by PLIP OLA.3: 6 residues within 4Å: Chain A: I.28, S.32, I.35, T.36, L.39 Ligands: OLA.24 Ligand excluded by PLIP OLA.4: 5 residues within 4Å: Chain A: H.100, F.158, M.165 Ligands: OLA.6, OLA.21 Ligand excluded by PLIP OLA.6: 7 residues within 4Å: Chain A: A.98, C.99, H.100, G.101, F.104 Ligands: OLA.4, CLR.9 Ligand excluded by PLIP OLA.12: 6 residues within 4Å: Chain A: L.44, L.47, G.48, V.403, F.407, V.428 Ligand excluded by PLIP OLA.13: 6 residues within 4Å: Chain A: V.50, C.53, W.54, W.57, I.78 Ligands: OLC.15 Ligand excluded by PLIP OLA.14: 6 residues within 4Å: Chain A: I.358, G.361, L.362, A.364, L.368 Ligands: OLA.19 Ligand excluded by PLIP OLA.17: 10 residues within 4Å: Chain A: Y.68, V.71, S.72, A.75, L.79, G.143, A.147, W.154, F.158 Ligands: OLC.15 Ligand excluded by PLIP OLA.18: 6 residues within 4Å: Chain A: L.217, G.220, V.221, L.223, R.224, A.227 Ligand excluded by PLIP OLA.19: 7 residues within 4Å: Chain A: L.215, L.219, Y.222, A.357, A.360 Ligands: CLR.11, OLA.14 Ligand excluded by PLIP OLA.20: 9 residues within 4Å: Chain A: L.83, P.86, F.87, T.90, F.95, C.96 Ligands: OLA.1, CLR.9, OLA.23 Ligand excluded by PLIP OLA.21: 3 residues within 4Å: Chain A: M.165, L.166 Ligands: OLA.4 Ligand excluded by PLIP OLA.22: 4 residues within 4Å: Chain A: F.208, L.212, F.379 Ligands: CLR.11 Ligand excluded by PLIP OLA.23: 2 residues within 4Å: Ligands: OLA.1, OLA.20 Ligand excluded by PLIP OLA.24: 3 residues within 4Å: Chain A: L.39 Ligands: OLA.1, OLA.3 Ligand excluded by PLIP

3 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 1 residues within 4Å: Chain A: W.389 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.389, A:W.389, A:W.389 OLC.15: 10 residues within 4Å: Chain A: C.53, V.56, W.57, Q.63, Y.68, V.71, A.75, I.78 Ligands: OLA.13, OLA.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.57, A:V.71, A:A.75, A:I.78, A:I.78 Hydrogen bonds: A:Y.68, A:Y.68 OLC.16: 8 residues within 4Å: Chain A: G.30, Y.34, W.389, Y.392, L.393, V.396, L.397, T.400 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.392, A:V.396, A:L.397, A:T.400

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: H.385, A.386, L.388, M.391 No protein-ligand interaction detected (PLIP)

1 x LJX: (2R,3R,4R)-2-[(8P)-6-amino-2-(hex-1-yn-1-yl)-8-(thiophen-2-yl)-9H-purin-9-yl]oxolane-3,4-diol(Non-covalent)

LJX.8: 17 residues within 4Å: Chain A: A.88, I.91, S.92, V.109, L.110, F.193, E.194, M.202, W.367, L.370, H.371, N.374, L.388, M.391, Y.392, I.395, H.399 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.91, A:L.110, A:F.193, A:W.367, A:L.388, A:M.391, A:Y.392, A:I.395 Hydrogen bonds: A:E.194, A:N.374 Water bridges: A:Y.34, A:A.88 pi-Stacking: A:F.193, A:F.193

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 9 residues within 4Å: Chain A: F.87, F.95, A.97, A.98, G.101, C.102, I.105 Ligands: OLA.6, OLA.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.87, A:F.87, A:F.95, A:A.97, A:A.98 Hydrogen bonds: A:A.98 CLR.10: 8 residues within 4Å: Chain A: L.365, P.369, I.372, I.373, F.376, C.383, S.384, L.390 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.365, A:P.369, A:I.372, A:I.373, A:F.376, A:L.390 Hydrogen bonds: A:S.384, A:S.384 CLR.11: 9 residues within 4Å: Chain A: L.212, L.368, I.372, C.375, F.376, F.379, C.380 Ligands: OLA.19, OLA.22 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.212, A:L.368, A:I.372, A:F.376, A:F.376, A:F.376, A:F.379, A:F.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shiriaeva, A. et al., GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A 2A Adenosine Receptor. J.Med.Chem. (2022)

Release Date

2022-08-31

Peptides

Adenosine receptor A2a,Soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Adenosine receptor A2a,Soluble cytochrome b562