SMTL ID : 8cu7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: R.127, A.130, P.134, E.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.134 Water bridges: A:N.138 PEG.35: 6 residues within 4Å: Chain A: Y.204, F.378, F.379, P.381 Ligands: OLA.21, OLA.33 No protein-ligand interaction detected (PLIP) PEG.36: 3 residues within 4Å: Chain A: G.183, C.184, G.185 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.185, A:E.186, A:Q.188 PEG.37: 7 residues within 4Å: Chain A: H.351, Y.411, R.412, I.413, R.414, E.415, R.417 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.411, A:R.414, A:E.415, A:R.417, A:R.417

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.2: 16 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 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 pi-Stacking: A:F.193, A:F.193

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: D.77, S.116, N.401 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.77, A:S.116 Water bridges: A:D.77, A:N.405

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

OLC.4: 8 residues within 4Å: Chain A: H.100, F.158, A.159, M.165, L.166 Ligands: OLA.27, OLA.32, OLC.40 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.158, A:F.158, A:L.166 Hydrogen bonds: A:H.100 OLC.6: 9 residues within 4Å: Chain A: G.30, Y.34, Y.392, V.396, L.397, T.400, V.404 Ligands: OLA.7, OLC.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.392, A:V.396, A:L.397, A:T.400, A:V.404 Water bridges: A:G.30 OLC.22: 3 residues within 4Å: Chain A: W.389 Ligands: OLC.6, OLA.15 No protein-ligand interaction detected (PLIP) OLC.23: 2 residues within 4Å: Chain A: W.57, L.58 No protein-ligand interaction detected (PLIP) OLC.38: 6 residues within 4Å: Chain A: I.28, S.31, I.35, T.93 Ligands: OLA.17, OLA.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.35, A:T.93 Hydrogen bonds: A:S.31 OLC.39: 3 residues within 4Å: Ligands: OLA.12, OLA.17, OLA.31 No protein-ligand interaction detected (PLIP) OLC.40: 5 residues within 4Å: Chain A: H.100, G.101 Ligands: OLC.4, CLR.9, OLA.27 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.100

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

OLA.5: 12 residues within 4Å: Chain A: C.53, V.56, W.57, Q.63, Y.68, V.71, A.75, I.78, L.79 Ligands: OLA.8, OLA.19, OLA.24 Ligand excluded by PLIP OLA.7: 10 residues within 4Å: Chain A: I.41, I.358, T.400, V.403, V.404, F.407, I.408, Y.411, R.412 Ligands: OLC.6 Ligand excluded by PLIP OLA.8: 4 residues within 4Å: Chain A: W.57 Ligands: OLA.5, OLA.24, OLA.27 Ligand excluded by PLIP OLA.12: 7 residues within 4Å: Chain A: V.82, T.90, T.93, F.95 Ligands: OLA.17, OLA.31, OLC.39 Ligand excluded by PLIP OLA.13: 6 residues within 4Å: Chain A: L.121, F.205, A.209, C.210, P.214, L.217 Ligand excluded by PLIP OLA.14: 8 residues within 4Å: Chain A: F.118, L.121, A.122, I.125, D.126, V.141, I.149 Ligands: OLA.30 Ligand excluded by PLIP OLA.15: 7 residues within 4Å: Chain A: P.387, W.389, L.390, L.393 Ligands: CLR.10, OLC.22, OLA.28 Ligand excluded by PLIP OLA.16: 5 residues within 4Å: Chain A: L.44, L.47, G.48, F.407, V.428 Ligand excluded by PLIP OLA.17: 3 residues within 4Å: Ligands: OLA.12, OLC.38, OLC.39 Ligand excluded by PLIP OLA.18: 5 residues within 4Å: Chain A: S.32, I.35, T.36, L.39 Ligands: OLC.38 Ligand excluded by PLIP OLA.19: 4 residues within 4Å: Chain A: C.53, W.54, W.57 Ligands: OLA.5 Ligand excluded by PLIP OLA.20: 4 residues within 4Å: Chain A: A.357, I.358, G.361 Ligands: OLA.26 Ligand excluded by PLIP OLA.21: 6 residues within 4Å: Chain A: Y.204, L.212, V.213, L.216 Ligands: OLA.33, PEG.35 Ligand excluded by PLIP OLA.24: 10 residues within 4Å: Chain A: Y.68, V.71, S.72, A.75, L.79, G.143, W.154, F.158 Ligands: OLA.5, OLA.8 Ligand excluded by PLIP OLA.25: 5 residues within 4Å: Chain A: L.216, G.220, L.223, R.224, A.227 Ligand excluded by PLIP OLA.26: 7 residues within 4Å: Chain A: L.212, L.215, L.216, L.219, Y.222 Ligands: CLR.11, OLA.20 Ligand excluded by PLIP OLA.27: 6 residues within 4Å: Chain A: F.104, F.158, L.162 Ligands: OLC.4, OLA.8, OLC.40 Ligand excluded by PLIP OLA.28: 5 residues within 4Å: Chain A: L.365, P.369, L.393 Ligands: CLR.10, OLA.15 Ligand excluded by PLIP OLA.29: 3 residues within 4Å: Chain A: Y.128, I.129, V.221 Ligand excluded by PLIP OLA.30: 2 residues within 4Å: Chain A: L.140 Ligands: OLA.14 Ligand excluded by PLIP OLA.31: 10 residues within 4Å: Chain A: V.82, L.83, P.86, F.87, T.90, F.95, C.96 Ligands: CLR.9, OLA.12, OLC.39 Ligand excluded by PLIP OLA.32: 3 residues within 4Å: Chain A: M.165, L.166 Ligands: OLC.4 Ligand excluded by PLIP OLA.33: 6 residues within 4Å: Chain A: F.208, L.212, F.379 Ligands: CLR.11, OLA.21, PEG.35 Ligand excluded by PLIP

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 6 residues within 4Å: Chain A: A.97, A.98, G.101, I.105 Ligands: OLA.31, OLC.40 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.97, A:A.98, A:I.105 Hydrogen bonds: A:A.98 Water bridges: A:Q.188 CLR.10: 9 residues within 4Å: Chain A: L.368, P.369, I.373, F.376, C.383, S.384, L.390 Ligands: OLA.15, OLA.28 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.368, A:P.369, A:P.369, 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.26, OLA.33 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 Water bridges: A:F.379

1 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.34: 8 residues within 4Å: Chain A: N.67, V.70, I.123, A.352, S.355, A.356, Y.409, I.413 No protein-ligand interaction detected (PLIP)

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

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