SMTL ID : 9h37.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: D.61, S.100, N.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.61, A:S.100 Water bridges: A:D.61

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 8 residues within 4Å: Chain A: F.71, F.79, A.81, A.82, G.85, F.88, I.89 Ligands: OLA.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.71, A:F.79, A:A.82, A:F.88 Hydrogen bonds: A:A.82 CLR.3: 13 residues within 4Å: Chain A: L.349, L.352, P.353, I.356, I.357, F.360, C.367, S.368, A.370, L.374 Ligands: OLA.7, OLA.17, OLA.18 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.349, A:L.352, A:P.353, A:P.353, A:I.356, A:I.357, A:F.360, A:L.374 Hydrogen bonds: A:S.368 CLR.4: 10 residues within 4Å: Chain A: F.191, L.196, L.352, I.356, C.359, F.360, F.363, C.364 Ligands: OLA.10, OLA.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.191, A:L.196, A:L.352, A:I.356, A:F.360, A:F.360, A:F.360, A:F.363

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

OLA.5: 8 residues within 4Å: Chain A: L.67, P.70, F.71, T.74, F.79, C.80 Ligands: CLR.2, OLA.16 Ligand excluded by PLIP OLA.6: 6 residues within 4Å: Chain A: L.199, L.203, Y.206, A.341, A.344, A.348 Ligand excluded by PLIP OLA.7: 2 residues within 4Å: Ligands: CLR.3, OLA.18 Ligand excluded by PLIP OLA.8: 3 residues within 4Å: Chain A: I.19, L.23 Ligands: OLA.16 Ligand excluded by PLIP OLA.9: 1 residues within 4Å: Chain A: V.17 Ligand excluded by PLIP OLA.10: 2 residues within 4Å: Chain A: F.363 Ligands: CLR.4 Ligand excluded by PLIP OLA.11: 11 residues within 4Å: Chain A: Y.52, V.55, S.56, L.63, F.92, G.127, A.131, I.134, W.138, F.142 Ligands: OLA.19 Ligand excluded by PLIP OLA.12: 2 residues within 4Å: Chain A: G.14, Y.376 Ligand excluded by PLIP OLA.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OLA.14: 6 residues within 4Å: Chain A: H.84, F.142, L.146, M.149 Ligands: OLA.19, OLA.24 Ligand excluded by PLIP OLA.15: 3 residues within 4Å: Chain A: S.16, T.20, L.23 Ligand excluded by PLIP OLA.16: 8 residues within 4Å: Chain A: V.66, P.70, I.73, T.74, T.77, F.79 Ligands: OLA.5, OLA.8 Ligand excluded by PLIP OLA.17: 5 residues within 4Å: Chain A: P.371, W.373, L.374, L.377 Ligands: CLR.3 Ligand excluded by PLIP OLA.18: 6 residues within 4Å: Chain A: I.356, F.360, C.367 Ligands: CLR.3, CLR.4, OLA.7 Ligand excluded by PLIP OLA.19: 7 residues within 4Å: Chain A: I.134, A.135, W.138, F.142 Ligands: OLA.11, OLA.14, OLA.24 Ligand excluded by PLIP OLA.20: 6 residues within 4Å: Chain A: C.37, V.40, W.41, Y.52, V.55, I.62 Ligand excluded by PLIP OLA.21: 6 residues within 4Å: Chain A: F.53, F.102, A.106, I.109, I.113, I.133 Ligand excluded by PLIP OLA.22: 2 residues within 4Å: Chain A: C.37, W.41 Ligand excluded by PLIP OLA.23: 4 residues within 4Å: Chain A: L.28, L.31, G.32, F.391 Ligand excluded by PLIP OLA.24: 4 residues within 4Å: Chain A: M.149, L.150 Ligands: OLA.14, OLA.19 Ligand excluded by PLIP OLA.25: 2 residues within 4Å: Chain A: Y.188, F.192 Ligand excluded by PLIP

1 x 01: 2-(furan-2-yl)-7-pyridin-4-yl-pyrrolo[2,3-d]pyrimidin-4-amine

01.26: 14 residues within 4Å: Chain A: A.72, I.75, A.90, V.93, L.94, F.177, E.178, M.186, W.351, L.354, H.355, N.358, M.375, I.379 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.94, A:F.177, A:F.177, A:W.351, A:I.379 Hydrogen bonds: A:N.358, A:N.358 pi-Stacking: A:F.177, A:F.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, M. et al., Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design. To Be Published

Release Date

2025-06-18

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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