SMTL ID : 7aro.1

Crystal structure of the non-ribose partial agonist LUF5833 bound to the adenosine A2A receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.12 Å

Oligo State

homo-dimer

Ligands

2 x RVZ: 2-azanyl-6-(1~{H}-imidazol-2-ylmethylsulfanyl)-4-phenyl-pyridine-3,5-dicarbonitrile(Non-covalent)

RVZ.1: 13 residues within 4Å: Chain A: A.72, V.93, L.94, F.177, E.178, M.186, W.351, L.354, N.358, L.372, M.375, Y.376, I.379 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.93, A:L.94, A:F.177, A:W.351, A:L.354, A:I.379 Hydrogen bonds: A:E.178, A:N.358 pi-Stacking: A:F.177 RVZ.8: 13 residues within 4Å: Chain B: A.72, V.93, L.94, F.177, E.178, M.186, W.351, L.354, N.358, L.372, M.375, Y.376, I.379 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.93, B:L.94, B:F.177, B:W.351, B:L.354, B:I.379 Hydrogen bonds: B:E.178, B:N.358 pi-Stacking: B:F.177

8 x OLA: OLEIC ACID(Non-covalent)

OLA.2: 5 residues within 4Å: Chain A: G.14, V.17, Y.18, V.21, Y.376 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.17, A:Y.18, A:Y.376 Hydrogen bonds: A:G.14 OLA.3: 4 residues within 4Å: Chain A: C.37, W.41, V.55, A.59 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.55 OLA.4: 2 residues within 4Å: Chain A: M.149, L.150 No protein-ligand interaction detected (PLIP) OLA.5: 2 residues within 4Å: Chain A: W.138, F.142 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.138 OLA.9: 5 residues within 4Å: Chain B: G.14, V.17, Y.18, V.21, Y.376 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.17, B:Y.18, B:Y.376 Hydrogen bonds: B:G.14 OLA.10: 4 residues within 4Å: Chain B: C.37, W.41, V.55, A.59 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.55 OLA.11: 2 residues within 4Å: Chain B: M.149, L.150 No protein-ligand interaction detected (PLIP) OLA.12: 2 residues within 4Å: Chain B: W.138, F.142 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.138

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 6 residues within 4Å: Chain A: F.191, L.196, C.359, F.360, F.363, C.364 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.191, A:L.196, A:F.360, A:F.360, A:F.360, A:F.360, A:F.363, A:F.363 CLR.13: 6 residues within 4Å: Chain B: F.191, L.196, C.359, F.360, F.363, C.364 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.191, B:L.196, B:F.360, B:F.360, B:F.360, B:F.360, B:F.363, B:F.363

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

NA.7: 3 residues within 4Å: Chain A: D.61, S.100, N.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.61, A:S.100 NA.14: 3 residues within 4Å: Chain B: D.61, S.100, N.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.100, B:N.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amelia, T. et al., Crystal Structure and Subsequent Ligand Design of a Nonriboside Partial Agonist Bound to the Adenosine A 2A Receptor. J.Med.Chem. (2021)

Release Date

2021-04-07

Peptides

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

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

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