SMTL ID : 8cic.1

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with clinical candidate Etrumadenant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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, A:N.385

1 x U30: 3-[2-azanyl-6-[1-[[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]methyl]-1,2,3-triazol-4-yl]pyrimidin-4-yl]-2-methyl-benzenecarbonitrile(Non-covalent)

U30.2: 18 residues within 4Å: Chain A: Y.18, A.72, I.75, S.76, V.93, L.94, A.97, L.176, F.177, E.178, M.186, W.351, L.354, H.355, N.358, L.372, Y.376, I.379 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.18, A:V.93, A:W.351, A:L.354, A:L.372, A:Y.376, A:I.379 Hydrogen bonds: A:N.358, A:N.358 Water bridges: A:I.75, A:N.190 Salt bridges: A:E.178 pi-Stacking: A:F.177

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 5 residues within 4Å: Chain A: H.84, G.85, M.149 Ligands: CLR.4, OLA.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.84 CLR.4: 8 residues within 4Å: Chain A: F.71, A.81, A.82, G.85, F.88, I.89 Ligands: CLR.3, OLC.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.71, A:F.88, A:I.89 Hydrogen bonds: A:A.82 CLR.5: 10 residues within 4Å: Chain A: L.349, L.352, P.353, I.357, F.360, C.367, S.368, A.370, L.374 Ligands: OLA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.349, A:L.352, A:P.353, A:I.357, A:F.360 Hydrogen bonds: A:S.368 Water bridges: A:S.368 CLR.6: 6 residues within 4Å: Chain A: I.356, C.359, F.360, F.363, C.364 Ligands: OLB.23 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.356, A:F.360, A:F.360, A:F.360, A:F.363

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

OLA.7: 5 residues within 4Å: Chain A: T.74, T.77, F.79 Ligands: OLC.25, OLC.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.74 Hydrogen bonds: A:T.77 OLA.8: 4 residues within 4Å: Chain A: P.371, W.373, L.377 Ligands: CLR.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.371, A:W.373, A:L.377 OLA.9: 7 residues within 4Å: Chain A: F.53, A.106, D.110, I.113, V.125, I.133, C.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.106, A:I.133 OLA.10: 5 residues within 4Å: Chain A: V.34, C.37, W.38, W.41 Ligands: OLB.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.34, A:W.41, A:W.41 Hydrogen bonds: A:W.41 OLA.11: 4 residues within 4Å: Chain A: L.199, L.203, Y.206, A.341 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.206 OLA.12: 6 residues within 4Å: Chain A: G.14, V.17, Y.376, V.380, T.384 Ligands: OLA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.17, A:Y.376, A:V.380 OLA.13: 4 residues within 4Å: Chain A: T.384, V.387, F.391 Ligands: OLA.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.384, A:V.387, A:F.391, A:F.391 OLA.14: 2 residues within 4Å: Chain A: G.345, L.346 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.346 OLA.15: 8 residues within 4Å: Chain A: H.84, F.142, A.143, L.146, M.149 Ligands: CLR.3, OLA.17, OLB.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.142, A:L.146 Salt bridges: A:H.84 OLA.16: 1 residues within 4Å: Ligands: OLC.27 No protein-ligand interaction detected (PLIP) OLA.17: 4 residues within 4Å: Chain A: A.135, F.142 Ligands: OLA.15, OLC.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.142, A:F.142 OLA.18: 1 residues within 4Å: Chain A: W.373 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.373, A:W.373 OLA.19: 5 residues within 4Å: Chain A: L.28, L.31, V.34, W.38, F.391 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.28, A:F.391 Hydrogen bonds: A:L.31 OLA.20: 3 residues within 4Å: Chain A: I.136 Ligands: OLA.21, OLB.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.136 OLA.21: 8 residues within 4Å: Chain A: T.128, R.129, G.132, I.136, V.139, L.140 Ligands: OLA.20, OLB.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.136, A:I.136, A:V.139, A:L.140

3 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.22: 7 residues within 4Å: Chain A: L.140, A.143, M.149, L.150 Ligands: OLA.15, OLA.20, OLA.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.140, A:A.143, A:L.150 OLB.23: 5 residues within 4Å: Chain A: F.192, F.363, P.365 Ligands: CLR.6, OLC.28 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.363, A:F.363, A:F.363 Hydrogen bonds: A:D.366 Water bridges: A:D.366 OLB.24: 11 residues within 4Å: Chain A: C.37, V.40, W.41, Q.47, Y.52, V.55, A.59, I.62, L.63 Ligands: OLA.10, OLC.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.41, A:I.62, A:L.63 Hydrogen bonds: A:Y.52, A:Y.52

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

OLC.25: 11 residues within 4Å: Chain A: V.66, L.67, P.70, F.71, T.74, F.79, C.80, Q.172 Ligands: CLR.4, OLA.7, OLC.27 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.66, A:L.67, A:P.70, A:F.71, A:T.74, A:F.79, A:F.79 Hydrogen bonds: A:C.80, A:C.80, A:Q.172, A:Q.172 OLC.26: 8 residues within 4Å: Chain A: Y.52, V.55, A.59, G.127, I.134, W.138 Ligands: OLA.17, OLB.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.55, A:I.134, A:W.138 OLC.27: 3 residues within 4Å: Ligands: OLA.7, OLA.16, OLC.25 No protein-ligand interaction detected (PLIP) OLC.28: 5 residues within 4Å: Chain A: Y.188, F.362, F.363, P.365 Ligands: OLB.23 No protein-ligand interaction detected (PLIP) OLC.29: 8 residues within 4Å: Chain A: P.11, I.12, S.15, S.16, I.19, T.20, S.76, T.77 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.12, A:I.19, A:T.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Claff, T. et al., Crystal structure of adenosine A 2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction. Commun Chem (2023)

Release Date

2023-05-31

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