SMTL ID : 6tos.1 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with GSK1059865

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

1 x NRE: [(2~{S},5~{S})-2-[[(5-bromanylpyridin-2-yl)amino]methyl]-5-methyl-piperidin-1-yl]-(3-fluoranyl-2-methoxy-phenyl)methanone(Non-covalent)

NRE.1: 18 residues within 4Å: Chain A: C.75, A.78, S.79, W.88, I.98, P.99, Q.102, A.103, V.106, Q.155, E.180, H.192, F.195, I.258, N.262, H.288, V.291, Y.292 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.99, A:Q.102, A:Q.102, A:A.103, A:F.195, A:F.195 Hydrogen bonds: A:N.262 Water bridges: A:Q.155 pi-Stacking: A:H.288

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: D.179, K.265, G.269, M.270, R.272 Ligands: CIT.3, CIT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.269 Water bridges: A:R.266

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 9 residues within 4Å: Chain A: W.182, D.185, P.188, K.189, K.265, R.266, G.269, R.272 Ligands: PG4.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.188 Hydrogen bonds: A:G.269, A:R.272 Water bridges: A:R.266 Salt bridges: A:K.189, A:R.266, A:R.272 CIT.4: 7 residues within 4Å: Chain A: K.265, F.271, R.277, V.280, Y.281, F.284 Ligands: PG4.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.280, A:Y.281, A:F.284 Hydrogen bonds: A:K.265, A:Y.281 Salt bridges: A:K.265, A:K.265, A:R.277

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: R.120, A.123, Q.233, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.233 Salt bridges: A:R.120, A:R.237 SO4.6: 4 residues within 4Å: Chain A: K.239, S.306, G.307, K.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.307, A:K.308 Salt bridges: A:K.308

12 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

SOG.7: 6 residues within 4Å: Chain A: D.185, L.186, K.189, S.193 Ligands: SOG.12, SOG.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.189 Hydrogen bonds: A:D.185 SOG.8: 4 residues within 4Å: Chain A: A.157, R.181, W.182, A.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.183 Water bridges: A:A.157 SOG.9: 5 residues within 4Å: Chain A: L.25, A.28, F.286, W.289 Ligands: SOG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.25, A:A.28, A:F.286, A:W.289 SOG.10: 7 residues within 4Å: Chain A: Y.17, Q.20, Y.21, V.24, A.282, T.285 Ligands: SOG.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.17, A:Q.20, A:Y.21, A:V.24, A:T.285 SOG.11: 4 residues within 4Å: Chain A: L.89, F.90, G.91, L.94 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.90 SOG.12: 4 residues within 4Å: Chain A: K.189, V.267, F.268 Ligands: SOG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.189, A:K.189 SOG.13: 6 residues within 4Å: Chain A: K.96, Y.100, L.149, V.153, A.156, A.157 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:Y.100, A:L.149 Water bridges: A:K.96 SOG.14: 4 residues within 4Å: Chain A: W.121, H.126, Q.213 Ligands: SOG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.121, A:Q.213 SOG.15: 2 residues within 4Å: Chain A: A.279, A.283 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.279, A:A.283 SOG.16: 8 residues within 4Å: Chain A: W.12, R.13, Y.17, A.274, S.275, D.276, R.277, E.278 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.277, A:E.278, A:E.278 Hydrogen bonds: A:W.12 Water bridges: A:R.13 SOG.17: 3 residues within 4Å: Chain A: Q.213, R.216 Ligands: SOG.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.213, A:R.216 SOG.18: 1 residues within 4Å: Ligands: SOG.7 No protein-ligand interaction detected (PLIP)

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

NA.19: 5 residues within 4Å: Chain A: D.68, A.109, F.251, Y.255, N.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.68, A:N.294 Water bridges: A:S.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rappas, M. et al., Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis. J.Med.Chem. (2020)

Release Date

2020-01-15

Peptides

Orexin receptor type 1: 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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Orexin receptor type 1

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