SMTL ID : 6tos.2 (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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.99, A:Q.102, A:A.103, A:F.195, A:F.195 Hydrogen bonds: A:N.262

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

SO4.2: 3 residues within 4Å: Chain A: R.120, A.123, R.237 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.120, A:R.237 SO4.3: 4 residues within 4Å: Chain A: K.239, S.306, G.307, K.308 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.306, A:G.307, A:K.308 Water bridges: A:S.306 Salt bridges: A:K.308

2 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.4: 11 residues within 4Å: Chain A: S.114, L.118, V.198, G.205, L.206, M.209, A.210, Q.213, R.216 Ligands: PGW.5, SOG.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.118, A:L.206, A:L.206, A:M.209, A:A.210, A:Q.213 Hydrogen bonds: A:Q.213 PGW.5: 19 residues within 4Å: Chain A: A.150, I.151, M.152, V.153, P.154, A.157, V.158, R.181, W.182, A.183, D.184, A.187, I.190, Y.191, C.194, F.195, V.198 Ligands: PGW.4, SOG.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.150, A:I.151, A:I.151, A:V.153, A:P.154, A:W.182, A:Y.191, A:Y.191, A:Y.191, A:F.195, A:V.198 Hydrogen bonds: A:A.157, A:A.183, A:D.184

15 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)

SOG.6: 5 residues within 4Å: Chain A: L.168, R.171, T.172, R.173, F.175 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.175 Hydrogen bonds: A:T.172, A:T.172, A:R.173 Water bridges: A:A.174 SOG.7: 3 residues within 4Å: Chain A: F.90, L.94, R.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.173, A:R.173 SOG.8: 6 residues within 4Å: Chain A: K.96, Y.100, V.153, A.156, A.157 Ligands: PGW.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.100, A:Y.100, A:V.153 SOG.9: 4 residues within 4Å: Chain A: K.189, V.267, F.268 Ligands: SOG.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.189, A:K.189 Water bridges: A:R.272 SOG.10: 6 residues within 4Å: Chain A: L.256, P.257, V.260, L.261, L.264, M.270 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.261, A:L.264 SOG.11: 5 residues within 4Å: Chain A: K.265, V.280, Y.281, F.284, H.288 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.281, A:F.284, A:F.284, A:F.284 SOG.12: 9 residues within 4Å: Chain A: F.115, R.136, G.139, S.140, G.143, I.144, V.147 Ligands: PGW.4, SOG.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.147 SOG.13: 5 residues within 4Å: Chain A: V.35, V.38, N.303, F.313, F.317 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.35, A:V.38, A:N.303, A:F.313, A:F.317 SOG.14: 3 residues within 4Å: Chain A: E.86, S.87, A.174 No protein-ligand interaction detected (PLIP) SOG.15: 2 residues within 4Å: Chain A: C.125, H.126 No protein-ligand interaction detected (PLIP) SOG.16: 8 residues within 4Å: Chain A: F.115, L.118, D.119, Y.122, A.123, F.130, S.132 Ligands: SOG.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.118, A:Y.122, A:Y.122 SOG.17: 4 residues within 4Å: Chain A: Q.222, P.224, G.225, T.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.223, A:G.225, A:T.226, A:T.226, A:T.226 SOG.18: 2 residues within 4Å: Chain A: F.268 Ligands: SOG.9 No protein-ligand interaction detected (PLIP) SOG.19: 6 residues within 4Å: Chain A: Y.211, F.212, F.215, M.245, V.248 Ligands: SOG.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.211, A:V.248 SOG.20: 7 residues within 4Å: Chain A: F.215, W.219, K.242, M.245, V.246, L.249 Ligands: SOG.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.242, A:M.245, A:V.246, A:L.249

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
B

Membrane

We predict this structure to be a membrane protein.
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Orexin receptor type 1

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