SMTL ID : 6tp6.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

1 x NT5: [(2~{R},5~{R})-5-[(5-fluoranylpyridin-2-yl)oxymethyl]-2-methyl-piperidin-1-yl]-(5-methyl-2-pyrimidin-2-yl-phenyl)methanone(Non-covalent)

NT5.1: 22 residues within 4Å: Chain A: C.75, A.78, S.79, V.82, W.88, I.98, P.99, Q.102, A.103, V.106, Q.155, E.180, H.192, F.195, Y.287, I.290, S.291, N.294, H.320, V.323, Y.324 Ligands: PG4.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.98, A:Q.102, A:Q.155, A:F.195, A:H.320 Hydrogen bonds: A:Q.102, A:N.294

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

PG4.2: 9 residues within 4Å: Chain A: D.83, E.86, M.159, E.180, K.297, F.316, T.317, H.320 Ligands: NT5.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.180, A:E.180, A:T.317, A:T.317 Water bridges: A:K.297

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

SO4.3: 4 residues within 4Å: Chain A: R.120, A.123, Q.265, R.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.265 Salt bridges: A:R.120, A:R.269 SO4.4: 5 residues within 4Å: Chain A: K.271, L.337, S.338, G.339, K.340 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.337, A:G.339, A:K.340 Salt bridges: A:K.271, A:K.340

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

SOG.5: 10 residues within 4Å: Chain A: R.13, D.14, Y.17, P.18, Y.21, A.22, L.25, I.84, E.310 Ligands: SOG.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.17, A:P.18, A:A.22, A:L.25, A:I.84 SOG.6: 4 residues within 4Å: Chain A: K.189, S.193, V.299, F.300 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.189, A:V.299 Hydrogen bonds: A:K.189 SOG.7: 4 residues within 4Å: Chain A: R.181, W.182, A.183, A.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.181, A:A.183 SOG.8: 4 residues within 4Å: Chain A: W.12, R.13, Y.17 Ligands: SOG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13 Water bridges: A:Y.17 SOG.9: 4 residues within 4Å: Chain A: L.25, A.28, F.318, W.321 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.25, A:F.318, A:W.321, A:W.321

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: V.82, C.178 Ligand excluded by PLIP

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

PGW.11: 10 residues within 4Å: Chain A: S.114, W.121, V.198, A.202, G.205, L.206, M.209, A.210, F.212, Q.213 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.121, A:L.206, A:M.209, A:A.210, A:Q.213 Hydrogen bonds: A:Q.213

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

2020-01-01

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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