SMTL ID : 6tp6.2 (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: 21 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, N.294, H.320, V.323, Y.324 Ligands: PG4.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.98, A:Q.102, A:Q.102, A:Q.155, A:F.195, A:F.195 Hydrogen bonds: A:Q.102, A:N.294

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

PG4.2: 9 residues within 4Å: Chain A: S.79, V.82, D.83, M.159, C.178, D.179, E.180, H.320 Ligands: NT5.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.82 Hydrogen bonds: A:D.179, A:E.180

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: 4 residues within 4Å: Chain A: K.271, S.338, G.339, K.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.339, A:K.340 Salt bridges: A:K.271, A:K.340

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

SOG.5: 6 residues within 4Å: Chain A: A.73, I.74, P.77, F.90, L.94, R.173 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.77, A:F.90, A:L.94 Hydrogen bonds: A:R.173, A:R.173 SOG.6: 4 residues within 4Å: Chain A: L.186, K.189, S.193, V.299 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.299 Hydrogen bonds: A:K.189 SOG.7: 6 residues within 4Å: Chain A: V.158, R.181, W.182, A.183, D.184, A.187 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.184 Hydrogen bonds: A:R.181, A:R.181, A:A.183, A:D.184, A:D.184 SOG.8: 2 residues within 4Å: Chain A: L.204, L.281 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.281

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.9: 10 residues within 4Å: Chain A: S.114, A.202, G.205, L.206, M.209, A.210, F.212, Q.213, R.216, R.221 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.206, A:M.209 Hydrogen bonds: A:Q.213, A:R.216, A:R.216

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
B

Membrane

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

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