SMTL ID : 6tq4.1 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with Compound 16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NV8: 2-[1-(phenylsulfonyl)-1,8-diazaspiro[4.5]decan-8-yl]-1,3-benzoxazole(Non-covalent)

NV8.1: 19 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, Y.287, I.290, S.291, N.294, Y.324 Ligands: SOG.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.88, A:I.98, A:Q.102, A:V.106, A:F.195, A:Y.287, A:I.290, A:I.290 Water bridges: A:N.294

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

SO4.2: 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 SO4.3: 4 residues within 4Å: Chain A: K.271, 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

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.4: 11 residues within 4Å: Chain A: S.114, L.118, W.121, V.198, A.202, P.203, L.206, M.209, A.210, Q.213, R.216 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.118, A:W.121, A:A.202, A:L.206, A:M.209, A:A.210 Hydrogen bonds: A:Q.213 Salt bridges: A:R.216

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

SOG.5: 8 residues within 4Å: Chain A: R.13, D.14, Y.17, P.18, Y.21, A.22, I.84, E.310 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.17, A:P.18, A:Y.21, A:A.22, A:I.84 Hydrogen bonds: A:D.14 SOG.6: 4 residues within 4Å: Chain A: F.115, R.136, G.139, S.140 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.115, A:F.115 SOG.7: 5 residues within 4Å: Chain A: K.189, S.193, V.299, F.300 Ligands: SOG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.299 SOG.8: 3 residues within 4Å: Chain A: L.186, K.189 Ligands: SOG.7 No protein-ligand interaction detected (PLIP) SOG.9: 1 residues within 4Å: Chain A: L.129 No protein-ligand interaction detected (PLIP) SOG.10: 15 residues within 4Å: Chain A: S.79, V.82, E.86, S.87, W.88, Q.102, V.177, C.178, D.179, K.297, H.320, V.323, Y.324 Ligands: NV8.1, SOG.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.323, A:Y.324 Hydrogen bonds: A:C.178, A:K.297, A:K.297 SOG.11: 4 residues within 4Å: Chain A: R.181, A.183, D.184, A.187 No protein-ligand interaction detected (PLIP) SOG.12: 3 residues within 4Å: Chain A: K.297, F.303 Ligands: SOG.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.297

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

NA.13: 4 residues within 4Å: Chain A: D.68, F.283, Y.287, N.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.68, A:N.326

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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