SMTL ID : 6tq7.1 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with SB-334867

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

monomer

Ligands

2 x NVK: 1-(2-methyl-1,3-benzoxazol-6-yl)-3-(1,5-naphthyridin-4-yl)urea(Non-covalent)

NVK.1: 18 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, M.152, Q.155, M.159, C.178, F.195, T.199, Y.324 Ligands: NVK.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.78, A:W.88, A:I.98, A:P.99, A:A.103, A:F.195, A:T.199 Water bridges: A:E.180 NVK.2: 17 residues within 4Å: Chain A: Y.29, C.75, S.79, D.83, Q.102, V.106, F.195, T.199, Y.200, Y.287, I.290, S.291, N.294, H.320, V.323, Y.324 Ligands: NVK.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.106, A:Y.200 Hydrogen bonds: A:T.199 pi-Stacking: A:H.320

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

SO4.3: 2 residues within 4Å: Chain A: R.120, R.269 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.120, A:R.269

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

SOG.4: 4 residues within 4Å: Chain A: R.171, T.172, R.173, F.175 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.175 Hydrogen bonds: A:T.172, A:T.172, A:R.173 SOG.5: 7 residues within 4Å: Chain A: A.157, E.160, R.181, W.182, A.183, D.184, A.187 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.160, A:R.181, A:R.181 Hydrogen bonds: A:A.183, A:D.184 SOG.6: 5 residues within 4Å: Chain A: D.185, L.186, K.189, S.193 Ligands: SOG.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.189 SOG.7: 4 residues within 4Å: Chain A: K.189, V.299, F.300 Ligands: SOG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.299 SOG.8: 4 residues within 4Å: Chain A: M.277, V.280, L.281 Ligands: SOG.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.280 SOG.9: 2 residues within 4Å: Chain A: F.215, W.219 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.215, A:W.219 SOG.10: 3 residues within 4Å: Chain A: F.212, F.215 Ligands: SOG.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.212, A:F.215, A:F.215

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: 8 residues within 4Å: Chain A: S.114, V.198, A.202, P.203, L.206, M.209, A.210, Q.213 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.202, A:P.203, A:L.206, A:L.206, A:M.209 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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