SMTL ID : 6tq9.2 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with SB-408124

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x NVN: 1-[6,8-bis(fluoranyl)-2-methyl-quinolin-4-yl]-3-[4-(dimethylamino)phenyl]urea(Non-covalent)

NVN.1: 19 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, D.179, Y.191, F.195, T.199, Y.292 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.102, A:A.103 Hydrogen bonds: A:P.99, A:Q.102 Water bridges: A:E.180 Halogen bonds: A:C.75

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

SOG.2: 3 residues within 4Å: Chain A: L.94, R.173 Ligands: SOG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.173, A:R.173 SOG.3: 7 residues within 4Å: Chain A: G.91, H.92, A.93, R.173 Ligands: SOG.2, SOG.4, SOG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.92 Hydrogen bonds: A:H.92, A:H.92, A:R.173 SOG.4: 4 residues within 4Å: Chain A: K.96, V.153 Ligands: SOG.3, SOG.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.96, A:V.153 SOG.5: 10 residues within 4Å: Chain A: K.96, A.157, E.160, R.181, W.182, A.183, D.184, A.187 Ligands: SOG.3, SOG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181, A:A.183, A:D.184 SOG.6: 2 residues within 4Å: Chain A: S.228, A.229 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.229 Hydrogen bonds: A:S.228

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

SO4.7: 4 residues within 4Å: Chain A: R.120, A.123, Q.233, R.237 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.233 Water bridges: A:R.120, A:R.120, A:R.120 Salt bridges: A:R.120, A:R.237

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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