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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

1 x NRK: (1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide(Non-covalent)

NRK.1: 20 residues within 4Å: Chain A: C.75, A.78, S.79, V.82, D.83, W.88, I.98, P.99, Q.102, A.103, V.106, Q.155, F.195, Y.255, I.258, S.259, N.262, H.288, V.291, Y.292 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.82, A:Q.102, A:F.195, A:I.258 Hydrogen bonds: A:Q.102, A:A.103 pi-Stacking: A:H.288

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

SO4.2: 2 residues within 4Å: Chain A: R.120, R.237 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.120 Salt bridges: A:R.120, A:R.237 SO4.3: 4 residues within 4Å: Chain A: K.239, S.306, G.307, K.308 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.306, A:G.307, A:K.308 Water bridges: A:S.306 Salt bridges: A:K.239, A:K.308

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

SOG.4: 6 residues within 4Å: Chain A: I.74, P.77, F.90, A.93, L.94, R.173 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.77, A:F.90, A:F.90 Hydrogen bonds: A:R.173, A:R.173 SOG.5: 3 residues within 4Å: Chain A: W.121, H.126, Q.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.213, A:Q.213 SOG.6: 5 residues within 4Å: Chain A: K.96, Y.100, L.149, V.153, A.157 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.100, A:Y.100, A:L.149 SOG.7: 6 residues within 4Å: Chain A: F.115, R.136, G.139, S.140, G.143, V.147 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.115, A:F.115, A:V.147 SOG.8: 5 residues within 4Å: Chain A: K.189, I.190, S.193, V.267, F.268 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.190 Hydrogen bonds: A:K.189

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

2020-01-15

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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