SMTL ID : 6tot.1 (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: 21 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, E.180, F.195, Y.255, I.258, S.259, N.262, H.288, V.291, Y.292 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.82, A:Q.102, A:F.195, A:I.258, A:I.258, A:I.258 Hydrogen bonds: A:Q.102 Water bridges: A:N.262 pi-Stacking: A:H.288

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

PG4.2: 4 residues within 4Å: Chain A: K.96, Y.100, V.153, A.156 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: R.120, Q.233, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.233 Salt bridges: A:R.120, A:R.237 SO4.4: 4 residues within 4Å: Chain A: K.239, S.306, G.307, K.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.307, A:K.308 Salt bridges: A:K.308

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

SOG.5: 9 residues within 4Å: Chain A: R.13, D.14, Y.17, P.18, Y.21, A.22, L.25, I.84, E.278 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.17, A:P.18, A:Y.21, A:A.22, A:L.25, A:I.84 Water bridges: A:D.14 SOG.6: 5 residues within 4Å: Chain A: K.189, S.193, V.267, F.268 Ligands: SOG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.189, A:V.267 Hydrogen bonds: A:K.189 SOG.7: 4 residues within 4Å: Chain A: D.185, L.186, K.189 Ligands: SOG.6 No protein-ligand interaction detected (PLIP) SOG.8: 4 residues within 4Å: Chain A: R.181, W.182, A.183 Ligands: PGW.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.181, A:A.183

2 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: 13 residues within 4Å: Chain A: A.150, I.151, M.152, V.153, P.154, A.157, V.158, I.190, Y.191, C.194, V.198 Ligands: SOG.8, PGW.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.150, A:I.151, A:V.153, A:V.153, A:P.154, A:V.158, A:I.190, A:Y.191, A:Y.191, A:V.198 Hydrogen bonds: A:A.157 PGW.10: 9 residues within 4Å: Chain A: S.114, L.118, W.121, A.202, L.206, M.209, A.210, Q.213 Ligands: PGW.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.118, A:W.121, A:M.209, A:A.210, 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

2020-01-15

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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