SMTL ID : 6tp3.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

monomer

Ligands

1 x NS2: [(2~{S})-2-(6-chloranyl-7-methyl-1~{H}-benzimidazol-2-yl)-2-methyl-pyrrolidin-1-yl]-[5-methoxy-2-(1,2,3-triazol-2-yl)phenyl]methanone(Non-covalent)

NS2.1: 19 residues within 4Å: Chain A: C.75, S.79, V.82, D.83, W.88, I.98, P.99, Q.102, A.103, V.106, Q.155, E.180, H.192, F.195, Y.287, N.294, H.320, V.323, Y.324 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.98, A:P.99, A:Q.102, A:Q.102, A:Q.155, A:H.320 Hydrogen bonds: A:N.294

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

SO4.2: 3 residues within 4Å: Chain A: R.120, A.123, R.269 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.120, A:R.269

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.3: 11 residues within 4Å: Chain A: S.114, L.118, W.121, V.198, G.205, L.206, M.209, A.210, F.212, Q.213, R.216 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.118, A:W.121, A:W.121, A:L.206, A:L.206, A:M.209, A:A.210, A:Q.213 Hydrogen bonds: A:Q.213 Salt bridges: A:R.216

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

SOG.4: 5 residues within 4Å: Chain A: D.184, D.185, L.186, K.189 Ligands: SOG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.184, A:D.185, A:L.186 Hydrogen bonds: A:K.189 SOG.5: 5 residues within 4Å: Chain A: K.189, S.193, V.299, F.300 Ligands: SOG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.189 SOG.6: 1 residues within 4Å: Chain A: W.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.219 SOG.7: 4 residues within 4Å: Chain A: L.25, A.28, F.318, W.321 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.25, A:F.318, A:W.321 SOG.8: 2 residues within 4Å: Chain A: L.89, F.90 No protein-ligand interaction detected (PLIP) SOG.9: 2 residues within 4Å: Chain A: H.126, Q.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.213 SOG.10: 7 residues within 4Å: Chain A: K.96, A.157, R.181, W.182, A.183, D.184, A.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181, A:A.183, A:D.184

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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