SMTL ID : 6tp3.1 (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, 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.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

2 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 SO4.3: 4 residues within 4Å: Chain A: K.271, S.338, G.339, K.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.339, A:K.340 Salt bridges: A:K.340

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.4: 9 residues within 4Å: Chain A: S.114, L.118, W.121, A.202, L.206, M.209, A.210, Q.213, R.216 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.118, A:W.121, A:A.202, A:L.206, A:M.209, A:Q.213 Salt bridges: A:R.216

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

SOG.5: 8 residues within 4Å: Chain A: I.74, P.77, A.78, F.90, A.93, L.94, I.98, R.173 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.77, A:A.78, A:I.98 Hydrogen bonds: A:R.173, A:R.173 SOG.6: 3 residues within 4Å: Chain A: L.168, R.171, T.172 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.168 Hydrogen bonds: A:T.172 SOG.7: 4 residues within 4Å: Chain A: D.184, D.185, L.186 Ligands: SOG.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.184 Hydrogen bonds: A:D.185 SOG.8: 1 residues within 4Å: Chain A: L.129 No protein-ligand interaction detected (PLIP) SOG.9: 6 residues within 4Å: Chain A: R.181, W.182, A.183, D.184, A.187 Ligands: SOG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.181, A:A.183 SOG.10: 3 residues within 4Å: Chain A: K.189, V.299, F.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.189, A:V.299 SOG.11: 2 residues within 4Å: Chain A: R.13, D.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.14, A:D.14

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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