SMTL ID : 6to7.2 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x SUV: [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone(Non-covalent)

SUV.1: 17 residues within 4Å: Chain A: A.78, S.79, V.82, W.88, I.98, P.99, Q.102, V.106, Q.155, E.180, H.192, F.195, I.258, N.262, H.288, V.291, Y.292 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.98, A:Q.102, A:Q.102, A:F.195, A:V.291 Hydrogen bonds: A:N.262

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

PG4.2: 10 residues within 4Å: Chain A: C.178, D.179, K.265, R.266, M.270, F.271, R.272, V.280, Y.281, F.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.179, A:K.265 Water bridges: A:R.272 PG4.3: 7 residues within 4Å: Chain A: L.204, A.208, Y.211, M.245, V.248, A.252 Ligands: SOG.11 No protein-ligand interaction detected (PLIP) PG4.4: 2 residues within 4Å: Chain A: R.49, N.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.50

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

SOG.5: 9 residues within 4Å: Chain A: K.189, I.190, S.193, V.267, F.268, G.269 Ligands: SOG.8, SOG.15, SOG.25 Ligand excluded by PLIP SOG.6: 11 residues within 4Å: Chain A: W.12, Y.17, Y.21, L.25, D.83, E.86, E.278, Y.281, A.282, T.285 Ligands: SOG.7 Ligand excluded by PLIP SOG.7: 11 residues within 4Å: Chain A: R.13, Y.17, P.18, A.22, W.23, I.26, I.84, T.85, E.86, R.277 Ligands: SOG.6 Ligand excluded by PLIP SOG.8: 6 residues within 4Å: Chain A: S.193, F.196, F.268 Ligands: SOG.5, SOG.14, SOG.15 Ligand excluded by PLIP SOG.9: 6 residues within 4Å: Chain A: P.77, L.81, L.89, F.90, G.91, L.94 Ligand excluded by PLIP SOG.10: 5 residues within 4Å: Chain A: K.96, Y.100, V.153, A.156, A.157 Ligand excluded by PLIP SOG.11: 6 residues within 4Å: Chain A: F.215, W.219, M.245, V.246, L.249 Ligands: PG4.3 Ligand excluded by PLIP SOG.12: 10 residues within 4Å: Chain A: K.96, A.157, V.158, M.159, E.160, R.181, W.182, A.183, D.184, A.187 Ligand excluded by PLIP SOG.13: 4 residues within 4Å: Chain A: W.121, H.126, Q.213 Ligands: PGW.26 Ligand excluded by PLIP SOG.14: 3 residues within 4Å: Chain A: F.268 Ligands: SOG.8, SOG.15 Ligand excluded by PLIP SOG.15: 9 residues within 4Å: Chain A: F.196, V.260, V.263, L.264, F.268, M.270 Ligands: SOG.5, SOG.8, SOG.14 Ligand excluded by PLIP SOG.16: 5 residues within 4Å: Chain A: M.270, F.271, Q.273, A.279, V.280 Ligand excluded by PLIP SOG.17: 2 residues within 4Å: Chain A: H.51, H.52 Ligand excluded by PLIP SOG.18: 2 residues within 4Å: Chain A: I.190 Ligands: SOG.25 Ligand excluded by PLIP SOG.19: 2 residues within 4Å: Chain A: T.41, V.69 Ligand excluded by PLIP SOG.20: 5 residues within 4Å: Chain A: T.55, V.56, R.120, Q.233, R.237 Ligand excluded by PLIP SOG.21: 7 residues within 4Å: Chain A: L.66, V.69, L.70, I.74, I.141, L.142, W.145 Ligand excluded by PLIP SOG.22: 4 residues within 4Å: Chain A: L.25, A.28, F.286, W.289 Ligand excluded by PLIP SOG.23: 2 residues within 4Å: Chain A: R.54, Y.59 Ligand excluded by PLIP SOG.24: 4 residues within 4Å: Chain A: W.319, W.320, G.323, L.324 Ligand excluded by PLIP SOG.25: 3 residues within 4Å: Chain A: I.190 Ligands: SOG.5, SOG.18 Ligand excluded by PLIP

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.26: 13 residues within 4Å: Chain A: S.114, A.117, L.118, W.121, L.201, G.205, L.206, M.209, A.210, F.212, Q.213, R.216 Ligands: SOG.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.117, A:L.118, A:W.121, A:L.206, A:M.209, A:A.210 Hydrogen bonds: A:Q.213

1 x NA: SODIUM ION(Non-functional Binders)

NA.27: 5 residues within 4Å: Chain A: D.68, A.109, F.251, Y.255, N.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.255, A:Y.255, A:N.294 Water bridges: A:S.105, A:S.295

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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