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

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

Coordinates

PDB Format

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

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

PG4.2: 7 residues within 4Å: Chain A: C.178, D.179, K.265, F.271, R.272, V.280, F.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.265

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 6 residues within 4Å: Chain A: T.55, V.56, T.57, R.120, Q.233, R.237 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.55, A:V.56, A:T.57, A:T.57, A:R.120, A:S.132 Salt bridges: A:R.120, A:R.120, A:R.237

22 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

SOG.4: 4 residues within 4Å: Chain A: F.90, L.94, V.97, R.173 Ligand excluded by PLIP SOG.5: 6 residues within 4Å: Chain A: S.193, F.196, I.197, V.263, F.268 Ligands: SOG.8 Ligand excluded by PLIP SOG.6: 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.7: 3 residues within 4Å: Chain A: H.126, Q.213 Ligands: SOG.25 Ligand excluded by PLIP SOG.8: 8 residues within 4Å: Chain A: F.196, V.260, V.263, L.264, F.268, M.270 Ligands: SOG.5, SOG.11 Ligand excluded by PLIP SOG.9: 6 residues within 4Å: Chain A: V.97, Y.100, L.149, V.153, A.156, A.157 Ligand excluded by PLIP SOG.10: 4 residues within 4Å: Chain A: K.189, I.190, S.193, V.267 Ligand excluded by PLIP SOG.11: 2 residues within 4Å: Chain A: V.260 Ligands: SOG.8 Ligand excluded by PLIP SOG.12: 7 residues within 4Å: Chain A: M.270, F.271, D.276, A.279, V.280, A.283 Ligands: SOG.20 Ligand excluded by PLIP SOG.13: 4 residues within 4Å: Chain A: Y.200, L.204, A.208, A.252 Ligand excluded by PLIP SOG.14: 2 residues within 4Å: Chain A: F.33, P.77 Ligand excluded by PLIP SOG.15: 5 residues within 4Å: Chain A: V.35, C.254, A.293, A.296, I.300 Ligand excluded by PLIP SOG.16: 4 residues within 4Å: Chain A: W.182, A.183, D.184, D.185 Ligand excluded by PLIP SOG.17: 7 residues within 4Å: Chain A: A.208, Y.211, F.212, F.215, M.245, V.248 Ligands: SOG.23 Ligand excluded by PLIP SOG.18: 4 residues within 4Å: Chain A: C.125, Q.213, R.216, K.217 Ligand excluded by PLIP SOG.19: 5 residues within 4Å: Chain A: L.253, L.256, P.257, F.286, L.290 Ligand excluded by PLIP SOG.20: 1 residues within 4Å: Ligands: SOG.12 Ligand excluded by PLIP SOG.21: 4 residues within 4Å: Chain A: P.257, V.260, L.261, S.287 Ligand excluded by PLIP SOG.22: 1 residues within 4Å: Chain A: I.301 Ligand excluded by PLIP SOG.23: 4 residues within 4Å: Chain A: A.208 Ligands: SOG.17, SOG.24, PGW.26 Ligand excluded by PLIP SOG.24: 3 residues within 4Å: Chain A: G.205 Ligands: SOG.23, PGW.26 Ligand excluded by PLIP SOG.25: 4 residues within 4Å: Chain A: H.126, P.127, L.128 Ligands: SOG.7 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: 12 residues within 4Å: Chain A: S.114, A.117, L.118, W.121, V.198, L.206, M.209, A.210, Q.213, R.216 Ligands: SOG.23, SOG.24 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.117, A:L.118, A:W.121, A:L.206, A:L.206, A:M.209 Hydrogen bonds: A:Q.213 Salt bridges: A:R.216

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

NA.27: 3 residues within 4Å: Chain A: D.68, Y.255, N.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.255, A:N.294

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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