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

Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

monomer

Ligands

13 x OLA: OLEIC ACID(Non-covalent)

OLA.1: 1 residues within 4Å: Chain A: V.476 No protein-ligand interaction detected (PLIP) OLA.4: 4 residues within 4Å: Chain A: Y.385, A.407, V.408, A.425 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.407, A:V.408 OLA.5: 6 residues within 4Å: Chain A: I.303, G.304, Y.374, E.395 Ligands: NH4.6, OLA.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.303 Hydrogen bonds: A:Y.374 OLA.7: 7 residues within 4Å: Chain A: R.305, G.338, K.339, E.363, M.364 Ligands: OLA.5, NH4.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.305, A:K.339 OLA.8: 4 residues within 4Å: Chain A: E.63, Y.64, T.509, A.512 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.64, A:A.512 Hydrogen bonds: A:T.509, A:T.509 OLA.9: 3 residues within 4Å: Chain A: I.81, V.84, L.85 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.84, A:L.85 OLA.10: 2 residues within 4Å: Chain A: W.549, W.550 No protein-ligand interaction detected (PLIP) OLA.11: 3 residues within 4Å: Chain A: I.193, I.196, P.197 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.196, A:P.197 OLA.12: 1 residues within 4Å: Chain A: N.182 No protein-ligand interaction detected (PLIP) OLA.13: 7 residues within 4Å: Chain A: L.247, V.251, Y.254, F.258, M.475, L.479, A.482 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.247, A:L.247, A:V.251, A:Y.254, A:F.258, A:L.479, A:A.482 OLA.14: 7 residues within 4Å: Chain A: G.82, L.85, N.533, F.534, R.540, F.543, F.547 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.85, A:N.533, A:F.534, A:F.543, A:F.547 Hydrogen bonds: A:N.533 OLA.15: 3 residues within 4Å: Chain A: K.232, V.497, F.498 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.497 Salt bridges: A:K.232 OLA.16: 2 residues within 4Å: Chain A: A.245, L.249 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.245, A:L.249

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.2: 21 residues within 4Å: Chain A: C.118, A.121, T.122, V.125, W.131, I.141, P.142, Q.145, T.146, V.149, Q.198, M.202, E.223, H.235, F.238, Y.485, I.488, N.492, H.518, V.521, Y.522 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.122, A:I.141, A:Q.145, A:Q.145, A:V.521 Hydrogen bonds: A:N.492

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 8 residues within 4Å: Chain A: V.315, V.423, K.424, A.425, G.426, D.427, E.430, L.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.427, A:D.427, A:L.431 NH4.6: 7 residues within 4Å: Chain A: I.303, I.337, E.363, M.364, L.365 Ligands: OLA.5, OLA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.365

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

PG4.17: 8 residues within 4Å: Chain A: C.221, D.222, K.495, M.500, F.501, V.510, Y.511, F.514 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.495 Water bridges: A:C.221, A:D.222

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 2,GlgA glycogen synthase,Hypocretin receptor-2: 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 2,GlgA glycogen synthase,Hypocretin receptor-2

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