SMTL ID : 6tq6.2 (1 other biounit)

Crystal structure of the Orexin-1 receptor in complex with Compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x NVH: 2-(5-methylsulfonylpyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one(Non-covalent)

NVH.1: 15 residues within 4Å: Chain A: C.75, S.79, W.88, I.98, P.99, Q.102, A.103, V.106, Q.155, H.192, F.195, Y.287, I.290, S.291, N.294 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.195, A:I.290 Hydrogen bonds: A:Q.155

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

SO4.2: 4 residues within 4Å: Chain A: R.120, A.123, Q.265, R.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.265 Salt bridges: A:R.120, A:R.269 SO4.3: 4 residues within 4Å: Chain A: K.271, S.338, G.339, K.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.338, 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: 12 residues within 4Å: Chain A: A.150, I.151, V.153, P.154, A.157, W.182, I.190, Y.191, C.194, F.195 Ligands: SOG.8, SOG.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.150, A:P.154, A:W.182, A:I.190, A:Y.191, A:Y.191, A:Y.191, A:F.195

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

SOG.5: 7 residues within 4Å: Chain A: I.74, P.77, A.78, F.90, L.94, I.98, R.173 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.77, A:A.78, A:F.90, A:L.94, 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.168 Hydrogen bonds: A:T.172, A:R.173 SOG.7: 3 residues within 4Å: Chain A: D.184, D.185, L.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.185, A:D.185, A:D.185 SOG.8: 6 residues within 4Å: Chain A: K.96, Y.100, L.149, A.156, A.157 Ligands: PGW.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.100, A:L.149, A:A.156 SOG.9: 4 residues within 4Å: Chain A: K.189, I.190, S.193, V.299 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.190, A:V.299 SOG.10: 7 residues within 4Å: Chain A: E.160, R.181, W.182, A.183, D.184, A.187 Ligands: PGW.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181, A:A.183, A:D.184

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

PG4.11: 11 residues within 4Å: Chain A: V.82, E.86, S.87, W.88, V.177, C.178, K.297, F.303, V.312, Y.313, F.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.178

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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