6TOD: Orexin-1 receptor

Crystal structure of the Orexin-1 receptor in complex with EMPA. Determined by X-ray diffraction at 2.11 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,949
Mol. weight: 94.73 kDa
Ligands: 7MA, CIT, SOG, PGW
Released: 1 Jan 2020

Explore 6TOD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TOD contains 36 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-73	28
α-helix	75-77	3
α-helix	80-94	15
α-helix	95-99	5
α-helix	100-109	10
α-helix	115-149	35
α-helix	158-175	18
α-helix	177-182	6
β-strand	183-187	5	1
α-helix	190-192	3
β-strand	200-204	5	1
α-helix	211-220	10
α-helix	221-225	5
α-helix	226-242	17
α-helix	245-247	3
α-helix	287-322	36
α-helix	330-332	3
α-helix	333-361	29
α-helix	363-371	9
α-helix	372-376	5

Chain B: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-35	6
α-helix	36-45	10
α-helix	46-72	27
α-helix	75-77	3
α-helix	80-94	15
α-helix	95-99	5
α-helix	100-109	10
α-helix	115-149	35
α-helix	158-175	18
α-helix	177-182	6
β-strand	183-186	4	2
β-strand	201-204	4	2
α-helix	211-220	10
α-helix	221-225	5
α-helix	226-242	17
α-helix	253-322	38
α-helix	333-361	29
α-helix	363-371	9
α-helix	372-376	5
α-helix	377-382	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Orexin receptor type 1	A, B	protein	336	Homo sapiens	O43613 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6TOD_1 Orexin receptor type 1 (chains A, B)
AASEDEFLRYLWRDYLYPKQYAWVLIAAYVAVFVVALVGNTLVCLAVWRNHHMRTVTNYF
LVNLSLADVLATAICLPASLLVDITESWLFGHALCKVIPYLQTVSVSVAVLTLSFIALDR
WYAICHPLLFKSTARRALGSILGIWAVSLAIMVPQAAVMECSSVLPELAARTRAFSVCDE
RWADDLAPKIYHSCFFIVTYLAPLGLMAMAYFQIFRKLWGRQIPGTTSAEVKQMRARRKT
AKMLMVVVLVFALCYLPISVLNVLKRVFGMFRQASDREAVYAAFTFSHWLVYANSAANPI
IYNFLSGKFREQFKAAFSWWLPGLAAAHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
7MA	N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3…	C23 H26 N4 O4 S	2
CIT	Citric acid	C6 H8 O7	1
SOG	octyl 1-thio-beta-D-glucopyranoside	C14 H28 O5 S	47
PGW	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexade…	C40 H77 O10 P	2

Water and common crystallization additives (SO4, PG4, NA) are not listed.

Primary citation

Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis. Rappas, M., Ali, A.A.E., Bennett, K.A. et al. J Med Chem (2020) 63:1528-1543. DOI 10.1021/acs.jmedchem.9b01787 · PubMed

Other PDB entries of the same protein (UniProt O43613 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TOS 2.13 Å, Crystal structure of the Orexin-1 receptor in complex with GSK1059865
6TOT 2.22 Å, Crystal structure of the Orexin-1 receptor in complex with lemborexant
6TO7 2.26 Å, Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution
6TQ4 2.3 Å, Crystal structure of the Orexin-1 receptor in complex with Compound 16
6TP6 2.34 Å, Crystal structure of the Orexin-1 receptor in complex with filorexant
6TQ6 2.55 Å, Crystal structure of the Orexin-1 receptor in complex with Compound 14
6TQ9 2.65 Å, Crystal structure of the Orexin-1 receptor in complex with SB-408124
6TQ7 2.66 Å, Crystal structure of the Orexin-1 receptor in complex with SB-334867
4ZJ8 2.75 Å, Structures of the human OX1 orexin receptor bound to selective and dual antagonists
4ZJC 2.83 Å, Structures of the human OX1 orexin receptor bound to selective and dual antagonists
6TP4 3.01 Å, Crystal structure of the Orexin-1 receptor in complex with ACT-462206
6TP3 3.04 Å, Crystal structure of the Orexin-1 receptor in complex with daridorexant

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