6TP3: Orexin-1 receptor

Crystal structure of the Orexin-1 receptor in complex with daridorexant. Determined by X-ray diffraction at 3.04 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 3.04 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,399
Mol. weight: 90.46 kDa
Ligands: PGW, SOG, NS2
Released: 1 Jan 2020

Explore 6TP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TP3 contains 32 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: 16 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	115-148	34
α-helix	158-175	18
α-helix	177-182	6
β-strand	183-187	5	1
α-helix	190-194	5
β-strand	200-204	5	1
α-helix	210-220	11
α-helix	221-225	5
α-helix	226-242	17
α-helix	246-247	2
α-helix	252-322	50
α-helix	333-361	29
α-helix	363-376	14

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-35	8
α-helix	36-40	5
α-helix	41-73	33
α-helix	75-77	3
α-helix	80-94	15
α-helix	95-99	5
α-helix	100-109	10
α-helix	115-148	34
α-helix	158-175	18
α-helix	177-182	6
β-strand	183-186	4	2
β-strand	201-204	4	2
α-helix	210-220	11
α-helix	221-225	5
α-helix	226-242	17
α-helix	286-322	37
α-helix	333-361	29
α-helix	363-375	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Orexin receptor type 1	A, B	protein	368	Homo sapiens	O43613 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6TP3_1 Orexin receptor type 1 (chains A, B)
AASEDEFLRYLWRDYLYPKQYAWVLIAAYVAVFVVALVGNTLVCLAVWRNHHMRTVTNYF
LVNLSLADVLATAICLPASLLVDITESWLFGHALCKVIPYLQAVSVSVAVLTLSFIALDR
WYAICHPLLFKSTARRALGSILGIWAVSLAIMVPQAAVMECSSVLPELAARTRAFSVCDE
RWADDLAPKIYHSCFFIVTYLAPLGLMAMAYFQIFRKLWGRQIPGTTSALVRNWKRPSDQ
LGDLEQGLSGEPQPRARAFLAEVKQMRARRKTAKMLMVVVLVFALCYLPISVLNVLKRVF
GMFRQASDREAVYAAFTFSHWLVYANSAANPIIYNFLSGKFREQFKAAFSWWLPGLAAAH
HHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PGW	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexade…	C40 H77 O10 P	2
SOG	octyl 1-thio-beta-D-glucopyranoside	C14 H28 O5 S	14
NS2	[(2~{S})-2-(6-chloranyl-7-methyl-1~{H}-benzimidazol-2-yl)-2-methyl-pyrrolidin-1…	C23 H23 Cl N6 O2	2

Water and common crystallization additives (SO4) 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:

6TOD 2.11 Å, Crystal structure of the Orexin-1 receptor in complex with EMPA
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

Browse structure collections

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