6V9S: PDB entry 6V9S

Structure-based development of subtype-selective orexin 1 receptor antagonists. Determined by X-ray diffraction at 3.5 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Pyrococcus abyssi (strain GE5 / Orsay)
Chains: 1
Atoms: 4,114
Mol. weight: 63.91 kDa
Ligands: JHC, CLR, OLA
Released: 15 Jul 2020

Explore 6V9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V9S contains 25 α-helices and 8 β-strands across 1 chain. 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: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
α-helix	46-73	28
α-helix	75-77	3
α-helix	80-109	30
α-helix	116-149	34
α-helix	151-153	3
α-helix	158-175	18
α-helix	177-182	6
β-strand	183-186	4	1
β-strand	201-204	4	1
α-helix	211-220	10
α-helix	221-225	5
α-helix	226-242	17
α-helix	1009-1011	3
α-helix	1016-1027	12
β-strand	1033-1041	9	2
α-helix	1048-1058	11
α-helix	1063-1066	4
β-strand	1067-1075	9	2
α-helix	1077-1089	13
β-strand	1093-1096	4	2
α-helix	1102-1109	8
β-strand	1114-1117	4	2
α-helix	1126-1132	7
α-helix	1136	1
β-strand	1137-1141	5	2
α-helix	1145-1149	5
β-strand	1156-1158	3	2
α-helix	1163-1177	15
α-helix	1182-310	38
α-helix	312-322	11
α-helix	334-361	28
α-helix	363-371	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Orexin receptor type 1,GlgA glycogen synthase chimera	A	protein	553	Homo sapiens, Pyrococcus abyssi (strain GE5 / Orsay)	O43613 (AlphaFold model), Q9V2J8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6V9S_1 Orexin receptor type 1,GlgA glycogen synthase chimera (chains A)
DYKDDDDAMEPSATPGAQMGVPPGSREPSPVPPDYEDEFLRYLWRDYLYPKQYEWVLIAA
YVAVFVVALVGNTLVCLAVWRNHHMRTVTNYFIVNLSLADVLVTAICLPASLLVDITESW
LFGHALCKVIPYLQAVSVSVKVLTLSFIALDRWYAICHPLLFKSTARRARGSILGIWAVS
LAIMVPQAAVMECSSVLPELANRTRLFSVCDERWADDLYPKIYHSCFFIVTYLAPLGLMA
MAYFQIFRKLWGRQGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQK
GVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVR
ELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGEL
ANAILKALELSRSDLSKFRENCKKRAMSFSKQMRARRKTAKMLMVVLLVFALCYLPISVL
NILKRVFGMFRQASDREAVYACFTFSHWLVYANSAANPIIYNFLSGKFREQFKAAFSCCL
PGLHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
JHC	[(2S)-2-[(2S)-butan-2-yl]-4-(5-chloro-1,3-benzoxazol-2-yl)-1,4-diazepan-1-yl][5…	C26 H29 Cl N6 O2	1
CLR	Cholesterol	C27 H46 O	1
OLA	Oleic acid	C18 H34 O2	1

Primary citation

Structure-based development of a subtype-selective orexin 1 receptor antagonist. Hellmann, J., Drabek, M., Yin, J. et al. Proc Natl Acad Sci U S A (2020) 117:18059-18067. DOI 10.1073/pnas.2002704117 · 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

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