PDB
6TOT
Resolution
2.2 Å
Released
Jan. 15, 2020
Receptor
OX1
Class
A
Species
Homo sapiens
Ligand
lemborexant
Function
Antagonist
Reference
10.1021/acs.jmedchem.9b01787

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Ligand Amino Acid Generic Number Segment Interaction Type
lemborexant S103 2.61x60 TM2 polar (hydrogen bond)
lemborexant S103 2.61x60 TM2 polar (hydrogen bond)
lemborexant S103 2.61x60 TM2 polar (hydrogen bond with backbone)
lemborexant V106 2.64x63 TM2 Van der Waals
lemborexant V106 2.64x63 TM2 hydrophobic
lemborexant D107 2.65x64 TM2 Van der Waals
lemborexant W112 23.50x50 ECL1 Van der Waals
lemborexant I122 3.28x28 TM3 Van der Waals
lemborexant P123 3.29x29 TM3 Van der Waals
lemborexant P123 3.29x29 TM3 polar (hydrogen bond with backbone)
lemborexant Q126 3.32x32 TM3 polar (hydrogen bond)
lemborexant Q126 3.32x32 TM3 polar (hydrogen bond)
lemborexant A127 3.33x33 TM3 Van der Waals
lemborexant Q179 4.60x61 TM4 Van der Waals
lemborexant F219 5.42x43 TM5 hydrophobic
lemborexant F219 5.42x43 TM5 Van der Waals
lemborexant Y311 6.48x48 TM6 Van der Waals
lemborexant I314 6.51x51 TM6 hydrophobic
lemborexant I314 6.51x51 TM6 Van der Waals
lemborexant S315 6.52x52 TM6 Van der Waals
lemborexant N318 6.55x55 TM6 polar (hydrogen bond)
lemborexant H344 7.39x38 TM7 aromatic (face-to-face)
lemborexant H344 7.39x38 TM7 polar (hydrogen bond)
lemborexant H344 7.39x38 TM7 Van der Waals
lemborexant Y348 7.43x42 TM7 polar (hydrogen bond)

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Snake plot — Download: PNG | SVG
ICL1 H H M R ICL1ECL1 S W L F ECL1ICL2 P L L F K S ICL2ECL2 E C S S V L P E L A N R T R L F S V C D E R W A D D ECL2ICL3 G T T S A L V R N W K R P S D Q L G D L E Q G L S G E P Q P R A R A ICL3ECL3 G M F R Q A S ECL3N-term M E P S A T P G A Q M G V P P G S R E P S P V P P D Y E D E F L R Y L W R D Y L Y P K Q Y N-termC-term G L G P C G S L K A P S P R S S A S H K S L S L Q S R C S I S K I S E H V V L T S V T T V L P C-term E W V L I A A Y V A V F V V A L V G N T L V C L A V W R N T V T N Y F I V N L S L A D V L V T A I C L P A S L L V D I T E G H A L C K V I P Y L Q A V S V S V A V L T L S F I A L D R W Y A I C H T A R R A R G S I L G I W A V S L A I M V P Q A A V M L Y P K I Y H S C F F I V T Y L A P L G L M A M A Y F Q I F R K L W G R Q I P F L A E V K Q M R A R R K T A K M L M V V L L V F A L C Y L P I S V L N V L K R V F D R E A V Y A C F T F S H W L V Y A N S A A N P I I Y N F L S G K F K A C L P F R E Q A F S C
Helix box plot — Download: PNG | SVG T N G V L A V V F V A V Y A A I L V W E 1 V N L S L A D V L V T I A C L P A S L L V 2 F S L T L V A V S V S V A Q L Y P I V K 3 A R G S I L G I W A V S L A I M V P Q 4 Y A M A M L G L P A L Y T V I F F C S H Y 5 M V V L L V F A L C Y L P I S V L N V L 6 I P N A A S N A Y V L W H S F T F C A 7

GPCRdb(A)
GPCRdb(A)
OX1 receptor
TM2
2x60 2.61x60 S103
2x63 2.64x63 V106
2x64 2.65x64 D107
ECL1
23x50 23.50x50 W112
TM3
3x28 3.28x28 I122
3x29 3.29x29 P123
3x32 3.32x32 Q126
3x33 3.33x33 A127
TM4
4x61 4.60x61 Q179
TM5
5x43 5.42x43 F219
TM6
6x48 6.48x48 Y311
6x51 6.51x51 I314
6x52 6.52x52 S315
6x55 6.55x55 N318
TM7
7x38 7.39x38 H344
7x42 7.43x42 Y348