PDB
6TOD
Resolution
2.1 Å
Released
Jan. 1, 2020
Receptor
OX1
Class
A
Species
Homo sapiens
Ligand
Function
EMPA
Antagonist
Reference
10.1021/acs.jmedchem.9b01787

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Ligand Amino Acid Generic Number Segment Interaction Type
EMPA S103 2.61x60 TM2 Van der Waals
EMPA W112 23.50x50 ECL1 hydrophobic
EMPA P123 3.29x29 TM3 hydrophobic
EMPA Q126 3.32x32 TM3 hydrophobic
EMPA T127 3.33x33 TM3 Van der Waals
EMPA V130 3.36x36 TM3 Van der Waals
EMPA Q179 4.60x61 TM4 polar (hydrogen bond)
EMPA M183 4.64x65 TM4 hydrophobic
EMPA C202 45.50x50 ECL2 Van der Waals
EMPA E204 45.52x52 ECL2 Van der Waals
EMPA H216 5.39x40 TM5 Van der Waals
EMPA F219 5.42x43 TM5 aromatic (edge-to-face)
EMPA F219 5.42x43 TM5 hydrophobic
EMPA Y311 6.48x48 TM6 Van der Waals
EMPA I314 6.51x51 TM6 hydrophobic
EMPA S315 6.52x52 TM6 Van der Waals
EMPA N318 6.55x55 TM6 Van der Waals
EMPA H344 7.39x38 TM7 aromatic (face-to-face)
EMPA V347 7.42x41 TM7 Van der Waals
EMPA Y348 7.43x42 TM7 Van der Waals

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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
ECL1
23x50 23.50x50 W112
TM3
3x29 3.29x29 P123
3x32 3.32x32 Q126
3x33 3.33x33 A127
3x36 3.36x36 V130
TM4
4x61 4.60x61 Q179
4x65 4.64x65 M183
ECL2
45x50 45.50x50 C202
45x52 45.52x52 E204
TM5
5x40 5.39x40 H216
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
7x41 7.42x41 V347
7x42 7.43x42 Y348