PDB
9JEQ
Resolution
3.1 Å
Released
Sept. 24, 2025
Receptor
H3
Class
A
Species
Homo sapiens
Ligand
histamine
Function
Agonist
Reference
10.1038/S41401-025-01633-4

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Ligand Amino Acid Generic Number Segment Interaction Type
histamine D114 3.32x32 TM3 polar (charge-assisted hydrogen bond)
histamine Y115 3.33x33 TM3 hydrophobic
histamine Y115 3.33x33 TM3 Van der Waals
histamine C118 3.36x36 TM3 Van der Waals
histamine Y167 4.57x57 TM4 polar (hydrogen bond)
histamine Y167 4.57x57 TM4 Van der Waals
histamine E206 5.46x461 TM5 Van der Waals
histamine Y374 6.51x51 TM6 Van der Waals
histamine Y374 6.51x51 TM6 aromatic (face-to-edge)
histamine Y374 6.51x51 TM6 polar (hydrogen bond)
histamine F398 7.39x38 TM7 hydrophobic
histamine F398 7.39x38 TM7 Van der Waals
histamine L401 7.42x41 TM7 hydrophobic
histamine L401 7.42x41 TM7 Van der Waals
histamine W402 7.43x42 TM7 aromatic (face-to-edge)
histamine W402 7.43x42 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
H3 receptor
TM3
3x32 3.32x32 D114
3x33 3.33x33 Y115
3x36 3.36x36 C118
TM4
4x57 4.57x57 Y167
TM5
5x461 5.46x461 E206
TM6
6x51 6.51x51 Y374
TM7
7x38 7.39x38 F398
7x41 7.42x41 L401
7x42 7.43x42 W402