PDB
8YN3
Resolution
2.6 Å
Released
Oct. 9, 2024
Receptor
H2
Class
A
Species
Homo sapiens
Ligand
histamine
Function
Agonist
Reference
10.1038/S41467-024-52585-Y

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Ligand Amino Acid Generic Number Segment Interaction Type
histamine D98 3.32x32 TM3 polar (charge-assisted hydrogen bond)
histamine V99 3.33x33 TM3 Van der Waals
histamine V99 3.33x33 TM3 hydrophobic
histamine C102 3.36x36 TM3 hydrophobic
histamine C102 3.36x36 TM3 Van der Waals
histamine D186 5.42x43 TM5 polar (charge-assisted hydrogen bond)
histamine W247 6.48x48 TM6 Van der Waals
histamine Y250 6.51x51 TM6 aromatic (edge-to-face)
histamine Y250 6.51x51 TM6 polar (hydrogen bond)
histamine Y250 6.51x51 TM6 Van der Waals
histamine F251 6.52x52 TM6 Van der Waals
histamine F254 6.55x55 TM6 aromatic (face-to-edge)
histamine F254 6.55x55 TM6 Van der Waals
histamine Y278 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
H2 receptor
TM3
3x32 3.32x32 D98
3x33 3.33x33 V99
3x36 3.36x36 C102
TM5
5x43 5.42x43 D186
TM6
6x48 6.48x48 W247
6x51 6.51x51 Y250
6x52 6.52x52 F251
6x55 6.55x55 F254
TM7
7x42 7.43x42 Y278