PDB
6K41
Resolution
2.9 Å
Released
April 15, 2020
Receptor
α2B
Class
A
Species
Homo sapiens
Ligand
dexmedetomidine
Function
Agonist
Reference
10.1038/S41589-020-0492-2

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Ligand Amino Acid Generic Number Segment Interaction Type
dexmedetomidine V93 3.33x33 TM3 hydrophobic
dexmedetomidine C96 3.36x36 TM3 hydrophobic
dexmedetomidine W384 6.48x48 TM6 hydrophobic
dexmedetomidine F387 6.51x51 TM6 aromatic (face-to-edge)
dexmedetomidine F388 6.52x52 TM6 aromatic (edge-to-face)
dexmedetomidine Y391 6.55x55 TM6 hydrophobic
dexmedetomidine F412 7.39x38 TM7 polar (hydrogen bond with backbone)
dexmedetomidine F412 7.39x38 TM7 Van der Waals
dexmedetomidine Y416 7.43x42 TM7 aromatic (face-to-edge)
dexmedetomidine Y416 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
α2B-adrenoceptor
TM3
3x33 3.33x33 V93
3x36 3.36x36 C96
TM6
6x48 6.48x48 W384
6x51 6.51x51 F387
6x52 6.52x52 F388
6x55 6.55x55 Y391
TM7
7x38 7.39x38 F412
7x42 7.43x42 Y416