PDB
6J21
Resolution
3.2 Å
Released
March 6, 2019
Receptor
NK1
Class
A
Species
Homo sapiens
Ligand
aprepitant
Function
Antagonist
Reference
10.1038/S41467-019-08568-5

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Ligand Amino Acid Generic Number Segment Interaction Type
aprepitant P112 3.32x32 TM3 hydrophobic
aprepitant I113 3.33x33 TM3 hydrophobic
aprepitant W184 ECL2 polar (hydrogen bond)
aprepitant W184 ECL2 Van der Waals
aprepitant E193 5.35x36 TM5 polar (charge-assisted hydrogen bond)
aprepitant Y196 5.38x39 TM5 Van der Waals
aprepitant H197 5.39x40 TM5 Van der Waals
aprepitant V200 5.42x43 TM5 hydrophobic
aprepitant V200 5.42x43 TM5 Van der Waals
aprepitant T201 5.43x44 TM5 Van der Waals
aprepitant T201 5.43x44 TM5 polar (hydrogen bond)
aprepitant W261 6.48x48 TM6 Van der Waals
aprepitant W261 6.48x48 TM6 hydrophobic
aprepitant F264 6.51x51 TM6 Van der Waals
aprepitant F264 6.51x51 TM6 hydrophobic
aprepitant H265 6.52x52 TM6 Van der Waals
aprepitant F268 6.55x55 TM6 Van der Waals
aprepitant F268 6.55x55 TM6 aromatic (face-to-edge)

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

GPCRdb(A)
GPCRdb(A)
NK1 receptor
TM3
3x32 3.32x32 P112
3x33 3.33x33 I113
TM5
5x36 5.35x36 E193
5x39 5.38x39 Y196
5x40 5.39x40 H197
5x43 5.42x43 V200
5x44 5.43x44 T201
TM6
6x48 6.48x48 W261
6x51 6.51x51 F264
6x52 6.52x52 H265
6x55 6.55x55 F268