PDB
8JPF
Resolution
3.0 Å
Released
Aug. 9, 2023
Receptor
NTS1
Class
A
Species
Homo sapiens
Ligands
NTS8–13
SBI-553
Function
Agonist
Ago-PAM
Reference
10.1038/S41586-023-06395-9
NTS8–13 SBI-553

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Ligand Amino Acid Generic Number Segment Interaction Type
NTS8–13 L54 N-term Van der Waals
NTS8–13 L54 N-term polar (hydrogen bond with backbone)
SBI-553 L105 2.43x43 TM2 hydrophobic
NTS8–13 H132 ECL1 Van der Waals
NTS8–13 Y145 3.29x29 TM3 polar (hydrogen bond)
NTS8–13 Y145 3.29x29 TM3 polar (hydrogen bond)
SBI-553 V159 3.43x43 TM3 hydrophobic
SBI-553 L162 3.46x46 TM3 hydrophobic
SBI-553 R166 3.50x50 TM3 polar (charge-assisted hydrogen bond)
SBI-553 I170 3.54x54 TM3 Van der Waals
SBI-553 I170 3.54x54 TM3 hydrophobic
NTS8–13 M207 4.64x65 TM4 Van der Waals
NTS8–13 V223 ECL2 hydrophobic
NTS8–13 T225 45.51x51 ECL2 polar (hydrogen bond)
NTS8–13 T225 45.51x51 ECL2 Van der Waals
NTS8–13 I237 5.39x40 TM5 hydrophobic
NTS8–13 I237 5.39x40 TM5 Van der Waals
SBI-553 N256 5.58x58 TM5 Van der Waals
SBI-553 L305 6.37x37 TM6 hydrophobic
SBI-553 L305 6.37x37 TM6 Van der Waals
SBI-553 V308 6.40x40 TM6 hydrophobic
SBI-553 V308 6.40x40 TM6 Van der Waals
NTS8–13 R322 6.54x54 TM6 polar (charge-assisted hydrogen bond)
NTS8–13 R323 6.55x55 TM6 Van der Waals
NTS8–13 F326 6.58x58 TM6 Van der Waals
NTS8–13 F326 6.58x58 TM6 polar (hydrogen bond with backbone)
NTS8–13 I329 ECL3 Van der Waals
NTS8–13 I329 ECL3 polar (hydrogen bond with backbone)
NTS8–13 W334 ECL3 Van der Waals
NTS8–13 W334 ECL3 hydrophobic
NTS8–13 P336 7.25x24 TM7 Van der Waals
NTS8–13 Y339 7.28x27 TM7 hydrophobic
NTS8–13 Y339 7.28x27 TM7 Van der Waals
NTS8–13 Y342 7.31x30 TM7 Van der Waals
NTS8–13 Y342 7.31x30 TM7 polar (hydrogen bond)
NTS8–13 H343 7.32x31 TM7 Van der Waals
NTS8–13 Y346 7.35x34 TM7 polar (hydrogen bond)
NTS8–13 Y346 7.35x34 TM7 Van der Waals
SBI-553 V367 7.56x56 TM7 hydrophobic
SBI-553 V367 7.56x56 TM7 Van der Waals
SBI-553 F371 8.50x50 H8 Van der Waals
SBI-553 F371 8.50x50 H8 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
NTS1 receptor
TM2
2x43 2.43x43 L105
TM3
3x29 3.29x29 Y145
3x43 3.43x43 V159
3x46 3.46x46 L162
3x50 3.50x50 R166
3x54 3.54x54 I170
TM4
4x65 4.64x65 M207
ECL2
45x51 45.51x51 T225
TM5
5x40 5.39x40 I237
5x58 5.58x58 N256
TM6
6x37 6.37x37 L305
6x40 6.40x40 V308
6x54 6.54x54 R322
6x55 6.55x55 R323
6x58 6.58x58 F326
TM7
7x24 7.25x24 P336
7x27 7.28x27 Y339
7x30 7.31x30 Y342
7x31 7.32x31 H343
7x34 7.35x34 Y346
7x56 7.56x56 V367
H8
8x50 8.50x50 F371