PDB
9M54
Resolution
3.2 Å
Released
July 23, 2025
Receptor
NPFF2
Class
A
Species
Homo sapiens
Ligand
Neuropeptide VF
Function
Agonist
Reference
10.1016/J.CELREP.2025.116160

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Ligand Amino Acid Generic Number Segment Interaction Type
Neuropeptide VF D207 2.64x63 TM2 polar (charge-assisted hydrogen bond)
Neuropeptide VF Q227 3.32x32 TM3 polar (hydrogen bond)
Neuropeptide VF Q227 3.32x32 TM3 polar (hydrogen bond)
Neuropeptide VF G228 3.33x33 TM3 Van der Waals
Neuropeptide VF V231 3.36x36 TM3 Van der Waals
Neuropeptide VF V231 3.36x36 TM3 hydrophobic
Neuropeptide VF M277 4.57x57 TM4 Van der Waals
Neuropeptide VF M277 4.57x57 TM4 hydrophobic
Neuropeptide VF E289 ECL2 polar (charge-assisted hydrogen bond)
Neuropeptide VF W307 ECL2 polar (hydrogen bond)
Neuropeptide VF W307 ECL2 Van der Waals
Neuropeptide VF C308 45.50x50 ECL2 Van der Waals
Neuropeptide VF C308 45.50x50 ECL2 polar (hydrogen bond with backbone)
Neuropeptide VF R309 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
Neuropeptide VF W393 6.52x52 TM6 hydrophobic
Neuropeptide VF W393 6.52x52 TM6 Van der Waals
Neuropeptide VF M396 6.55x55 TM6 Van der Waals
Neuropeptide VF M396 6.55x55 TM6 hydrophobic
Neuropeptide VF N413 7.31x30 TM7 Van der Waals
Neuropeptide VF Y417 7.35x34 TM7 hydrophobic
Neuropeptide VF Y417 7.35x34 TM7 Van der Waals
Neuropeptide VF H421 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
NPFF2 receptor
TM2
2x63 2.64x63 D207
TM3
3x32 3.32x32 Q227
3x33 3.33x33 G228
3x36 3.36x36 V231
TM4
4x57 4.57x57 M277
ECL2
45x50 45.50x50 C308
45x51 45.51x51 R309
TM6
6x52 6.52x52 W393
6x55 6.55x55 M396
TM7
7x30 7.31x30 N413
7x34 7.35x34 Y417
7x38 7.39x38 H421