PDB
7YON
Resolution
3.0 Å
Released
March 22, 2023
Receptor
Y2
Class
A
Species
Homo sapiens
Ligand
CHEMBL439904
Function
Agonist
Reference
10.1016/J.STR.2022.11.010

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Ligand Amino Acid Generic Number Segment Interaction Type
CHEMBL439904 L40 N-term hydrophobic
CHEMBL439904 T107 2.61x60 TM2 polar (hydrogen bond)
CHEMBL439904 T107 2.61x60 TM2 polar (hydrogen bond with backbone)
CHEMBL439904 T107 2.61x60 TM2 polar (hydrogen bond)
CHEMBL439904 Y110 2.64x63 TM2 Van der Waals
CHEMBL439904 Y110 2.64x63 TM2 hydrophobic
CHEMBL439904 T111 2.65x64 TM2 polar (hydrogen bond)
CHEMBL439904 T111 2.65x64 TM2 Van der Waals
CHEMBL439904 Q130 3.32x32 TM3 Van der Waals
CHEMBL439904 I192 ECL2 Van der Waals
CHEMBL439904 E193 ECL2 Van der Waals
CHEMBL439904 E193 ECL2 polar (hydrogen bond with backbone)
CHEMBL439904 I194 ECL2 Van der Waals
CHEMBL439904 I194 ECL2 hydrophobic
CHEMBL439904 T204 45.51x51 ECL2 polar (hydrogen bond)
CHEMBL439904 T204 45.51x51 ECL2 Van der Waals
CHEMBL439904 E205 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
CHEMBL439904 Y219 5.38x39 TM5 hydrophobic
CHEMBL439904 Y219 5.38x39 TM5 Van der Waals
CHEMBL439904 S220 5.39x40 TM5 Van der Waals
CHEMBL439904 Q288 6.55x55 TM6 polar (hydrogen bond)
CHEMBL439904 Q288 6.55x55 TM6 polar (hydrogen bond)
CHEMBL439904 V291 6.58x58 TM6 Van der Waals
CHEMBL439904 S295 ECL3 Van der Waals
CHEMBL439904 L298 ECL3 Van der Waals
CHEMBL439904 L298 ECL3 polar (hydrogen bond with backbone)
CHEMBL439904 D299 ECL3 Van der Waals
CHEMBL439904 L300 ECL3 Van der Waals
CHEMBL439904 K301 ECL3 Van der Waals
CHEMBL439904 Y303 7.31x30 TM7 hydrophobic
CHEMBL439904 Y303 7.31x30 TM7 Van der Waals
CHEMBL439904 K304 7.32x31 TM7 Van der Waals
CHEMBL439904 F307 7.35x34 TM7 hydrophobic
CHEMBL439904 F307 7.35x34 TM7 Van der Waals
CHEMBL439904 H311 7.39x38 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
Y2 receptor
TM2
2x60 2.61x60 T107
2x63 2.64x63 Y110
2x64 2.65x64 T111
TM3
3x32 3.32x32 Q130
ECL2
45x51 45.51x51 T204
45x52 45.52x52 E205
TM5
5x39 5.38x39 Y219
5x40 5.39x40 S220
TM6
6x55 6.55x55 Q288
6x58 6.58x58 V291
TM7
7x30 7.31x30 Y303
7x31 7.32x31 K304
7x34 7.35x34 F307
7x38 7.39x38 H311