PDB
7DDZ
Resolution
2.8 Å
Released
Jan. 27, 2021
Receptor
Y2
Class
A
Species
Homo sapiens
Ligand
Function
CHEMBL1823342
Antagonist
Reference
10.1038/S41467-021-21030-9

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Ligand Amino Acid Generic Number Segment Interaction Type
CHEMBL1823342 Y57 1.39x39 TM1 Van der Waals
CHEMBL1823342 T107 2.61x60 TM2 hydrophobic
CHEMBL1823342 Y110 2.64x63 TM2 Van der Waals
CHEMBL1823342 T111 2.65x64 TM2 Van der Waals
CHEMBL1823342 W116 23.50x50 ECL1 hydrophobic
CHEMBL1823342 P127 3.29x29 TM3 Van der Waals
CHEMBL1823342 Q130 3.32x32 TM3 Van der Waals
CHEMBL1823342 G131 3.33x33 TM3 Van der Waals
CHEMBL1823342 V134 3.36x36 TM3 hydrophobic
CHEMBL1823342 Q135 3.37x37 TM3 Van der Waals
CHEMBL1823342 L183 4.60x61 TM4 hydrophobic
CHEMBL1823342 R187 ECL2 Van der Waals
CHEMBL1823342 C203 45.50x50 ECL2 Van der Waals
CHEMBL1823342 Y219 5.38x39 TM5 hydrophobic
CHEMBL1823342 S220 5.39x40 TM5 Van der Waals
CHEMBL1823342 S223 5.42x43 TM5 Van der Waals
CHEMBL1823342 L224 5.43x44 TM5 Van der Waals
CHEMBL1823342 L227 5.46x461 TM5 hydrophobic
CHEMBL1823342 Y228 5.47x47 TM5 Van der Waals
CHEMBL1823342 W281 6.48x48 TM6 Van der Waals
CHEMBL1823342 H285 6.52x52 TM6 aromatic (edge-to-face)
CHEMBL1823342 Q288 6.55x55 TM6 polar (hydrogen bond)
CHEMBL1823342 F307 7.35x34 TM7 hydrophobic
CHEMBL1823342 T308 7.36x35 TM7 hydrophobic
CHEMBL1823342 H311 7.39x38 TM7 Van der Waals

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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
TM1
1x39 1.39x39 Y57
TM2
2x60 2.61x60 T107
2x63 2.64x63 Y110
2x64 2.65x64 T111
ECL1
23x50 23.50x50 W116
TM3
3x29 3.29x29 P127
3x32 3.32x32 Q130
3x33 3.33x33 G131
3x36 3.36x36 V134
3x37 3.37x37 Q135
TM4
4x61 4.60x61 L183
ECL2
45x50 45.50x50 C203
TM5
5x39 5.38x39 Y219
5x40 5.39x40 S220
5x43 5.42x43 S223
5x44 5.43x44 L224
5x461 5.46x461 L227
5x47 5.47x47 Y228
TM6
6x48 6.48x48 W281
6x52 6.52x52 H285
6x55 6.55x55 Q288
TM7
7x34 7.35x34 F307
7x35 7.36x35 T308
7x38 7.39x38 H311