Structure information

Y1 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

7X9A

SPECIES

Homo sapiens

RESOLUTION

3.200

PREFERRED CHAIN

R

REFERENCE

10.1126/SCIADV.ABM1232

PUBLICATION DATE

May 18, 2022

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
neuropeptide Y F28 N-term hydrophobic
neuropeptide Y E29 N-term polar (hydrogen bond with backbone)
neuropeptide Y E29 N-term polar (charge-assisted hydrogen bond)
neuropeptide Y N30 N-term Van der Waals
neuropeptide Y D32 N-term polar (hydrogen bond with backbone)
neuropeptide Y D32 N-term polar (charge-assisted hydrogen bond)
neuropeptide Y C33 N-term Van der Waals
neuropeptide Y C93 2.57x56 TM2 Van der Waals
neuropeptide Y F96 2.60x59 TM2 Van der Waals
neuropeptide Y T97 2.61x60 TM2 polar (hydrogen bond)
neuropeptide Y T97 2.61x60 TM2 Van der Waals
neuropeptide Y Y100 2.64x63 TM2 hydrophobic
neuropeptide Y Y100 2.64x63 TM2 Van der Waals
neuropeptide Y T101 2.65x64 TM2 Van der Waals
neuropeptide Y D104 ECL1 Van der Waals
neuropeptide Y N116 3.28x28 TM3 polar (hydrogen bond)
neuropeptide Y Q120 3.32x32 TM3 Van der Waals
neuropeptide Y Q120 3.32x32 TM3 polar (hydrogen bond)
neuropeptide Y C121 3.33x33 TM3 Van der Waals
neuropeptide Y I124 3.36x36 TM3 hydrophobic
neuropeptide Y F173 4.60x61 TM4 hydrophobic
neuropeptide Y F173 4.60x61 TM4 Van der Waals
neuropeptide Y E182 ECL2 polar (hydrogen bond with backbone)
neuropeptide Y E182 ECL2 Van der Waals
neuropeptide Y P183 ECL2 Van der Waals
neuropeptide Y P183 ECL2 polar (hydrogen bond with backbone)
neuropeptide Y F184 ECL2 hydrophobic
neuropeptide Y F184 ECL2 Van der Waals
neuropeptide Y T188 ECL2 polar (hydrogen bond)
neuropeptide Y D190 ECL2 polar (charge-assisted hydrogen bond)
neuropeptide Y Y192 ECL2 Van der Waals
neuropeptide Y F199 45.51x51 ECL2 hydrophobic
neuropeptide Y F199 45.51x51 ECL2 Van der Waals
neuropeptide Y D200 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
neuropeptide Y D205 5.32x33 TM5 polar (charge-assisted hydrogen bond)
neuropeptide Y R208 5.35x36 TM5 Van der Waals
neuropeptide Y T212 5.39x40 TM5 Van der Waals
neuropeptide Y T212 5.39x40 TM5 polar (hydrogen bond)
neuropeptide Y L215 5.42x43 TM5 Van der Waals
neuropeptide Y Q219 5.46x461 TM5 polar (hydrogen bond)
neuropeptide Y Q219 5.46x461 TM5 polar (hydrogen bond)
neuropeptide Y F282 6.54x54 TM6 hydrophobic
neuropeptide Y F282 6.54x54 TM6 Van der Waals
neuropeptide Y N283 6.55x55 TM6 polar (hydrogen bond)
neuropeptide Y N283 6.55x55 TM6 Van der Waals
neuropeptide Y N283 6.55x55 TM6 polar (hydrogen bond)
neuropeptide Y F286 6.58x58 TM6 Van der Waals
neuropeptide Y F286 6.58x58 TM6 hydrophobic
neuropeptide Y D287 6.59x59 TM6 polar (charge-assisted hydrogen bond)
neuropeptide Y N289 ECL3 Van der Waals
neuropeptide Y I292 ECL3 Van der Waals
neuropeptide Y I292 ECL3 hydrophobic
neuropeptide Y T295 ECL3 polar (hydrogen bond)
neuropeptide Y C296 ECL3 polar (hydrogen bond)
neuropeptide Y H298 7.31x30 TM7 polar (hydrogen bond)
neuropeptide Y H298 7.31x30 TM7 polar (hydrogen bond)
neuropeptide Y N299 7.32x31 TM7 Van der Waals
neuropeptide Y N299 7.32x31 TM7 polar (hydrogen bond)
neuropeptide Y F302 7.35x34 TM7 hydrophobic
neuropeptide Y F302 7.35x34 TM7 Van der Waals
neuropeptide Y H306 7.39x38 TM7 Van der Waals
neuropeptide Y H306 7.39x38 TM7 polar (hydrogen bond)

Ligands

neuropeptide Y

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Residue Diagrams

L N G S V G L I I V A G Y A L A L T F I 1 V N L S F S D L L V A M I C L P F T F V Y 2 L V L S F I S V T I S V C Q V F P N L K 3 A Y V G I A V I W V L A V A S S L P F 4 Y C I F I F C L P G F Y Q L V L L L T T Y 5 L S I V V A F A V C W L P L T I F N T V 6 I P N V C T S I M A T L H C L L F L L 7
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ICL1 K E M R ICL1ECL1 H W V F ECL1ICL2 P R G W R P ICL2ECL2 V M T D E P F Q N V T L D A Y K D K Y V C F D Q F P ECL2ICL3 K M R ICL3ECL3 H Q I I A ECL3N-term M N S T L F S Q V E N H S V H S N F S E K N A Q L L A F E N D D C H L N-termC-term N F C D F R S R D D D Y E T I A M S T M H T D V S K T S L K Q A S P V A F K K I N N N D D N E K I C-term P L A M I F T L A L A Y G A V I I L G V S G N L A L I I I I L K Q N V T N I L I V N L S F S D L L V A I M C L P F T F V Y T L M D G E A M C K L N P F V Q C V S I T V S I F S L V L I A V E R H Q L I I N N N R H A Y V G I A V I W V L A V A S S L P F L I Y Q S D S H R L S Y T T L L L V L Q Y F G P L C F I F I C Y F K I Y I R L K R R N N M M D D N K Y R S S E T K R I N I M L L S I V V A F A V C W L P L T I F N T V F D W N T C N H N L L F L L C H L T A M I S T C V N P I F Y G F L N K N L Q F F Q R D F F
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Residue Table


GPCRdb(A)
GPCRdb(A)
Y1 receptor
TM2
2x56 2.57x56 C93
2x59 2.60x59 F96
2x60 2.61x60 T97
2x63 2.64x63 Y100
2x64 2.65x64 T101
TM3
3x28 3.28x28 N116
3x32 3.32x32 Q120
3x33 3.33x33 C121
3x36 3.36x36 I124
TM4
4x61 4.60x61 F173
ECL2
45x51 45.51x51 F199
45x52 45.52x52 D200
TM5
5x33 5.32x33 D205
5x36 5.35x36 R208
5x40 5.39x40 T212
5x43 5.42x43 L215
5x461 5.46x461 Q219
TM6
6x54 6.54x54 F282
6x55 6.55x55 N283
6x58 6.58x58 F286
6x59 6.59x59 D287
TM7
7x30 7.31x30 H298
7x31 7.32x31 N299
7x34 7.35x34 F302
7x38 7.39x38 H306