Structure information

Y1 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

7VGX

SPECIES

Homo sapiens

RESOLUTION

3.200

PREFERRED CHAIN

R

REFERENCE

10.1038/S41467-022-28510-6

PUBLICATION DATE

Feb. 23, 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 C93 2.57x56 TM2 polar (hydrogen bond)
neuropeptide Y C93 2.57x56 TM2 Van der Waals
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 D104 2.68x67 TM2 polar (charge-assisted hydrogen bond)
neuropeptide Y N116 3.28x28 TM3 polar (hydrogen bond)
neuropeptide Y Q120 3.32x32 TM3 polar (hydrogen bond)
neuropeptide Y Q120 3.32x32 TM3 Van der Waals
neuropeptide Y C121 3.33x33 TM3 Van der Waals
neuropeptide Y C121 3.33x33 TM3 hydrophobic
neuropeptide Y I124 3.36x36 TM3 hydrophobic
neuropeptide Y I124 3.36x36 TM3 Van der Waals
neuropeptide Y F173 4.60x61 TM4 hydrophobic
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 V197 ECL2 hydrophobic
neuropeptide Y F199 45.51x51 ECL2 Van der Waals
neuropeptide Y F199 45.51x51 ECL2 hydrophobic
neuropeptide Y D200 45.52x52 ECL2 polar (hydrogen bond with backbone)
neuropeptide Y D200 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
neuropeptide Y R208 5.35x36 TM5 polar (charge-assisted hydrogen bond)
neuropeptide Y T212 5.39x40 TM5 Van der Waals
neuropeptide Y Q219 5.46x461 TM5 polar (hydrogen bond)
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 H290 ECL3 Van der Waals
neuropeptide Y C296 ECL3 Van der Waals
neuropeptide Y H298 7.31x30 TM7 Van der Waals
neuropeptide Y F302 7.35x34 TM7 Van der Waals
neuropeptide Y F302 7.35x34 TM7 hydrophobic
neuropeptide Y H306 7.39x38 TM7 polar (hydrogen bond)
neuropeptide Y H306 7.39x38 TM7 Van der Waals

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
2x60 2.61x60 T97
2x63 2.64x63 Y100
2x67 2.68x67 D104
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
5x36 5.35x36 R208
5x40 5.39x40 T212
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
7x34 7.35x34 F302
7x38 7.39x38 H306