PDB
8YKW
Resolution
2.8 Å
Released
May 29, 2024
Receptor
succinate
Class
A
Species
Homo sapiens
Ligand
succinic acid
Function
Agonist
Reference
10.1038/S41422-024-00984-7

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Ligand Amino Acid Generic Number Segment Interaction Type
succinic acid Y30 1.39x39 TM1 polar (hydrogen bond)
succinic acid Y30 1.39x39 TM1 Van der Waals
succinic acid L79 2.60x60 TM2 Van der Waals
succinic acid Y83 2.64x64 TM2 Van der Waals
succinic acid Y83 2.64x64 TM2 polar (hydrogen bond)
succinic acid R99 3.29x29 TM3 polar (charge-assisted hydrogen bond)
succinic acid L102 3.32x32 TM3 hydrophobic
succinic acid L102 3.32x32 TM3 Van der Waals
succinic acid H103 3.33x33 TM3 Van der Waals
succinic acid F175 ECL2 Van der Waals
succinic acid R281 7.39x38 TM7 polar (charge-assisted hydrogen bond)
succinic acid F285 7.43x42 TM7 Van der Waals
succinic acid F285 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
succinate receptor
TM1
1x39 1.39x39 Y30
TM2
2x60 2.60x60 L79
2x64 2.64x64 Y83
TM3
3x29 3.29x29 R99
3x32 3.32x32 L102
3x33 3.33x33 H103
TM7
7x38 7.39x38 R281
7x42 7.43x42 F285