PDB
8JPN
Resolution
2.9 Å
Released
May 22, 2024
Receptor
succinate
Class
A
Species
Homo sapiens
Ligand
cis-epoxysuccinic acid
Function
Agonist
Reference
10.1038/S41422-024-00968-7

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Ligand Amino Acid Generic Number Segment Interaction Type
cis-epoxysuccinic acid Y30 1.39x39 TM1 polar (hydrogen bond)
cis-epoxysuccinic acid L79 2.60x60 TM2 Van der Waals
cis-epoxysuccinic acid Y83 2.64x64 TM2 polar (hydrogen bond)
cis-epoxysuccinic acid Y83 2.64x64 TM2 Van der Waals
cis-epoxysuccinic acid R99 3.29x29 TM3 polar (charge-assisted hydrogen bond)
cis-epoxysuccinic acid L102 3.32x32 TM3 Van der Waals
cis-epoxysuccinic acid D174 45.52x52 ECL2 Van der Waals
cis-epoxysuccinic acid Y175 ECL2 polar (hydrogen bond with backbone)
cis-epoxysuccinic acid Y175 ECL2 Van der Waals
cis-epoxysuccinic acid R281 7.39x38 TM7 polar (charge-assisted hydrogen bond)

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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
ECL2
45x52 45.52x52 D174
TM7
7x38 7.39x38 R281