PDB
8YKV
Resolution
2.5 Å
Released
May 29, 2024
Receptor
succinate
Class
A
Species
Homo sapiens
Ligand
compound 31 [PMID: 29968758]
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
compound 31 [PMID: 29968758] L79 2.60x60 TM2 hydrophobic
compound 31 [PMID: 29968758] Y83 2.64x64 TM2 polar (hydrogen bond)
compound 31 [PMID: 29968758] Y83 2.64x64 TM2 Van der Waals
compound 31 [PMID: 29968758] G86 ECL1 Van der Waals
compound 31 [PMID: 29968758] G86 ECL1 polar (hydrogen bond with backbone)
compound 31 [PMID: 29968758] W88 23.50x50 ECL1 Van der Waals
compound 31 [PMID: 29968758] W88 23.50x50 ECL1 hydrophobic
compound 31 [PMID: 29968758] N98 3.28x28 TM3 Van der Waals
compound 31 [PMID: 29968758] R99 3.29x29 TM3 polar (charge-assisted hydrogen bond)
compound 31 [PMID: 29968758] L102 3.32x32 TM3 hydrophobic
compound 31 [PMID: 29968758] L102 3.32x32 TM3 Van der Waals
compound 31 [PMID: 29968758] H103 3.33x33 TM3 Van der Waals
compound 31 [PMID: 29968758] H103 3.33x33 TM3 polar (hydrogen bond)
compound 31 [PMID: 29968758] D174 45.52x52 ECL2 polar (hydrogen bond with backbone)
compound 31 [PMID: 29968758] D174 45.52x52 ECL2 Van der Waals
compound 31 [PMID: 29968758] F175 ECL2 Van der Waals
compound 31 [PMID: 29968758] 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
TM2
2x60 2.60x60 L79
2x64 2.64x64 Y83
ECL1
23x50 23.50x50 W88
TM3
3x28 3.28x28 N98
3x29 3.29x29 R99
3x32 3.32x32 L102
3x33 3.33x33 H103
ECL2
45x52 45.52x52 D174
TM7
7x38 7.39x38 R281