PDB
5YWY
Resolution
3.2 Å
Released
Dec. 5, 2018
Receptor
EP4
Class
A
Species
Homo sapiens
Ligands
Fab001 (chain H)
ONO-AE3-208
Fab001 (chain L)
Function
Allosteric antagonist
Antagonist
Allosteric antagonist
Reference
10.1038/S41589-018-0131-3
Fab001 (chain H) ONO-AE3-208 Fab001 (chain L)

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Ligand Amino Acid Generic Number Segment Interaction Type
Fab001 (chain H) P20 1.35x35 TM1 hydrophobic
ONO-AE3-208 I23 1.38x38 TM1 hydrophobic
ONO-AE3-208 P24 1.39x39 TM1 hydrophobic
ONO-AE3-208 T76 2.61x61 TM2 Van der Waals
ONO-AE3-208 T76 2.61x61 TM2 polar (hydrogen bond)
ONO-AE3-208 Y80 2.65x65 TM2 polar (hydrogen bond)
ONO-AE3-208 Y80 2.65x65 TM2 polar (hydrogen bond)
Fab001 (chain H) Y80 2.65x65 TM2 hydrophobic
Fab001 (chain H) G83 ECL1 polar (hydrogen bond with backbone)
Fab001 (chain H) G83 ECL1 Van der Waals
Fab001 (chain H) Q84 23.49x49 ECL1 Van der Waals
Fab001 (chain H) G87 23.52x52 ECL1 Van der Waals
Fab001 (chain H) G88 3.21x21 TM3 Van der Waals
Fab001 (chain H) Q89 3.22x22 TM3 Van der Waals
ONO-AE3-208 L99 3.32x32 TM3 Van der Waals
Fab001 (chain H) L163 ECL2 polar (hydrogen bond with backbone)
Fab001 (chain H) L163 ECL2 Van der Waals
Fab001 (chain H) Q164 ECL2 Van der Waals
Fab001 (chain H) Q164 ECL2 polar (hydrogen bond with backbone)
Fab001 (chain H) Y165 ECL2 Van der Waals
Fab001 (chain H) Y165 ECL2 aromatic (edge-to-face)
Fab001 (chain H) Y165 ECL2 polar (hydrogen bond with backbone)
Fab001 (chain H) P166 ECL2 Van der Waals
Fab001 (chain H) P166 ECL2 hydrophobic
Fab001 (chain H) D167 ECL2 polar (charge-assisted hydrogen bond)
Fab001 (chain H) T168 ECL2 Van der Waals
ONO-AE3-208 W169 ECL2 hydrophobic
ONO-AE3-208 W169 ECL2 Van der Waals
Fab001 (chain H) L302 ECL3 Van der Waals
Fab001 (chain H) L302 ECL3 hydrophobic
Fab001 (chain L) R304 ECL3 polar (charge-assisted hydrogen bond)
Fab001 (chain H) R304 ECL3 polar (charge-assisted hydrogen bond)
Fab001 (chain L) E305 ECL3 polar (charge-assisted hydrogen bond)
ONO-AE3-208 L312 7.36x35 TM7 Van der Waals
ONO-AE3-208 L312 7.36x35 TM7 hydrophobic
ONO-AE3-208 I315 7.39x38 TM7 hydrophobic
ONO-AE3-208 I315 7.39x38 TM7 Van der Waals
ONO-AE3-208 R316 7.40x39 TM7 polar (charge-assisted hydrogen bond)
ONO-AE3-208 S319 7.43x42 TM7 Van der Waals
ONO-AE3-208 V320 7.44x43 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
EP4 receptor
TM1
1x35 1.35x35 P20
1x38 1.38x38 I23
1x39 1.39x39 P24
TM2
2x61 2.61x61 T76
2x65 2.65x65 Y80
ECL1
23x49 23.49x49 Q84
23x52 23.52x52 G87
TM3
3x21 3.21x21 G88
3x22 3.22x22 Q89
3x32 3.32x32 L99
TM7
7x35 7.36x35 L312
7x38 7.39x38 I315
7x39 7.40x39 R316
7x42 7.43x42 S319
7x43 7.44x43 V320