PDB
5YWY
Resolution
3.2 Å
Released
Dec. 5, 2018
Receptor
EP4
Class
A
Species
Homo sapiens
Ligands
Function
Fab001 (chain H)
Allosteric antagonist
ONO-AE3-208
Antagonist
Fab001 (chain L)
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 Van der Waals
ONO-AE3-208 P24 1.39x39 TM1 hydrophobic
ONO-AE3-208 M27 1.42x42 TM1 hydrophobic
ONO-AE3-208 V72 2.57x57 TM2 Van der Waals
ONO-AE3-208 T76 2.61x61 TM2 polar (hydrogen bond)
ONO-AE3-208 Y80 2.65x65 TM2 polar (hydrogen bond)
Fab001 (chain H) Y80 2.65x65 TM2 aromatic (edge-to-face)
Fab001 (chain H) Y80 2.65x65 TM2 hydrophobic
Fab001 (chain H) G83 ECL1 polar (hydrogen bond with backbone)
Fab001 (chain H) Q84 23.49x49 ECL1 Van der Waals
Fab001 (chain H) W85 23.50x50 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 hydrophobic
Fab001 (chain H) C92 3.25x25 TM3 Van der Waals
ONO-AE3-208 L99 3.32x32 TM3 Van der Waals
Fab001 (chain H) L163 ECL2 hydrophobic
Fab001 (chain H) Q164 ECL2 Van der Waals
Fab001 (chain H) Y165 ECL2 hydrophobic
Fab001 (chain H) Y165 ECL2 aromatic (edge-to-face)
Fab001 (chain H) P166 ECL2 Van der Waals
Fab001 (chain H) D167 ECL2 polar (hydrogen bond)
ONO-AE3-208 T168 ECL2 Van der Waals
Fab001 (chain H) T168 ECL2 hydrophobic
ONO-AE3-208 W169 ECL2 hydrophobic
ONO-AE3-208 W169 ECL2 aromatic (edge-to-face)
Fab001 (chain H) L302 ECL3 hydrophobic
Fab001 (chain L) R304 ECL3 aromatic (pi-cation)
Fab001 (chain L) R304 ECL3 polar (charge-charge)
Fab001 (chain L) R304 ECL3 polar (hydrogen bond)
Fab001 (chain H) R304 ECL3 polar (charge-charge)
Fab001 (chain L) E305 ECL3 polar (charge-charge)
Fab001 (chain L) E305 ECL3 polar (hydrogen bond)
ONO-AE3-208 L312 7.36x35 TM7 hydrophobic
ONO-AE3-208 I315 7.39x38 TM7 hydrophobic
ONO-AE3-208 R316 7.40x39 TM7 hydrophobic
ONO-AE3-208 R316 7.40x39 TM7 polar (charge-charge)
ONO-AE3-208 R316 7.40x39 TM7 polar (hydrogen bond)
ONO-AE3-208 R316 7.40x39 TM7 aromatic (pi-cation)
ONO-AE3-208 S319 7.43x42 TM7 Van der Waals
ONO-AE3-208 V320 7.44x43 TM7 hydrophobic

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NGL is a WebGL based 3D viewer powered by MMTF.

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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
1x42 1.42x42 M27
TM2
2x57 2.57x57 V72
2x61 2.61x61 T76
2x65 2.65x65 Y80
ECL1
23x49 23.49x49 Q84
23x50 23.50x50 W85
23x52 23.52x52 G87
TM3
3x21 3.21x21 G88
3x22 3.22x22 Q89
3x25 3.25x25 C92
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