Structure of PDB 8gdc Chain R Binding Site BS01

Receptor Information
>8gdc Chain R (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VAFPITMLLTGFVGNALAMLLVSRSKSFLLCIGWLALTDLVGQLLTTPVV
IVVYLSKQRWEHIDPSGRLCTFFGLTMTVFGLSSLFIASAMAVERALAIR
APHWYASHMKTRATRAVLLGVWLAVLAFALLPVLGVGQYTVQWPGTWCFI
STGGNLFFASAFAFLGLLALTVTFSCNLATIKALVSRCRAKAAQWGRITT
ETAIQLMGIMCVLSVCWSPLLIMMLKMIFCNFFLIAVRLASLNQILDPWV
YLLLRKIL
Ligand information
Ligand IDP2E
InChIInChI=1S/C20H32O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h4,7,12-13,15-17,19,21,23H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,19+/m0/s1
InChIKeyXEYBRNLFEZDVAW-ARSRFYASSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCC(C=CC1C(CC(=O)C1CC=CCCCC(=O)O)O)O
CACTVS 3.341CCCCC[CH](O)C=C[CH]1[CH](O)CC(=O)[CH]1CC=CCCCC(O)=O
OpenEye OEToolkits 1.5.0CCCCC[C@@H](\C=C\[C@H]1[C@@H](CC(=O)[C@@H]1C\C=C/CCCC(=O)O)O)O
CACTVS 3.341CCCCC[C@H](O)/C=C/[C@H]1[C@H](O)CC(=O)[C@@H]1C\C=C/CCCC(O)=O
ACDLabs 10.04O=C1CC(O)C(/C=C/C(O)CCCCC)C1C\C=C/CCCC(=O)O
FormulaC20 H32 O5
Name(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid;
Prostaglandin E2
ChEMBLCHEMBL548
DrugBankDB00917
ZINCZINC000003830713
PDB chain8gdc Chain R Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8gdc Single hormone or synthetic agonist induces G s /G i coupling selectivity of EP receptors via distinct binding modes and propagating paths.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		M58 G102 Q103 M137 W207 R333 S336
Binding residue
(residue number reindexed from 1)		M7 G42 Q43 M77 W147 R238 S241
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004930 G protein-coupled receptor activity
GO:0004955 prostaglandin receptor activity
GO:0004957 prostaglandin E receptor activity
Biological Process
GO:0006954 inflammatory response
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007189 adenylate cyclase-activating G protein-coupled receptor signaling pathway
GO:0007200 phospholipase C-activating G protein-coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0008219 cell death
GO:0014827 intestine smooth muscle contraction
GO:0031622 positive regulation of fever generation
GO:0060455 negative regulation of gastric acid secretion
Cellular Component
GO:0005635 nuclear envelope
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gdc, PDBe:8gdc, PDBj:8gdc
PDBsum8gdc
PubMed37478163
UniProtP43115|PE2R3_HUMAN Prostaglandin E2 receptor EP3 subtype (Gene Name=PTGER3)

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