Structure of PDB 7yu3 Chain R Binding Site BS01

Receptor Information
>7yu3 Chain R (length=290) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFIMLANLLVMV
AIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGPNTRRLTVSTWL
LRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVIW
TMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMV
VLYAHIFGYVRQRTMRMDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVC
CPQCDVLAYEKFFLLLAEFNSAMNPIIYSYRDKEMSATFR
Ligand information
Ligand IDK6L
InChIInChI=1S/C20H34NO6P/c1-2-3-4-5-10-17-11-6-7-12-18(17)13-8-9-14-20(23)21-19(15-22)16-27-28(24,25)26/h6-7,11-12,19,22H,2-5,8-10,13-16H2,1H3,(H,21,23)(H2,24,25,26)/t19-/m1/s1
InChIKeyLYWONSBDWRVEKO-LJQANCHMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCc1ccccc1CCCCC(=O)N[CH](CO)CO[P](O)(O)=O
OpenEye OEToolkits 2.0.7CCCCCCc1ccccc1CCCCC(=O)N[C@H](CO)COP(=O)(O)O
OpenEye OEToolkits 2.0.7CCCCCCc1ccccc1CCCCC(=O)NC(CO)COP(=O)(O)O
CACTVS 3.385CCCCCCc1ccccc1CCCCC(=O)N[C@H](CO)CO[P](O)(O)=O
FormulaC20 H34 N O6 P
Name[(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7yu3 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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PDB7yu3 Structure of the active G i -coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		K39 T109 R124 Y202 W210 E293 K294 L297
Binding residue
(residue number reindexed from 1)		K17 T87 R102 Y180 W188 E260 K261 L264
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001965 G-protein alpha-subunit binding
GO:0004930 G protein-coupled receptor activity
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0008289 lipid binding
GO:0030165 PDZ domain binding
GO:0035727 lysophosphatidic acid binding
GO:0070915 lysophosphatidic acid receptor activity
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007189 adenylate cyclase-activating G protein-coupled receptor signaling pathway
GO:0007193 adenylate cyclase-inhibiting 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:0008360 regulation of cell shape
GO:0010977 negative regulation of neuron projection development
GO:0014003 oligodendrocyte development
GO:0019222 regulation of metabolic process
GO:0021549 cerebellum development
GO:0021554 optic nerve development
GO:0022008 neurogenesis
GO:0022038 corpus callosum development
GO:0032060 bleb assembly
GO:0035025 positive regulation of Rho protein signal transduction
GO:0042552 myelination
GO:0043065 positive regulation of apoptotic process
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0043410 positive regulation of MAPK cascade
GO:0043951 negative regulation of cAMP-mediated signaling
GO:0051496 positive regulation of stress fiber assembly
GO:0060326 cell chemotaxis
GO:0060999 positive regulation of dendritic spine development
GO:0071453 cellular response to oxygen levels
GO:0071673 positive regulation of smooth muscle cell chemotaxis
GO:0098693 regulation of synaptic vesicle cycle
GO:0099149 regulation of postsynaptic neurotransmitter receptor internalization
GO:1902018 negative regulation of cilium assembly
GO:1904566 cellular response to 1-oleoyl-sn-glycerol 3-phosphate
Cellular Component
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0030139 endocytic vesicle
GO:0042734 presynaptic membrane
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0043198 dendritic shaft
GO:0045211 postsynaptic membrane
GO:0098978 glutamatergic synapse
GO:0098982 GABA-ergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7yu3, PDBe:7yu3, PDBj:7yu3
PDBsum7yu3
PubMed36109516
UniProtQ92633|LPAR1_HUMAN Lysophosphatidic acid receptor 1 (Gene Name=LPAR1)

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