Structure of PDB 7td4 Chain R Binding Site BS01

Receptor Information
>7td4 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]
DYVNYDIIVRHYNYTGKLNIKLTSVVFILICCFIILENIFVLLTIWKTKK
FHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLREGSMF
VALSASVFSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILG
GLPIMGWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIY
SLVRTRSRRLTFRKSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCK
VKTCDILFRAEYFLVLAVLNSGTNPIIYTLTNKEMRRAFI
Ligand information
Ligand IDJ8C
InChIInChI=1S/C29H35F3N2O3/c1-3-21-14-23(10-11-24(21)15-34-16-25(17-34)28(35)36)19(2)33-37-18-20-9-12-26(22-7-5-4-6-8-22)27(13-20)29(30,31)32/h9-14,22,25H,3-8,15-18H2,1-2H3,(H,35,36)/b33-19+
InChIKeyKIHYPELVXPAIDH-HNSNBQBZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCc1cc(ccc1CN2CC(C2)C(O)=O)C(C)=NOCc3ccc(C4CCCCC4)c(c3)C(F)(F)F
OpenEye OEToolkits 2.0.7CCc1cc(ccc1CN2CC(C2)C(=O)O)C(=NOCc3ccc(c(c3)C(F)(F)F)C4CCCCC4)C
OpenEye OEToolkits 2.0.7CCc1cc(ccc1CN2CC(C2)C(=O)O)/C(=N/OCc3ccc(c(c3)C(F)(F)F)C4CCCCC4)/C
CACTVS 3.385CCc1cc(ccc1CN2CC(C2)C(O)=O)/C(C)=N/OCc3ccc(C4CCCCC4)c(c3)C(F)(F)F
FormulaC29 H35 F3 N2 O3
Name1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid
ChEMBLCHEMBL2336071
DrugBankDB12371
ZINCZINC000006717453
PDB chain7td4 Chain R Residue 402 [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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PDB7td4 Differential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K34 N101 R120 E121 F125 L128 S129 L195 C206 V209 L213 L276 L297
Binding residue
(residue number reindexed from 1)		K17 N76 R95 E96 F100 L103 S104 L170 C181 V184 L188 L243 L264
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001664 G protein-coupled receptor binding
GO:0004930 G protein-coupled receptor activity
GO:0005515 protein binding
GO:0038036 sphingosine-1-phosphate receptor activity
GO:0046625 sphingolipid binding
Biological Process
GO:0001525 angiogenesis
GO:0001955 blood vessel maturation
GO:0003245 cardiac muscle tissue growth involved in heart morphogenesis
GO:0003376 sphingosine-1-phosphate receptor signaling pathway
GO:0006935 chemotaxis
GO:0007155 cell adhesion
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:0007420 brain development
GO:0008283 cell population proliferation
GO:0008284 positive regulation of cell population proliferation
GO:0016477 cell migration
GO:0019222 regulation of metabolic process
GO:0019226 transmission of nerve impulse
GO:0030032 lamellipodium assembly
GO:0030036 actin cytoskeleton organization
GO:0030155 regulation of cell adhesion
GO:0030182 neuron differentiation
GO:0030335 positive regulation of cell migration
GO:0030500 regulation of bone mineralization
GO:0030595 leukocyte chemotaxis
GO:0045124 regulation of bone resorption
GO:0045446 endothelial cell differentiation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0050927 positive regulation of positive chemotaxis
GO:0051497 negative regulation of stress fiber assembly
GO:0061384 heart trabecula morphogenesis
GO:0072678 T cell migration
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0045121 membrane raft
GO:0098793 presynapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7td4, PDBe:7td4, PDBj:7td4
PDBsum7td4
PubMed35136060
UniProtP21453|S1PR1_HUMAN Sphingosine 1-phosphate receptor 1 (Gene Name=S1PR1)

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