Structure of PDB 5fi9 Chain A Binding Site BS03

Receptor Information
>5fi9 Chain A (length=523) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLNLTCPACKVLFTALNHGLKKEPNVARVGSVAIKICKMLNIAPLDVCQS
AVHLFEDDVVEVWTRSVLSPSEACGLLLGSSCFSTWNISLPSVPKPPPKP
PSPPAPGAPVSRVLFLTDLHWDHEYLEGTDPYCADPLCCRRGSGWPPNSQ
KGAGFWGEYSKCDLPLRTLESLLKGLGPAGPFEMVYWTGDIPAHDVWQQS
RQDQLRALTTITDLVRKFLGPVPVYPAVGNHESTPVNGFPPPFIKGNQSS
QWLYEAMAKAWEPWLPADALHTLRIGGFYALTPRPGLRLISLNMNFCSRE
NFWLLINSTDPAGQLQWLVEELQAAENRGDKVHIIGHIPPGHCLKSWSWN
YYKIIARYENTLAGQFFGHTHVDEFEIFYDEETLSRPLAVAFLAPSATTF
INLNPGYRVYQIDGNYPGSSHVVLDHETYILNLTQANAAGGTPSWKRLYR
ARETYGLPDAMPASWHNLVYRMRDDEQLFQTFWFLYHKGHPPSEPCGTPC
RLATLCAQLSARADSPALCRHLM
Ligand information
Ligand IDNT8
InChIInChI=1S/C10H25NO6P2/c1-2-3-4-5-6-7-8-9-10(11,18(12,13)14)19(15,16)17/h2-9,11H2,1H3,(H2,12,13,14)(H2,15,16,17)
InChIKeyTWYYYYAFACTHMV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CCCCCCCCCC(N)(P(=O)(O)O)P(=O)(O)O
CACTVS 3.385CCCCCCCCCC(N)([P](O)(O)=O)[P](O)(O)=O
FormulaC10 H25 N O6 P2
Name(1-azanyl-1-phosphono-decyl)phosphonic acid
ChEMBLCHEMBL5288063
DrugBank
ZINCZINC000100166436
PDB chain5fi9 Chain A Residue 718 [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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PDB5fi9 Crystal structure of mammalian acid sphingomyelinase.
Resolution2.543 Å
Binding residue
(original residue number in PDB)		H206 D276 H280 N316 H317 H455 H457 H573
Binding residue
(residue number reindexed from 1)		H120 D190 H194 N230 H231 H369 H371 H487
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.12: sphingomyelin phosphodiesterase.
3.1.4.3: phospholipase C.
Gene Ontology
Molecular Function
GO:0004767 sphingomyelin phosphodiesterase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0034480 phosphatidylcholine phospholipase C activity
GO:0046872 metal ion binding
GO:0061750 acid sphingomyelin phosphodiesterase activity
Biological Process
GO:0001778 plasma membrane repair
GO:0006629 lipid metabolic process
GO:0006672 ceramide metabolic process
GO:0006685 sphingomyelin catabolic process
GO:0008203 cholesterol metabolic process
GO:0009410 response to xenobiotic stimulus
GO:0009615 response to virus
GO:0010212 response to ionizing radiation
GO:0023021 termination of signal transduction
GO:0034340 response to type I interferon
GO:0034612 response to tumor necrosis factor
GO:0034644 cellular response to UV
GO:0042060 wound healing
GO:0042220 response to cocaine
GO:0043065 positive regulation of apoptotic process
GO:0043407 negative regulation of MAP kinase activity
GO:0045807 positive regulation of endocytosis
GO:0046513 ceramide biosynthetic process
GO:0046598 positive regulation of viral entry into host cell
GO:0046718 symbiont entry into host cell
GO:0070555 response to interleukin-1
GO:0071277 cellular response to calcium ion
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005768 endosome
GO:0005811 lipid droplet
GO:0005886 plasma membrane
GO:0036019 endolysosome
GO:0042599 lamellar body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5fi9, PDBe:5fi9, PDBj:5fi9
PDBsum5fi9
PubMed27435900
UniProtQ04519|ASM_MOUSE Sphingomyelin phosphodiesterase (Gene Name=Smpd1)

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