Structure of PDB 5fi9 Chain B Binding Site BS01

Receptor Information
>5fi9 Chain B (length=529) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLNLTCPACKVLFTALNHGLKKEPNVARVGSVAIKICKMLNIAPLDVCQS
AVHLFEDDVVEVWTRSVLSPSEACGLLLGSSCGHWDIFSTWNISLPSVPK
PPPKPPSPPAPGAPVSRVLFLTDLHWDHEYLEGTDPYCADPLCCRRGSGW
PPNSQKGAGFWGEYSKCDLPLRTLESLLKGLGPAGPFEMVYWTGDIPAHD
VWQQSRQDQLRALTTITDLVRKFLGPVPVYPAVGNHESTPVNGFPPPFIK
GNQSSQWLYEAMAKAWEPWLPADALHTLRIGGFYALTPRPGLRLISLNMN
FCSRENFWLLINSTDPAGQLQWLVEELQAAENRGDKVHIIGHIPPGHCLK
SWSWNYYKIIARYENTLAGQFFGHTHVDEFEIFYDEETLSRPLAVAFLAP
SATTFINLNPGYRVYQIDGNYPGSSHVVLDHETYILNLTQANAAGGTPSW
KRLYRARETYGLPDAMPASWHNLVYRMRDDEQLFQTFWFLYHKGHPPSEP
CGTPCRLATLCAQLSARADSPALCRHLMP
Ligand information
Ligand IDFUC
InChIInChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6+/m0/s1
InChIKeySHZGCJCMOBCMKK-SXUWKVJYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)C
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)O)O)O)O
OpenEye OEToolkits 1.5.0C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O
CACTVS 3.341C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
FormulaC6 H12 O5
Namealpha-L-fucopyranose;
alpha-L-fucose;
6-deoxy-alpha-L-galactopyranose;
L-fucose;
fucose
ChEMBLCHEMBL1232862
DrugBankDB04473
ZINCZINC000001532814
PDB chain5fi9 Chain K Residue 5 [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)		N122 P125
Binding residue
(residue number reindexed from 1)		N41 P44
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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