Structure of PDB 5i85 Chain A Binding Site BS04

Receptor Information
>5i85 Chain A (length=528) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVCQS
IVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTVPK
PPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGL
PPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHD
VWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIE
GNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLNMN
FCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHCLK
SWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFLAP
SATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHW
QLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEP
CGTPCRLATLCAQLSARADSPALCRHLM
Ligand information
Ligand IDPC
InChIInChI=1S/C5H14NO4P/c1-6(2,3)4-5-10-11(7,8)9/h4-5H2,1-3H3,(H-,7,8,9)/p+1
InChIKeyYHHSONZFOIEMCP-UHFFFAOYSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCC[N+](C)(C)C
CACTVS 3.341C[N+](C)(C)CCO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C[N+](C)(C)CCOP(=O)(O)O
FormulaC5 H15 N O4 P
NamePHOSPHOCHOLINE
ChEMBLCHEMBL1235161
DrugBankDB03945
ZINCZINC000001532692
PDB chain5i85 Chain A Residue 727 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5i85 Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		H208 D278 H282 N318 H319 H457 H459
Binding residue
(residue number reindexed from 1)		H125 D195 H199 N235 H236 H374 H376
Annotation score5
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:0005515 protein binding
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:0006684 sphingomyelin metabolic process
GO:0006685 sphingomyelin catabolic process
GO:0007165 signal transduction
GO:0007399 nervous system development
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:0046479 glycosphingolipid catabolic process
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
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5i85, PDBe:5i85, PDBj:5i85
PDBsum5i85
PubMed27725636
UniProtP17405|ASM_HUMAN Sphingomyelin phosphodiesterase (Gene Name=SMPD1)

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