Structure of PDB 5ebe Chain A Binding Site BS03

Receptor Information
>5ebe Chain A (length=418) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPPAIGQFWHVTDLHLDPTYHITDDHTKVCASSKGANASNPGPFGDVLCD
SPYQLILSAFDFIKNSGQEASFMIWTGDSPPHVPVPELSTDTVINVITNM
TTTIQSLFPNLQVFPALGNHDYWPQDQLPVVTSKVYNAVANLWKPWLDEE
AISTLRKGGFYSQKVTTNPNLRIISLNTNLYYGPNIMTLNKTDPANQFEW
LESTLNNSQQNKEKVYIIAHVPVGYLPSSQNITAMREYYNEKLIDIFQKY
SDVIAGQFYGHTHRDSIMVLSDKKGSPVNSLFVAPAVTPVKSVLEKQTNN
PGIRLFQYDPRDYKLLDMLQYYLNLTEANLKGESIWKLEYILTQTYDIED
LQPESLYGLAKQFTILDSKQFIKYYNYFFVSYDSSVTCDKTCKAFQICAI
MNLDNISYADCLKQLYIK
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain5ebe Chain A Residue 607 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ebe The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D110 H114 N151 H152 H293 H295 V322 K323
Binding residue
(residue number reindexed from 1)		D78 H82 N119 H120 H261 H263 V290 K291
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.-
3.6.1.15: nucleoside-triphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0004767 sphingomyelin phosphodiesterase activity
GO:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
Biological Process
GO:0006685 sphingomyelin catabolic process
GO:0009143 nucleoside triphosphate catabolic process
GO:0160049 negative regulation of cGAS/STING signaling pathway
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ebe, PDBe:5ebe, PDBj:5ebe
PDBsum5ebe
PubMed26783088
UniProtQ92484|ASM3A_HUMAN Cyclic GMP-AMP phosphodiesterase SMPDL3A (Gene Name=SMPDL3A)

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