Structure of PDB 5y48 Chain A Binding Site BS01

Receptor Information
>5y48 Chain A (length=246) Species: 3672 (Momordica balsamina) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVSFRLSGADPSSYGMFIKDLRNALPHTEKVYNIPLLLPSVSGAGRYLLM
HLFNYDGNTITVAVDVTNVYIMGYLALTTSYFFNEPAADLASQYVFRSAR
RKITLPYSGNYERLQIAAGKPREKIPIGLPALDTAISTLLHYDSTAAAGA
LLVLIQTTAEAARFKYIEQQIQERAYRDEVPSSATISLENSWSGLSKQIQ
LAQGNNGVFRTPTVLVDSKGNRVQITNVTSNVVTSNIQLLLNTKNI
Ligand information
Ligand IDURA
InChIInChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
InChIKeyISAKRJDGNUQOIC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O=C1NC=CC(=O)N1
ACDLabs 10.04O=C1C=CNC(=O)N1
OpenEye OEToolkits 1.5.0C1=CNC(=O)NC1=O
FormulaC4 H4 N2 O2
NameURACIL
ChEMBLCHEMBL566
DrugBankDB03419
ZINCZINC000000895045
PDB chain5y48 Chain A Residue 301 [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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PDB5y48 Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Y70 I71 E85 G109 N110
Binding residue
(residue number reindexed from 1)		Y70 I71 E85 G109 N110
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=5.85,Kd=1.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) I71 E160 R163
Catalytic site (residue number reindexed from 1) I71 E160 R163
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0030598 rRNA N-glycosylase activity
GO:0090729 toxin activity
Biological Process
GO:0017148 negative regulation of translation
GO:0035821 modulation of process of another organism

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Molecular Function
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Biological Process
External links
PDB RCSB:5y48, PDBe:5y48, PDBj:5y48
PDBsum5y48
PubMed30007053
UniProtD9J2T9

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