Structure of PDB 3ivd Chain A Binding Site BS03

Receptor Information
>3ivd Chain A (length=499) Species: 217992 (Escherichia coli O6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAKDVTIIYTNDLHAHVEPYKVPWIADGKRDIGGWANITTLVKQEKAKNK
ATWFFDAGDYFTGPYISSLTKGKAIIDIMNTMPFDAVTIGNHEFDHGWDN
TLLQLSQAKFPIVQGNIFYQNSSKSFWDKPYTIIEKDGVKIGVIGLHGVF
AFNDTVSAATRVGIEARDEIKWLQRYIDELKGKVDLTVALIHEGVPARQS
SMGGTDVRRALDKDIQTASQVKGLDILITGHAHVGTPEPIKVGNTLILST
DSGGIDVGKLVLDYKEKPHNFTVKNFELKTIYADEWKPDQQTKQVIDGWN
KKLDEVVQQTVAQSPVELKRAYGESASLGNLAADALLAAAGKNTQLALTN
SGGIRNEIPAGAITMGGVISTFPFPNELVTMELTGKQLRSLMEHGASLSN
GVLQVSKGLEMKYDSSKPVGQRVITLTLNGKPIEDATVYHIATQSFLADG
GDGFTAFTEGKARNITGGYYVYHAVVDYFKAGNTITDEQLNGMRVKDIK
Ligand information
Ligand IDURI
InChIInChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChIKeyDRTQHJPVMGBUCF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
FormulaC9 H12 N2 O6
NameURIDINE
ChEMBLCHEMBL100259
DrugBankDB02745
ZINCZINC000002583633
PDB chain3ivd Chain A Residue 603 [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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PDB3ivd Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Uridine
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H112 T175 N370 G372 R375 F394 N396 F466 D472
Binding residue
(residue number reindexed from 1)		H92 T155 N350 G352 R355 F374 N376 F446 D452
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D32 H34 D79 N111 H112 D115 H212 H251 H253 Y342 R375
Catalytic site (residue number reindexed from 1) D12 H14 D59 N91 H92 D95 H192 H231 H233 Y322 R355
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0046872 metal ion binding
Biological Process
GO:0009166 nucleotide catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3ivd, PDBe:3ivd, PDBj:3ivd
PDBsum3ivd
PubMed
UniProtA0A0H2VD83

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