Structure of PDB 3ivd Chain B Binding Site BS03

Receptor Information
>3ivd Chain B (length=499) Species: 217992 (Escherichia coli O6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKDVTIIYTNDLHAHVEPYKVPWIADGKRDIGGWANITTLVKQEKAKNKA
TWFFDAGDYFTGPYISSLTKGKAIIDIMNTMPFDAVTIGNHEFDHGWDNT
LLQLSQAKFPIVQGNIFYQNSSKSFWDKPYTIIEKDGVKIGVIGLHGVFA
FNDTVSAATRVGIEARDEIKWLQRYIDELKGKVDLTVALIHEGVPARQSS
MGGTDVRRALDKDIQTASQVKGLDILITGHAHVGTPEPIKVGNTLILSTD
SGGIDVGKLVLDYKEKPHNFTVKNFELKTIYADEWKPDQQTKQVIDGWNK
KLDEVVQQTVAQSPVELKRAYGESASLGNLAADALLAAAGKNTQLALTNS
GGIRNEIPAGAITMGGVISTFPFPNELVTMELTGKQLRSLMEHGASLSNG
VLQVSKGLEMKYDSSKPVGQRVITLTLNGKPIEDATVYHIATQSFLADGG
DGFTAFTEGKARNITGGYYVYHAVVDYFKAGNTITDEQLNGMRVKDIKE
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 B Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		H91 T154 N349 G351 R354 F373 N375 F445 D451
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) D11 H13 D58 N90 H91 D94 H191 H230 H232 Y321 R354
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

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

[Back to BioLiP]