Structure of PDB 2pau Chain A Binding Site BS02

Receptor Information
>2pau Chain A (length=176) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFG
GNVNAERIALLAMYHDASAVLTGDLPTPIAQEYKAIEKIAQQKLVDMVPE
ELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAK
TRLEATLEARRSQEMDYFMEIFVPSF
Ligand information
Ligand IDD5M
InChIInChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeyKHWCHTKSEGGWEX-RRKCRQDMSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H14 N5 O6 P
Name2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL1206239
DrugBank
ZINCZINC000001713574
PDB chain2pau Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2pau Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R18 W19 H33 D77 T80 D137
Binding residue
(residue number reindexed from 1)		R15 W16 H30 D74 T77 D127
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.3.89: 5'-deoxynucleotidase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002953 5'-deoxynucleotidase activity
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0050340 thymidylate 5'-phosphatase activity
GO:0050897 cobalt ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0010139 pyrimidine deoxyribonucleotide salvage
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2pau, PDBe:2pau, PDBj:2pau
PDBsum2pau
PubMed18353368
UniProtP76491|5DNU_ECOLI 5'-deoxynucleotidase YfbR (Gene Name=yfbR)

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