Structure of PDB 2par Chain A Binding Site BS02

Receptor Information
>2par Chain A (length=175) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRK
FGGNVNAERIALLAMYHDASAVLTGDLPTEYKAIEKIAQQKLVDMVPEEL
RDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTR
LEATLEARRSQEMDYFMEIFVPSFH
Ligand information
Ligand IDTMP
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-PHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain2par 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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PDB2par 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 L163
Binding residue
(residue number reindexed from 1)		R17 W18 H32 D76 T79 D125 L151
Annotation score3
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:2par, PDBe:2par, PDBj:2par
PDBsum2par
PubMed18353368
UniProtP76491|5DNU_ECOLI 5'-deoxynucleotidase YfbR (Gene Name=yfbR)

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