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BioLiP

Structure of PDB 2yb0 Chain D Binding Site BS02

Receptor Information
>2yb0 Chain D (length=255) Species: 5664 (Leishmania major) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYP
WKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPL
KEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVI
IECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNS
LLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFA
LAKEN
Ligand information
Ligand IDDUR
InChIInChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
InChIKeyMXHRCPNRJAMMIM-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CO
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)CO)O
CACTVS 3.341OC[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O
CACTVS 3.341OC[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O
FormulaC9 H12 N2 O5
Name2'-DEOXYURIDINE
ChEMBLCHEMBL353955
DrugBankDB02256
ZINCZINC000000155696
PDB chain2yb0 Chain E Residue 1266 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yb0 The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		W60 W61
Binding residue
(residue number reindexed from 1)		W53 W54
Annotation score2
Binding affinityMOAD: Kd=140uM
Enzymatic activity
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0004170 dUTP diphosphatase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Cellular Component
GO:0005654 nucleoplasm

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Molecular Function
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Cellular Component
External links

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