Structure of PDB 2yaz Chain D Binding Site BS01

Receptor Information
>2yaz Chain D (length=257) 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
LAKENRL
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain2yaz Chain D Residue 1265 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yaz The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Q21 I28 W41 D79 H82 F83 N183 R186 Y191
Binding residue
(residue number reindexed from 1)		Q14 I21 W34 D72 H75 F76 N176 R179 Y184
Annotation score3
Binding affinityMOAD: Kd=7.3uM
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

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:2yaz, PDBe:2yaz, PDBj:2yaz
PDBsum2yaz
PubMed21454646
UniProtO15826

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