Structure of PDB 2yb0 Chain A Binding Site BS02

Receptor Information

>2yb0 Chain A (length=258) Species: 5664 (Leishmania major)

ANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSY
PWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKP
LKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDV
IIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDN
SLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWF
ALAKENRL

Ligand information

• Ligand ID: DUR
• InChI: InChI=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
• InChIKey: MXHRCPNRJAMMIM-SHYZEUOFSA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CO
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)CO)O
  CACTVS 3.341: OC[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O
  CACTVS 3.341: OC[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O
• Formula: C9 H12 N2 O5
• Name: 2'-DEOXYURIDINE
• ChEMBL: CHEMBL353955
• DrugBank: DB02256
• ZINC: ZINC000000155696
• PDB chain: 2yb0 Chain B Residue 1266

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yb0 The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine.
• Resolution: 2.28 Å
• Binding residue (original residue number in PDB): W60 W61
• Binding residue (residue number reindexed from 1): W54 W55
• Annotation score: 2
• Binding affinity: MOAD: Kd=140uM
  PDBbind-CN: -logKd/Ki=3.85,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

External links

• PDB: RCSB:2yb0, PDBe:2yb0, PDBj:2yb0
• PDBsum: 2yb0
• PubMed: 21454646
• UniProt: O15826