Structure of PDB 4apz Chain B Binding Site BS01

Receptor Information

>4apz Chain B (length=142) Species: 1423 (Bacillus subtilis)

MQIKIKYLDETQTRISKIEQGDWIDLRAAEDVTIKKDEFKLVPLGVAMEL
PEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDT
EIKKGDRICQFRIMKKMPAVELVEVEHLGNEDRGGLGSTGTK

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: 4apz Chain B Residue 1145

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4apz Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism
• Resolution: 2.01 Å
• Binding residue (original residue number in PDB): N76 I81 D82 Y85 W92 F93
• Binding residue (residue number reindexed from 1): N74 I79 D80 Y83 W90 F91
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.6.1.23: dUTP diphosphatase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004170 dUTP diphosphatase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006226 dUMP biosynthetic process
• GO:0009117 nucleotide metabolic process
• GO:0046081 dUTP catabolic process

External links

• PDB: RCSB:4apz, PDBe:4apz, PDBj:4apz
• PDBsum: 4apz
• PubMed: 23897460
• UniProt: O31801|YNCF_BACSU Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF (Gene Name=yncF)