Structure of PDB 5y5p Chain D Binding Site BS01

Receptor Information

>5y5p Chain D (length=171) Species: 654913 (Shrimp white spot syndrome virus (isolate Tongan))

MDSSASVVFMRFAPPGEETALPPRRATPGSVAYDLFPSEEMDIEPMGLAK
ISTGYGIDKFPDGCYGQIVSRSGMTWKNNTSVPTGTIDVDYRGELKVILR
NHSAEKSVPIRKGTSIAQLIFLRYCDVEEEQIVYINETTGERTIIDSSSK
KDNKNQARSVRGTGGFGSTDN

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: 5y5p Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5y5p The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner.
• Resolution: 2.03 Å
• Binding residue (original residue number in PDB): T84 G85 I87 D88 Y91 K96 G165 F166
• Binding residue (residue number reindexed from 1): T84 G85 I87 D88 Y91 K96 G165 F166
• 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

Biological Process

• GO:0006226 dUMP biosynthetic process
• GO:0046081 dUTP catabolic process

External links

• PDB: RCSB:5y5p, PDBe:5y5p, PDBj:5y5p
• PDBsum: 5y5p
• PubMed: 29187596
• UniProt: Q77J78