Structure of PDB 4dvn Chain B Binding Site BS02

Receptor Information

>4dvn Chain B (length=161) Species: 268305 (Bovine viral diarrhea virus 1-CP7)

ENITQWNLQDNGTEGIQRAMFQRGVNRSLHGIWPEKICTGVPSHLATDTE
LKAIHGMMDASEKTNYTCCRLQRHEWNKHGWCNWYNIEPWILLMNKTQAN
LTEGQPLRECAVTCRYDRDSDLNVVTQARDSPTPLTGCKKGKNFSFAGIL
VQGPCNFEIAV

Ligand information

• Ligand ID: U2P
• InChI: InChI=1S/C9H13N2O9P/c12-3-4-6(14)7(20-21(16,17)18)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: HQIDPEYTETUCNF-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2OP(=O)(O)O)CO
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)OP(=O)(O)O
  CACTVS 3.341: OC[CH]1O[CH]([CH](O[P](O)(O)=O)[CH]1O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)OP(=O)(O)O
  CACTVS 3.341: OC[C@H]1O[C@H]([C@H](O[P](O)(O)=O)[C@@H]1O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER;
  URIDINE-2'-PHOSPHATE;
  2'-URIDINEMONOPHOSPHATE
• ChEMBL: CHEMBL447360
• ZINC: ZINC000004095997
• PDB chain: 4dvn Chain B Residue 1113

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dvn Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity.
• Resolution: 2.38 Å
• Binding residue (original residue number in PDB): N9 I18 Q19 H32 A62
• Binding residue (residue number reindexed from 1): N7 I16 Q17 H30 A60
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.113: pestivirus NS3 polyprotein peptidase.
  3.4.22.-
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.
  4.6.1.19: ribonuclease T2.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0033897 ribonuclease T2 activity

External links

• PDB: RCSB:4dvn, PDBe:4dvn, PDBj:4dvn
• PDBsum: 4dvn
• PubMed: 22579253
• UniProt: Q96662|POLG_BVDVC Genome polyprotein