Structure of PDB 4dvl Chain B Binding Site BS03

Receptor Information

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

ENITQWNLQDNGTEGIQRAMFQRGVNRSLHGIWPEKICTGVPSHLATDTE
LKAIHGMMDASEKTNYTCCRLQRHEWNKHGWCNWYNIEPWILLMNKTQAN
LTEGQPLRECAVTCRYDRDSDLNVVTQARDSPTPLTGCKKGKNFSFAGIL
VQGPCNFEIAV

Ligand information

• Ligand ID: JKM
• InChI: InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7+,8+/m1/s1
• InChIKey: HWDMHJDYMFRXOX-GVYWOMJSSA-N
• SMILES:
  CACTVS 3.370: OC[CH]1O[CH]([CH]2O[P](O)(=O)O[CH]12)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)[C@@H]2[C@@H]3[C@@H]([C@H](O2)CO)O[P@@](=O)(O3)O
  CACTVS 3.370: OC[C@H]1O[C@@H]([C@H]2O[P](O)(=O)O[C@H]12)N3C=CC(=O)NC3=O
  ACDLabs 12.01: O=C1C=CN(C(=O)N1)C2OC(C3OP(=O)(O)OC23)CO
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C3C(C(O2)CO)OP(=O)(O3)O
• Formula: C9 H11 N2 O8 P
• Name: 1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4( 1H,3H)-dione;
  Uridine 2',3'-cyclophosphate
• ZINC: ZINC000098209050
• PDB chain: 4dvl Chain B Residue 1114

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dvl Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity.
• Resolution: 2.75 Å
• Binding residue (original residue number in PDB): N9 H32 A62
• Binding residue (residue number reindexed from 1): N7 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:4dvl, PDBe:4dvl, PDBj:4dvl
• PDBsum: 4dvl
• PubMed: 22579253
• UniProt: Q96662|POLG_BVDVC Genome polyprotein