Structure of PDB 3gqo Chain A Binding Site BS01

Receptor Information

>3gqo Chain A (length=161) Species: 36385 (Venezuelan equine encephalitis virus (strain P676))

KAPSYHVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESFDLQP
IEVGKARLVKGAAKHIIHAVGPNFNKVSEVEGDKQLAEAYESIAKIVNDN
NYKSVAIPLLSTGIFSGNKDRLTQSLNHLLTALDTTDADVAIYCRDKKWE
MTLKEAVARRE

Ligand information

• Ligand ID: APR
• InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
• InChIKey: SRNWOUGRCWSEMX-KEOHHSTQSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
• Formula: C15 H23 N5 O14 P2
• Name: ADENOSINE-5-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL1231026
• ZINC: ZINC000017654550
• PDB chain: 3gqo Chain A Residue 167

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gqo The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G9 D10 I11 A22 A23 N24 G30 G31 G32 V33 C34 L108 S110 T111 G112 I113 F114 R144
• Binding residue (residue number reindexed from 1): G10 D11 I12 A23 A24 N25 G31 G32 G33 V34 C35 L109 S111 T112 G113 I114 F115 R145
• Annotation score: 5
• Binding affinity: PDBbind-CN: -logKd/Ki=5.41,Kd=3.9uM

Enzymatic activity

• Enzyme Commision number: 2.1.1.-
  2.7.7.-
  2.7.7.19: polynucleotide adenylyltransferase.
  2.7.7.48: RNA-directed RNA polymerase.
  3.1.3.84: ADP-ribose 1''-phosphate phosphatase.
  3.4.22.-
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.1.74: mRNA 5'-phosphatase.
  3.6.4.13: RNA helicase.

External links

• PDB: RCSB:3gqo, PDBe:3gqo, PDBj:3gqo
• PDBsum: 3gqo
• PubMed: 19386706
• UniProt: P36328|POLN_EEVVP Polyprotein P1234