Structure of PDB 5ikm Chain A Binding Site BS02

Receptor Information

>5ikm Chain A (length=259) Species: 11053 (dengue virus type 1)

GETLGEKWKRQLNQLSKSEFNTYKRSGIMEVDRSEAKEGLKRGETTKHAV
SRGTAKLRWFVERNLVKPEGKVIDLGCGRGGWSYYCAGLKKVTEVKGYTK
GGPGHEEPIPMATYGWNLVKLHSGKDVFFIPPEKCDTLLCDIGESSPNPT
IEEGRTLRVLKMVEPWLRGNQFCIKILNPYMPSVVETLEQMQRKHGGMLV
RNPLSRNSTHEMYWVSCGTGNIVSAVNMTSRMLLNRFTMAHRKPTYERDV
DLGAGTRHV

Ligand information

• Ligand ID: BDF
• InChI: InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4-,5+,6-/m1/s1
• InChIKey: LKDRXBCSQODPBY-ARQDHWQXSA-N
• SMILES:
  CACTVS 3.341: OC[C]1(O)OC[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
  ACDLabs 10.04: OC1C(O)(OCC(O)C1O)CO
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)(CO)O)O)O)O
• Formula: C6 H12 O6
• Name: beta-D-fructopyranose;
  beta-D-fructose;
  D-fructose;
  fructose
• ZINC: ZINC000003861095
• PDB chain: 5ikm Chain A Residue 312

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ikm 1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): E169 P170 K199 H200
• Binding residue (residue number reindexed from 1): E164 P165 K194 H195
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.4.21.91: flavivirin.
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
• GO:0008168 methyltransferase activity

Biological Process

• GO:0032259 methylation

External links

• PDB: RCSB:5ikm, PDBe:5ikm, PDBj:5ikm
• PDBsum: 5ikm
• UniProt: I6XG39