Structure of PDB 5ec8 Chain A Binding Site BS01

Receptor Information

>5ec8 Chain A (length=256) Species: 408870 (Dengue virus 3 Philippines/H87/1956)

ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVS
RGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKG
GPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTV
EESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVR
NPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVD
LGAGTR

Ligand information

• Ligand ID: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 5ec8 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ec8 Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design.
• Resolution: 1.714 Å
• Binding residue (original residue number in PDB): S56 G81 G86 W87 T104 K105 H110 E111 K130 D131 V132 F133 D146
• Binding residue (residue number reindexed from 1): S50 G75 G80 W81 T98 K99 H104 E105 K124 D125 V126 F127 D140
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  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:5ec8, PDBe:5ec8, PDBj:5ec8
• PDBsum: 5ec8
• PubMed: 27750202
• UniProt: P27915|POLG_DEN3P Genome polyprotein