Structure of PDB 3emd Chain A Binding Site BS01

Receptor Information
>3emd Chain A (length=259) Species: 164416 (Wesselsbron virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTLGEVWKRQLNMLGKQEFERYKVSDITEVDRTAARRYLKEGRTDVGISV
SRGAAKIRWLHERGYLRITGRVLDLGCGRGGWSYYAAAQKEVMSVKGYTL
GIEGHEKPIHMQTLGWNIVKFKDKSNVFTMPTEPSDTLLCDIGESSSNPL
VERDRTMKVLENFERWKHVNTENFCVKVLAPYHPDVIEKLERLQLRFGGG
IVRVPFSRNSTHEMYYISGARNNITHMVNTTSRSLLRRMTRPSGKAIIEG
DVFLPTGTR
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain3emd Chain A Residue 293 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3emd Recognition of RNA Cap in the Wesselsbron Virus NS5 Methyltransferase Domain: Implications for RNA-Capping Mechanisms in Flavivirus
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S56 G58 G81 G86 W87 T104 L105 E111 S130 N131 V132 F133 D146 I147
Binding residue
(residue number reindexed from 1)		S51 G53 G76 G81 W82 T99 L100 E106 S125 N126 V127 F128 D141 I142
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.57: methyltransferase cap1.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0006370 7-methylguanosine mRNA capping
GO:0032259 methylation
GO:0106005 RNA 5'-cap (guanine-N7)-methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3emd, PDBe:3emd, PDBj:3emd
PDBsum3emd
PubMed18976670
UniProtD0VX01

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