Structure of PDB 3p8z Chain A Binding Site BS01

Receptor Information
>3p8z Chain A (length=257) Species: 11069 (dengue virus type 3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAV
SRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK
GGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPT
VEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLV
RNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDV
DLGAGTR
Ligand information
Ligand ID36A
InChIInChI=1S/C21H25ClN6O5S/c22-12-3-1-2-11(6-12)7-24-18-15-19(26-9-25-18)28(10-27-15)20-17(30)16(29)14(33-20)8-34-5-4-13(23)21(31)32/h1-3,6,9-10,13-14,16-17,20,29-30H,4-5,7-8,23H2,(H,31,32)(H,24,25,26)/t13-,14+,16+,17+,20+/m0/s1
InChIKeyVGYBDYWAAOWMTJ-SWQDORGXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)Cl)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CSCC[C@@H](C(=O)O)N)O)O
CACTVS 3.370N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCc4cccc(Cl)c4)ncnc23)C(O)=O
OpenEye OEToolkits 1.7.0c1cc(cc(c1)Cl)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CSCCC(C(=O)O)N)O)O
ACDLabs 12.01O=C(O)C(N)CCSCC4OC(n2cnc1c(ncnc12)NCc3cccc(Cl)c3)C(O)C4O
CACTVS 3.370N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCc4cccc(Cl)c4)ncnc23)C(O)=O
FormulaC21 H25 Cl N6 O5 S
Name(S)-2-amino-4-(((2S,3S,4R,5R)-5-(6-(3-chlorobenzylamino)-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methylthio)butanoic acid
ChEMBLCHEMBL1230055
DrugBank
ZINCZINC000058633002
PDB chain3p8z Chain A Residue 263 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3p8z Small molecule inhibitors that selectively block dengue virus methyltransferase
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S56 G58 G81 G86 W87 T104 K105 H110 K130 D131 V132 D146 I147 R163 M167
Binding residue
(residue number reindexed from 1)		S51 G53 G76 G81 W82 T99 K100 H105 K125 D126 V127 D141 I142 R158 M162
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.09,Ki=0.82uM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3p8z, PDBe:3p8z, PDBj:3p8z
PDBsum3p8z
PubMed21147775
UniProtP27915|POLG_DEN3P Genome polyprotein

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