Structure of PDB 5dto Chain A Binding Site BS06

Receptor Information
>5dto Chain A (length=852) 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
DLGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYH
GSYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFK
EKVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTN
AQWDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMRAIWYMWLGVR
YLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYA
DDTAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQR
PTPTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKA
DLENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLAL
NDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQ
DELIGRARISQGAGWSIRETACLGKAYAQMWSLMYFHRRDLRLASNAICS
AVPVHWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVT
TWENVPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLD
YM
Ligand information
Ligand IDM7G
InChIInChI=1S/C11H17N5O11P2/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(26-10)2-25-29(23,24)27-28(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H5-,12,13,14,19,20,21,22,23,24)/p+1/t4-,6-,7-,10-/m1/s1
InChIKeySBASPRRECYVBRF-KQYNXXCUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC1OC(n2c[n+](C)c3c2N=C(N)NC3=O)C(O)C1O
OpenEye OEToolkits 2.0.7C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.385C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)c3N=C(N)NC(=O)c13
CACTVS 3.385C[n+]1cn([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
FormulaC11 H18 N5 O11 P2
Name7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB01960
ZINCZINC000013548083
PDB chain5dto Chain B Residue 0 [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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PDB5dto Molecular basis for specific viral RNA recognition and 2'-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5)
Resolution2.603 Å
Binding residue
(original residue number in PDB)		K14 L17 N18 L20 F25 K29 S151 P152 S213
Binding residue
(residue number reindexed from 1)		K9 L12 N13 L15 F20 K24 S146 P147 S208
Annotation score2
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:0003968 RNA-dependent RNA polymerase activity
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0005524 ATP binding
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dto, PDBe:5dto, PDBj:5dto
PDBsum5dto
PubMed26578813
UniProtQ6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)

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