Structure of PDB 5jjs Chain A Binding Site BS05

Receptor Information
>5jjs Chain A (length=849) 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
WDSAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYL
EFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADD
TAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPT
PTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADL
ENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALND
MGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDE
LIGRARISQGWSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPV
HWVPTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWEN
VPYLGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMP
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain5jjs Chain A Residue 1009 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jjs Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling
Resolution1.65 Å
Binding residue
(original residue number in PDB)		S56 G58 G81 G86 W87 T104 K105 H110 E111 D131 V132 F133 D146
Binding residue
(residue number reindexed from 1)		S51 G53 G76 G81 W82 T99 K100 H105 E106 D126 V127 F128 D141
Annotation score5
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:5jjs, PDBe:5jjs, PDBj:5jjs
PDBsum5jjs
PubMed27500641
UniProtQ6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)

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