Structure of PDB 5jjs Chain A Binding Site BS03

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 ID6L2
InChIInChI=1S/C23H27NO7S2/c1-29-15-6-4-8-17(12-15)33(27,28)24-23(26)19-13-18(20(30-2)14-21(19)31-3)22-10-9-16(32-22)7-5-11-25/h9-10,13-15,17,25H,4,6,8,11-12H2,1-3H3,(H,24,26)/t15-,17-/m1/s1
InChIKeyCOCQFOUTOAHOEQ-NVXWUHKLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO[C@@H]1CCC[C@H](C1)[S](=O)(=O)NC(=O)c2cc(c(OC)cc2OC)c3sc(cc3)C#CCO
ACDLabs 12.01COC1CC(CCC1)S(NC(c2c(cc(OC)c(c2)c3sc(cc3)C#CCO)OC)=O)(=O)=O
OpenEye OEToolkits 2.0.4COc1cc(c(cc1c2ccc(s2)C#CCO)C(=O)NS(=O)(=O)C3CCCC(C3)OC)OC
OpenEye OEToolkits 2.0.4COc1cc(c(cc1c2ccc(s2)C#CCO)C(=O)NS(=O)(=O)[C@@H]3CCC[C@H](C3)OC)OC
CACTVS 3.385CO[CH]1CCC[CH](C1)[S](=O)(=O)NC(=O)c2cc(c(OC)cc2OC)c3sc(cc3)C#CCO
FormulaC23 H27 N O7 S2
Name5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-{[(1R,3R)-3-methoxycyclohexyl]sulfonyl}benzamide
ChEMBL
DrugBank
ZINCZINC000584904685
PDB chain5jjs Chain A Residue 1004 [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)		L511 C709 H711 R729 R737 M765 T794 W795 S796 H798 A799 H800 Q802 W803
Binding residue
(residue number reindexed from 1)		L478 C676 H678 R696 R704 M730 T759 W760 S761 H763 A764 H765 Q767 W768
Annotation score1
Binding affinityMOAD: ic50=0.048uM
PDBbind-CN: -logKd/Ki=7.32,IC50=0.048uM
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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