Structure of PDB 5f3z Chain A Binding Site BS03

Receptor Information
>5f3z Chain A (length=585) Species: 11069 (dengue virus type 3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMIN
GVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRK
VMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAADSAKAAVEDEEFWK
LVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYLEFEALGFLNEDHWFS
RENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHN
EEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQR
GSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLE
TKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSK
GWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSL
RETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIH
AHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCG
SLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM
Ligand information
Ligand ID5V5
InChIInChI=1S/C13H12O3S/c1-16-11-5-4-9(8-13(14)15)7-10(11)12-3-2-6-17-12/h2-7H,8H2,1H3,(H,14,15)
InChIKeyHCAVDRSGOUZCSD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(CC(O)=O)cc1c2sccc2
OpenEye OEToolkits 2.0.4COc1ccc(cc1c2cccs2)CC(=O)O
FormulaC13 H12 O3 S
Name2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid
ChEMBLCHEMBL5182967
DrugBank
ZINCZINC000584905221
PDB chain5f3z Chain A Residue 1003 [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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PDB5f3z A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L511 C709 R729 M761 T794 S796 H798 A799 W803
Binding residue
(residue number reindexed from 1)		L213 C411 R431 M463 T496 S498 H500 A501 W505
Annotation score1
Binding affinityMOAD: Kd=29uM
PDBbind-CN: -logKd/Ki=4.54,Kd=29uM
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:0005524 ATP binding
Biological Process
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5f3z, PDBe:5f3z, PDBj:5f3z
PDBsum5f3z
PubMed26872970
UniProtQ6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)

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