Structure of PDB 5f41 Chain A Binding Site BS03

Receptor Information
>5f41 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 ID5V6
InChIInChI=1S/C13H12O3S/c1-16-12-3-2-9(7-13(14)15)6-11(12)10-4-5-17-8-10/h2-6,8H,7H2,1H3,(H,14,15)
InChIKeyJRNVDXIGCSDEEN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(CC(O)=O)cc1c2cscc2
OpenEye OEToolkits 2.0.4COc1ccc(cc1c2ccsc2)CC(=O)O
FormulaC13 H12 O3 S
Name2-(4-methoxy-3-thiophen-3-yl-phenyl)ethanoic acid
ChEMBLCHEMBL5205786
DrugBank
ZINCZINC000584905248
PDB chain5f41 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5f41 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 H711 R729 M761 T794 S796 H798 A799 W803
Binding residue
(residue number reindexed from 1)		L213 C411 H413 R431 M463 T496 S498 H500 A501 W505
Annotation score1
Binding affinityMOAD: Kd=67uM
PDBbind-CN: -logKd/Ki=4.17,Kd=67uM
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:5f41, PDBe:5f41, PDBj:5f41
PDBsum5f41
PubMed26872970
UniProtQ6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)

[Back to BioLiP]