Structure of PDB 5hmy Chain A Binding Site BS03

Receptor Information
>5hmy Chain A (length=591) 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
SLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYMPSMKRF
Ligand information
Ligand IDLNY
InChIInChI=1S/C17H14O5S/c18-5-1-2-14-3-4-15(23-14)13-7-11(9-16(19)20)6-12(8-13)10-17(21)22/h3-4,6-8,18H,5,9-10H2,(H,19,20)(H,21,22)
InChIKeyGUHLJLFVRKYNRL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OCC#Cc1sc(cc1)c2cc(CC(O)=O)cc(CC(O)=O)c2
OpenEye OEToolkits 2.0.4c1cc(sc1C#CCO)c2cc(cc(c2)CC(=O)O)CC(=O)O
ACDLabs 12.01C(C(=O)O)c1cc(cc(c1)c2ccc(s2)C#CCO)CC(O)=O
FormulaC17 H14 O5 S
Name2,2'-(5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-1,3-phenylene)diacetic acid
ChEMBLCHEMBL3810161
DrugBank
ZINCZINC000584905616
PDB chain5hmy Chain A Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5hmy Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L511 C709 R729 M761 M765 T794 S796 H798 A799 H800 Q802 W803
Binding residue
(residue number reindexed from 1)		L213 C411 R431 M463 M467 T496 S498 H500 A501 H502 Q504 W505
Annotation score1
Binding affinityMOAD: ic50=0.5uM
PDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5hmy, PDBe:5hmy, PDBj:5hmy
PDBsum5hmy
PubMed26984786
UniProtQ6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)

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