Structure of PDB 3ska Chain B Binding Site BS01

Receptor Information
>3ska Chain B (length=558) Species: 420174 (Hepatitis C virus isolate HC-J4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQK
KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSK
FGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQRK
PARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLV
NTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRS
LTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRA
AKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQ
PEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPI
NSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLGKALDCQIYGACYSIE
PLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRAR
SVRAKLLSQGGRAAICGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGY
SGGDIYHS
Ligand information
Ligand ID053
InChIInChI=1S/C21H15F3N4O3/c22-21(23,24)12-3-4-15-14(9-12)17(13-2-1-6-27-19(13)29)18(20(30)31)28(15)10-11-5-7-26-16(25)8-11/h1-9H,10H2,(H2,25,26)(H,27,29)(H,30,31)
InChIKeyCNFSTRPHYZHTGV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)c1cc2c(cc1)n(c(c2C3=CC=CNC3=O)C(=O)O)Cc4ccnc(N)c4
CACTVS 3.370Nc1cc(Cn2c3ccc(cc3c(C4=CC=CNC4=O)c2C(O)=O)C(F)(F)F)ccn1
OpenEye OEToolkits 1.7.2c1cc2c(cc1C(F)(F)F)c(c(n2Cc3ccnc(c3)N)C(=O)O)C4=CC=CNC4=O
FormulaC21 H15 F3 N4 O3
Name1-[(2-aminopyridin-4-yl)methyl]-3-(2-oxo-1,2-dihydropyridin-3-yl)-5-(trifluoromethyl)-1H-indole-2-carboxylic acid
ChEMBLCHEMBL1821963
DrugBank
ZINCZINC000043202982
PDB chain3ska Chain B Residue 577 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ska I. Novel HCV NS5B polymerase inhibitors: discovery of indole 2-carboxylic acids with C3-heterocycles.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		N316 C366 S368 L384 G410 M414 Y415 Q446 I447 Y448
Binding residue
(residue number reindexed from 1)		N311 C361 S363 L379 G405 M409 Y410 Q441 I442 Y443
Annotation score1
Binding affinityMOAD: ic50=0.017uM
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
3.4.21.98: hepacivirin.
3.4.22.-
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
Biological Process
GO:0039694 viral RNA genome replication

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Molecular Function
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Biological Process
External links
PDB RCSB:3ska, PDBe:3ska, PDBj:3ska
PDBsum3ska
PubMed21840715
UniProtO92972|POLG_HCVJ4 Genome polyprotein

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