Structure of PDB 3upi Chain B Binding Site BS01

Receptor Information
>3upi 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 ID0C2
InChIInChI=1S/C25H21F2N3O5S/c1-13-12-35-23-16(13)6-8-19-21(23)20(17-4-3-9-28-24(17)31)22(25(32)29-36(2,33)34)30(19)11-14-10-15(26)5-7-18(14)27/h3-10,13H,11-12H2,1-2H3,(H,28,31)(H,29,32)/t13-/m1/s1
InChIKeyLVGCEDOTDJKOGS-CYBMUJFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[CH]1COc2c1ccc3n(Cc4cc(F)ccc4F)c(C(=O)N[S](C)(=O)=O)c(C5=CC=CNC5=O)c23
CACTVS 3.370C[C@@H]1COc2c1ccc3n(Cc4cc(F)ccc4F)c(C(=O)N[S](C)(=O)=O)c(C5=CC=CNC5=O)c23
OpenEye OEToolkits 1.7.6CC1COc2c1ccc3c2c(c(n3Cc4cc(ccc4F)F)C(=O)NS(=O)(=O)C)C5=CC=CNC5=O
ACDLabs 12.01O=S(=O)(NC(=O)c1n(c4c(c1C2=CC=CNC2=O)c3OCC(c3cc4)C)Cc5cc(F)ccc5F)C
OpenEye OEToolkits 1.7.6C[C@@H]1COc2c1ccc3c2c(c(n3Cc4cc(ccc4F)F)C(=O)NS(=O)(=O)C)C5=CC=CNC5=O
FormulaC25 H21 F2 N3 O5 S
Name(3S)-6-(2,5-difluorobenzyl)-3-methyl-N-(methylsulfonyl)-8-(2-oxo-1,2-dihydropyridin-3-yl)-3,6-dihydro-2H-furo[2,3-e]indole-7-carboxamide
ChEMBL
DrugBank
ZINCZINC000098207786
PDB chain3upi Chain B Residue 586 [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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PDB3upi Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F193 P197 N316 C366 S367 G410 M414 Y415 I447 Y448 G449
Binding residue
(residue number reindexed from 1)		F188 P192 N311 C361 S362 G405 M409 Y410 I442 Y443 G444
Annotation score1
Binding affinityMOAD: ic50=6nM
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:3upi, PDBe:3upi, PDBj:3upi
PDBsum3upi
PubMed22220815
UniProtO92972|POLG_HCVJ4 Genome polyprotein

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