Structure of PDB 3gnw Chain B Binding Site BS01

Receptor Information
>3gnw Chain B (length=568) 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
FGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPG
RKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEF
LVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAI
RSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAAC
RAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDP
PQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHT
PINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYS
IEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHR
ARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVA
GYSGGDIYHSLSRARPRL
Ligand information
Ligand IDXNC
InChIInChI=1S/C34H32FN3O5S/c1-21-9-7-12-26(36-21)33(40)38-28-13-8-14-29(39)30(28)37-27-18-34(2,3)20-44(41,42)32(27)31(38)24-16-15-23(17-25(24)35)43-19-22-10-5-4-6-11-22/h4-17,31,37,39H,18-20H2,1-3H3/t31-/m0/s1
InChIKeyCLEOWFBQYYBWRR-HKBQPEDESA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cccc(n1)C(=O)N2[CH](c3ccc(OCc4ccccc4)cc3F)C5=C(CC(C)(C)C[S]5(=O)=O)Nc6c(O)cccc26
OpenEye OEToolkits 1.5.0Cc1cccc(n1)C(=O)N2c3cccc(c3NC4=C(C2c5ccc(cc5F)OCc6ccccc6)S(=O)(=O)CC(C4)(C)C)O
ACDLabs 10.04Fc2cc(OCc1ccccc1)ccc2C5C6=C(Nc3c(O)cccc3N5C(=O)c4nc(ccc4)C)CC(CS6(=O)=O)(C)C
CACTVS 3.341Cc1cccc(n1)C(=O)N2[C@@H](c3ccc(OCc4ccccc4)cc3F)C5=C(CC(C)(C)C[S]5(=O)=O)Nc6c(O)cccc26
OpenEye OEToolkits 1.5.0Cc1cccc(n1)C(=O)N2c3cccc(c3NC4=C([C@@H]2c5ccc(cc5F)OCc6ccccc6)S(=O)(=O)CC(C4)(C)C)O
FormulaC34 H32 F N3 O5 S
Name(11S)-11-[4-(benzyloxy)-2-fluorophenyl]-3,3-dimethyl-10-[(6-methylpyridin-2-yl)carbonyl]-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide
ChEMBLCHEMBL499826
DrugBank
ZINCZINC000044307926
PDB chain3gnw Chain B Residue 579 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gnw Structure-based design of a benzodiazepine scaffold yields a potent allosteric inhibitor of hepatitis C NS5B RNA polymerase.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		R200 C366 S367 S368 N411 M414 Y415 Q446 I447 Y448 G449 S556
Binding residue
(residue number reindexed from 1)		R197 C363 S364 S365 N408 M411 Y412 Q443 I444 Y445 G446 S553
Annotation score1
Binding affinityMOAD: Kd=0.79nM
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:3gnw, PDBe:3gnw, PDBj:3gnw
PDBsum3gnw
PubMed19507864
UniProtO92972|POLG_HCVJ4 Genome polyprotein

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