Structure of PDB 4kb7 Chain A Binding Site BS01

Receptor Information
>4kb7 Chain A (length=545) Species: 31647 (Hepatitis C virus subtype 1b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQK
KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSK
YGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRK
PARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLV
NTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKS
LTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRA
AKLQDCTMLVYGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQ
PEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPV
NSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIE
PLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRAR
SVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPVAGYSGGDIYHS
Ligand information
Ligand ID690
InChIInChI=1S/C29H28BFN2O6S/c1-32-29(34)27-22-15-21(17-7-8-17)24(16-26(22)38-28(27)18-9-11-19(31)12-10-18)33(40(2,36)37)14-13-25-20-5-3-4-6-23(20)30(35)39-25/h3-6,9-12,15-17,25,35H,7-8,13-14H2,1-2H3,(H,32,34)/t25-/m1/s1
InChIKeyNPAMWFMDBHAIAJ-RUZDIDTESA-N
SMILES
SoftwareSMILES
CACTVS 3.370CNC(=O)c1c(oc2cc(N(CC[C@H]3OB(O)c4ccccc34)[S](C)(=O)=O)c(cc12)C5CC5)c6ccc(F)cc6
CACTVS 3.370CNC(=O)c1c(oc2cc(N(CC[CH]3OB(O)c4ccccc34)[S](C)(=O)=O)c(cc12)C5CC5)c6ccc(F)cc6
ACDLabs 12.01O=S(=O)(N(c3c(cc1c(oc(c1C(=O)NC)c2ccc(F)cc2)c3)C4CC4)CCC6OB(O)c5ccccc56)C
OpenEye OEToolkits 1.7.6B1(c2ccccc2[C@H](O1)CCN(c3cc4c(cc3C5CC5)c(c(o4)c6ccc(cc6)F)C(=O)NC)S(=O)(=O)C)O
OpenEye OEToolkits 1.7.6B1(c2ccccc2C(O1)CCN(c3cc4c(cc3C5CC5)c(c(o4)c6ccc(cc6)F)C(=O)NC)S(=O)(=O)C)O
FormulaC29 H28 B F N2 O6 S
Name5-cyclopropyl-2-(4-fluorophenyl)-6-[{2-[(3R)-1-hydroxy-1,3-dihydro-2,1-benzoxaborol-3-yl]ethyl}(methylsulfonyl)amino]-N-methyl-1-benzofuran-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000204162954
PDB chain4kb7 Chain A Residue 601 [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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PDB4kb7 Discovery of a Potent Boronic Acid Derived Inhibitor of the HCV RNA-Dependent RNA Polymerase.
Resolution1.85 Å
Binding residue
(original residue number in PDB)
F193 R200 L204 L314 Y316 I363 S365 C366 S368 N411 M414 Y415 Y448
Binding residue
(residue number reindexed from 1)
F188 R195 L199 L309 Y311 I358 S360 C361 S363 N406 M409 Y410 Y443
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.49,IC50=32nM
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:4kb7, PDBe:4kb7, PDBj:4kb7
PDBsum4kb7
PubMed23672667
UniProtP26663|POLG_HCVBK Genome polyprotein

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