Structure of PDB 3h5s Chain A Binding Site BS01

Receptor Information

>3h5s Chain A (length=557) Species: 11105 (Hepatitis C virus (isolate BK))

HMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQK
KVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSK
FGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQRK
PARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLV
NTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKS
LTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRA
AKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQ
PEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPV
NSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIE
PLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRAR
SVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASRLDLSGWFVAGY
SGGDIYH

Ligand information

• Ligand ID: H5S
• InChI: InChI=1S/C27H30FN3O6S2/c1-15-12-16(6-9-20(15)28)13-31-25(27(2,3)4)23(32)21(26(31)33)22-18-8-7-17-10-11-30(38(5,34)35)14-19(17)24(18)39(36,37)29-22/h6-9,12,25,32H,10-11,13-14H2,1-5H3/t25-/m1/s1
• InChIKey: YRWZNTIWOPXYQZ-RUZDIDTESA-N
• SMILES:
  CACTVS 3.341: Cc1cc(CN2[C@H](C(=C(C2=O)C3=N[S](=O)(=O)c4c5CN(CCc5ccc34)[S](C)(=O)=O)O)C(C)(C)C)ccc1F
  OpenEye OEToolkits 1.5.0: Cc1cc(ccc1F)CN2C(C(=C(C2=O)C3=NS(=O)(=O)c4c3ccc5c4CN(CC5)S(=O)(=O)C)O)C(C)(C)C
  OpenEye OEToolkits 1.5.0: Cc1cc(ccc1F)CN2[C@H](C(=C(C2=O)C3=NS(=O)(=O)c4c3ccc5c4CN(CC5)S(=O)(=O)C)O)C(C)(C)C
  CACTVS 3.341: Cc1cc(CN2[CH](C(=C(C2=O)C3=N[S](=O)(=O)c4c5CN(CCc5ccc34)[S](C)(=O)=O)O)C(C)(C)C)ccc1F
  ACDLabs 10.04: Fc1ccc(cc1C)CN5C(=O)C(C3=NS(=O)(=O)c2c4c(ccc23)CCN(C4)S(=O)(=O)C)=C(O)C5C(C)(C)C
• Formula: C27 H30 F N3 O6 S2
• Name: (5S)-5-tert-butyl-1-(4-fluoro-3-methylbenzyl)-4-hydroxy-3-[8-(methylsulfonyl)-1,1-dioxido-6,7,8,9-tetrahydroisothiazolo[4,5-h]isoquinolin-3-yl]-1,5-dihydro-2H-pyrrol-2-one
• ZINC: ZINC000103544313
• PDB chain: 3h5s Chain A Residue 571

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3h5s Non-nucleoside inhibitors of HCV polymerase NS5B. Part 4: structure-based design, synthesis, and biological evaluation of benzo[d]isothiazole-1,1-dioxides
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): F193 P197 S288 N291 D318 M414 Y415 I447 Y448 G449 S556
• Binding residue (residue number reindexed from 1): F188 P192 S283 N286 D313 M409 Y410 I442 Y443 G444 S551
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.005uM
  PDBbind-CN: -logKd/Ki=8.30,IC50=5nM

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

External links

• PDB: RCSB:3h5s, PDBe:3h5s, PDBj:3h5s
• PDBsum: 3h5s
• PubMed: 19709881
• UniProt: P26663|POLG_HCVBK Genome polyprotein