Structure of PDB 3hky Chain A Binding Site BS01

Receptor Information

>3hky Chain A (length=564) Species: 31647 (Hepatitis C virus subtype 1b)

SSMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQ
KKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKS
KFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQP
EKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQ
RVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEA
RQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKA
TAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAP
PGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWET
ARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYG
ACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRT
WRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSG
WFVAGYSGGDIYHS

Ligand information

• Ligand ID: IX6
• InChI: InChI=1S/C30H32FN3O6S/c1-16(2)14-39-19-10-11-20(21(31)12-19)27-28-22(13-30(5,6)15-41(28,37)38)33-26-23(8-7-9-24(26)35)34(27)29(36)25-17(3)40-18(4)32-25/h7-12,27,33,35H,1,13-15H2,2-6H3/t27-/m0/s1
• InChIKey: NNKOFEVRZHVHLU-MHZLTWQESA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c(nc(o1)C)C(=O)N2c3cccc(c3NC4=C([C@@H]2c5ccc(cc5F)OCC(=C)C)S(=O)(=O)CC(C4)(C)C)O
  OpenEye OEToolkits 1.5.0: Cc1c(nc(o1)C)C(=O)N2c3cccc(c3NC4=C(C2c5ccc(cc5F)OCC(=C)C)S(=O)(=O)CC(C4)(C)C)O
  CACTVS 3.341: CC(=C)COc1ccc([C@@H]2N(C(=O)c3nc(C)oc3C)c4cccc(O)c4NC5=C2[S](=O)(=O)CC(C)(C)C5)c(F)c1
  ACDLabs 10.04: Fc1cc(OCC(=C)/C)ccc1C4C5=C(Nc2c(O)cccc2N4C(=O)c3nc(oc3C)C)CC(CS5(=O)=O)(C)C
  CACTVS 3.341: CC(=C)COc1ccc([CH]2N(C(=O)c3nc(C)oc3C)c4cccc(O)c4NC5=C2[S](=O)(=O)CC(C)(C)C5)c(F)c1
• Formula: C30 H32 F N3 O6 S
• Name: (11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide
• ZINC: ZINC000103546563
• PDB chain: 3hky Chain A Residue 579

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hky 1a/1b subtype profiling of nonnucleoside polymerase inhibitors of hepatitis C virus
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R200 C366 S367 L384 N411 Y448 S556
• Binding residue (residue number reindexed from 1): R201 C367 S368 L385 N412 Y449 S557
• Annotation score: 1
• Binding affinity: MOAD: Kd=2.3nM
  PDBbind-CN: -logKd/Ki=7.10,Kd=80nM

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:3hky, PDBe:3hky, PDBj:3hky
• PDBsum: 3hky
• PubMed: 20071590
• UniProt: O92972|POLG_HCVJ4 Genome polyprotein