Structure of PDB 3cj4 Chain A Binding Site BS01

Receptor Information

>3cj4 Chain A (length=558) Species: 31647 (Hepatitis C virus subtype 1b)

HHMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQ
KKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKS
KFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQR
KPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFL
VNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIK
SLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACR
AAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPP
QPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTP
VNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSI
EPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRA
RSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASRLDLSGWFVAG
YSGGDIYH

Ligand information

• Ligand ID: SX5
• InChI: InChI=1S/C18H23BrN2O4/c1-11-7-12(2)10-21(9-11)18(25)14-8-13(19)3-4-15(14)20-16(22)5-6-17(23)24/h3-4,8,11-12H,5-7,9-10H2,1-2H3,(H,20,22)(H,23,24)/t11-,12+
• InChIKey: JSVSGWHGYIDZFX-TXEJJXNPSA-N
• SMILES:
  CACTVS 3.341: C[CH]1C[CH](C)CN(C1)C(=O)c2cc(Br)ccc2NC(=O)CCC(O)=O
  OpenEye OEToolkits 1.5.0: C[C@@H]1C[C@@H](CN(C1)C(=O)c2cc(ccc2NC(=O)CCC(=O)O)Br)C
  OpenEye OEToolkits 1.5.0: CC1CC(CN(C1)C(=O)c2cc(ccc2NC(=O)CCC(=O)O)Br)C
  CACTVS 3.341: C[C@@H]1C[C@H](C)CN(C1)C(=O)c2cc(Br)ccc2NC(=O)CCC(O)=O
  ACDLabs 10.04: O=C(c1cc(Br)ccc1NC(=O)CCC(=O)O)N2CC(CC(C)C2)C
• Formula: C18 H23 Br N2 O4
• Name: 4-[(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)amino]-4-oxobutanoic acid
• ChEMBL: CHEMBL256528
• DrugBank: DB08581
• ZINC: ZINC000024978147
• PDB chain: 3cj4 Chain A Residue 571

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3cj4 Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): L419 R422 M423 H475 S476 I482 R501 W528
• Binding residue (residue number reindexed from 1): L415 R418 M419 H471 S472 I478 R497 W524
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.31uM
  PDBbind-CN: -logKd/Ki=6.51,Kd=0.31uM

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:3cj4, PDBe:3cj4, PDBj:3cj4
• PDBsum: 3cj4
• PubMed: 18400495
• UniProt: P26663|POLG_HCVBK Genome polyprotein