Structure of PDB 3cj5 Chain A Binding Site BS01

Receptor Information

>3cj5 Chain A (length=562) Species: 31647 (Hepatitis C virus subtype 1b)

HHMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQ
KKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKS
KFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQP
EGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRV
EFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQ
AIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASA
ACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPG
DPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETAR
HTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGAC
YSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWR
HRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASRLDLSGWF
VAGYSGGDIYHS

Ligand information

• Ligand ID: SX6
• InChI: InChI=1S/C22H30BrN3O4/c1-15-11-16(2)14-26(13-15)22(29)18-12-17(23)3-4-19(18)24-20(27)5-6-21(28)25-7-9-30-10-8-25/h3-4,12,15-16H,5-11,13-14H2,1-2H3,(H,24,27)/t15-,16+
• InChIKey: DELARNBPJXTDBD-IYBDPMFKSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1CC(CN(C1)C(=O)c2cc(ccc2NC(=O)CCC(=O)N3CCOCC3)Br)C
  OpenEye OEToolkits 1.5.0: C[C@H]1C[C@H](CN(C1)C(=O)c2cc(ccc2NC(=O)CCC(=O)N3CCOCC3)Br)C
  CACTVS 3.341: C[C@H]1C[C@@H](C)CN(C1)C(=O)c2cc(Br)ccc2NC(=O)CCC(=O)N3CCOCC3
  ACDLabs 10.04: O=C(N1CCOCC1)CCC(=O)Nc3ccc(Br)cc3C(=O)N2CC(C)CC(C)C2
  CACTVS 3.341: C[CH]1C[CH](C)CN(C1)C(=O)c2cc(Br)ccc2NC(=O)CCC(=O)N3CCOCC3
• Formula: C22 H30 Br N3 O4
• Name: N-(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)-4-morpholin-4-yl-4-oxobutanamide
• ChEMBL: CHEMBL402315
• DrugBank: DB08582
• ZINC: ZINC000024978180
• PDB chain: 3cj5 Chain A Residue 571

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3cj5 Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.
• Resolution: 1.92 Å
• Binding residue (original residue number in PDB): R422 M423 H475 S476 L497 R498 R501 W528
• Binding residue (residue number reindexed from 1): R421 M422 H474 S475 L496 R497 R500 W527
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.46uM
  PDBbind-CN: -logKd/Ki=6.34,Kd=0.46uM

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:3cj5, PDBe:3cj5, PDBj:3cj5
• PDBsum: 3cj5
• PubMed: 18400495
• UniProt: P26663|POLG_HCVBK Genome polyprotein