Structure of PDB 3knx Chain A Binding Site BS04

Receptor Information

>3knx Chain A (length=181) Species: 63746 (Hepatitis C virus (isolate H77))

APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCING
VCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCG
SSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHA
VGLFRAAVCTRGVAKAVDFIPVENLETTMRS

Ligand information

• Ligand ID: JZT
• InChI: InChI=1S/C39H64N6O7/c1-9-19-40-34(50)32(48)25-17-15-13-11-10-12-14-16-18-26(35(51)45-22-24-30(39(24,7)8)31(45)33(49)41-25)42-36(52)43-27(37(2,3)4)23-44-28(46)20-38(5,6)21-29(44)47/h9,24-27,30-32,48H,1,10-23H2,2-8H3,(H,40,50)(H,41,49)(H2,42,43,52)/t24-,25-,26-,27+,30-,31-,32+/m0/s1
• InChIKey: OCBUWZICDFQHBN-MHXQYHMZSA-N
• SMILES:
  CACTVS 3.352: CC(C)(C)[CH](CN1C(=O)CC(C)(C)CC1=O)NC(=O)N[CH]2CCCCCCCCC[CH](NC(=O)[CH]3[CH]4[CH](CN3C2=O)C4(C)C)[CH](O)C(=O)NCC=C
  OpenEye OEToolkits 1.7.0: CC1(CC(=O)N(C(=O)C1)CC(C(C)(C)C)NC(=O)NC2CCCCCCCCCC(NC(=O)C3C4C(C4(C)C)CN3C2=O)C(C(=O)NCC=C)O)C
  OpenEye OEToolkits 1.7.0: CC1(CC(=O)N(C(=O)C1)C[C@H](C(C)(C)C)NC(=O)N[C@H]2CCCCCCCCC[C@H](NC(=O)[C@@H]3[C@@H]4[C@@H](C4(C)C)CN3C2=O)[C@H](C(=O)NCC=C)O)C
  CACTVS 3.352: CC(C)(C)[C@@H](CN1C(=O)CC(C)(C)CC1=O)NC(=O)N[C@H]2CCCCCCCCC[C@H](NC(=O)[C@@H]3[C@@H]4[C@H](CN3C2=O)C4(C)C)[C@@H](O)C(=O)NCC=C
• Formula: C39 H64 N6 O7
• Name: (2R)-2-{(3S,13S,16aS,17aR,17bS)-13-[({(1S)-1-[(4,4-dimethyl-2,6-dioxopiperidin-1-yl)methyl]-2,2-dimethylpropyl}carbamoyl)amino]-17,17-dimethyl-1,14-dioxooctadecahydro-2H-cyclopropa[3,4]pyrrolo[1,2-a][1,4]diazacyclohexadecin-3-yl}-2-hydroxy-N-prop-2-en-1-ylethanamide
• ZINC: ZINC000058649759
• PDB chain: 3knx Chain A Residue 999

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3knx Discovery and structure-activity relationship of P1-P3 ketoamide derived macrocyclic inhibitors of hepatitis C virus NS3 protease.
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): H57 I132 L135 G137 S139 R155 A156 A157 V158 C159
• Binding residue (residue number reindexed from 1): H57 I132 L135 G137 S139 R155 A156 A157 V158 C159
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D81 G137 S139
• Catalytic site (residue number reindexed from 1): H57 D81 G137 S139
• Enzyme Commision number: 3.4.21.98: hepacivirin.
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0019087 transformation of host cell by virus

External links

• PDB: RCSB:3knx, PDBe:3knx, PDBj:3knx
• PDBsum: 3knx
• PubMed: 19102654
• UniProt: Q9ELS8