Structure of PDB 5vp9 Chain A Binding Site BS01

Receptor Information

>5vp9 Chain A (length=198)

MASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGE
VQIVSTATQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDL
VGWQAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPI
SYLKGSSGGPLLCPAGHAVGIFRAAVSTRGVAKAVDFIPVESLETTMR

Ligand information

• Ligand ID: 9H7
• InChI: InChI=1S/C38H46N6O8S2/c1-37(2,3)52-36(48)41-28-15-8-6-4-5-7-12-23-21-38(23,35(47)43-54(49,50)25-17-18-25)42-32(45)29-20-24(22-44(29)34(28)46)51-33-31(30-16-11-19-53-30)39-26-13-9-10-14-27(26)40-33/h7,9-14,16,19,23-25,28-29H,4-6,8,15,17-18,20-22H2,1-3H3,(H,41,48)(H,42,45)(H,43,47)/b12-7-/t23-,24-,28+,29+,38-/m1/s1
• InChIKey: XPJKLRKWYFSTBR-LZFWIHPHSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C)OC(=O)N[C@H]1CCCCC\C=C/[C@@H]2C[C@]2(NC(=O)[C@@H]3C[C@H](CN3C1=O)Oc4nc5ccccc5nc4c6sccc6)C(=O)N[S](=O)(=O)C7CC7
  CACTVS 3.385: CC(C)(C)OC(=O)N[CH]1CCCCCC=C[CH]2C[C]2(NC(=O)[CH]3C[CH](CN3C1=O)Oc4nc5ccccc5nc4c6sccc6)C(=O)N[S](=O)(=O)C7CC7
  OpenEye OEToolkits 2.0.6: CC(C)(C)OC(=O)NC1CCCCCC=CC2CC2(NC(=O)C3CC(CN3C1=O)Oc4c(nc5ccccc5n4)c6cccs6)C(=O)NS(=O)(=O)C7CC7
  OpenEye OEToolkits 2.0.6: CC(C)(C)OC(=O)N[C@H]1CCCCC/C=C\[C@@H]2C[C@]2(NC(=O)[C@@H]3C[C@H](CN3C1=O)Oc4c(nc5ccccc5n4)c6cccs6)C(=O)NS(=O)(=O)C7CC7
  ACDLabs 12.01: c3(c1cccs1)c(nc2ccccc2n3)OC4CN5C(C4)C(NC6(C(C=CCCCCCC(C5=O)NC(=O)OC(C)(C)C)C6)C(NS(C7CC7)(=O)=O)=O)=O
• Formula: C38 H46 N6 O8 S2
• PDB chain: 5vp9 Chain A Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vp9 Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.
• Resolution: 1.859 Å
• Binding residue (original residue number in PDB): Q1041 F1043 Y1056 H1057 V1078 D1081 L1135 K1136 G1137 S1139 F1154 R1155 A1156 A1157
• Binding residue (residue number reindexed from 1): Q59 F61 Y74 H75 V96 D99 L153 K154 G155 S157 F172 R173 A174 A175
• Annotation score: 1
• Binding affinity: MOAD: Ki=1.03nM
  PDBbind-CN: -logKd/Ki=8.99,Ki=1.03nM

Enzymatic activity

• Catalytic site (original residue number in PDB): H1057 D1081 G1137 S1139
• Catalytic site (residue number reindexed from 1): H75 D99 G155 S157
• 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:0008236 serine-type peptidase activity

Biological Process

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

External links

• PDB: RCSB:5vp9, PDBe:5vp9, PDBj:5vp9
• PDBsum: 5vp9
• PubMed: 28594175
• UniProt: P26664|POLG_HCV1 Genome polyprotein