Structure of PDB 3su4 Chain A Binding Site BS01

Receptor Information

>3su4 Chain A (length=192)

GSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQ
GSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSA
GGPLLCPAGHAVGIFKAAVSTRGVAKAVDFIPVESLETTMRS

Ligand information

• Ligand ID: SU3
• InChI: InChI=1S/C38H55N5O9S/c1-7-25-18-38(25,33(46)41-53(49,50)27-14-15-27)40-31(44)29-17-26-20-43(29)32(45)30(36(2,3)4)39-34(47)51-22-37(5,6)16-9-8-11-23-12-10-13-24-19-42(21-28(23)24)35(48)52-26/h10,12-13,25-27,29-30H,7-9,11,14-22H2,1-6H3,(H,39,47)(H,40,44)(H,41,46)/t25-,26-,29+,30-,38-/m1/s1
• InChIKey: KUQWGLQLLVFLSM-ONAXAZCASA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: CC[C@@H]1C[C@@]1(C(=O)NS(=O)(=O)C2CC2)NC(=O)[C@@H]3C[C@@H]4CN3C(=O)[C@@H](NC(=O)OCC(CCCCc5cccc6c5CN(C6)C(=O)O4)(C)C)C(C)(C)C
  CACTVS 3.370: CC[CH]1C[C]1(NC(=O)[CH]2C[CH]3C[N]2C(=O)[CH](NC(=O)OCC(C)(C)CCCCc4cccc5C[N](Cc45)C(=O)O3)C(C)(C)C)C(=O)N[S](=O)(=O)C6CC6
  ACDLabs 12.01: O=S(=O)(NC(=O)C5(NC(=O)C2N3C(=O)C(NC(=O)OCC(C)(C)CCCCc1cccc4c1CN(C(=O)OC(C2)C3)C4)C(C)(C)C)CC5CC)C6CC6
  OpenEye OEToolkits 1.7.2: CCC1CC1(C(=O)NS(=O)(=O)C2CC2)NC(=O)C3CC4CN3C(=O)C(NC(=O)OCC(CCCCc5cccc6c5CN(C6)C(=O)O4)(C)C)C(C)(C)C
  CACTVS 3.370: CC[C@@H]1C[C@]1(NC(=O)[C@@H]2C[C@@H]3C[N@@]2C(=O)[C@@H](NC(=O)OCC(C)(C)CCCCc4cccc5C[N@@](Cc45)C(=O)O3)C(C)(C)C)C(=O)N[S](=O)(=O)C6CC6
• Formula: C38 H55 N5 O9 S
• Name: (5R,7S,10S)-10-tert-butyl-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethylcyclopropyl}-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19-dodecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosine-7(3H)-carboxamide;
  vaniprevir;
  MK-7009
• ChEMBL: CHEMBL4525964
• DrugBank: DB11929
• ZINC: ZINC000095627836
• PDB chain: 3su4 Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3su4 The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
• Resolution: 2.255 Å
• Binding residue (original residue number in PDB): Q1041 F1043 H1057 V1078 D1081 R1123 I1132 L1135 K1136 G1137 A1139 F1154 K1155 A1156 A1157
• Binding residue (residue number reindexed from 1): Q52 F54 H68 V89 D92 R134 I143 L146 K147 G148 A150 F165 K166 A167 A168
• Annotation score: 1
• Binding affinity: MOAD: Ki=554nM
  PDBbind-CN: -logKd/Ki=6.26,Ki=554nM

Enzymatic activity

• Catalytic site (original residue number in PDB): H1057 D1081 G1137 A1139
• Catalytic site (residue number reindexed from 1): H68 D92 G148 A150
• 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:3su4, PDBe:3su4, PDBj:3su4
• PDBsum: 3su4
• PubMed: 22910833
• UniProt: P26664|POLG_HCV1 Genome polyprotein