Structure of PDB 1rtl Chain A Binding Site BS04

Receptor Information
>1rtl Chain A (length=180) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCING
VCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCG
SSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHA
VGLFRAAVCTRGVTKAVDFIPVENLETTMR
Ligand information
Ligand IDCPX
InChIInChI=1S/C24H38N4O4/c1-15(2)19(27-23(32)25-17-6-3-4-7-17)22(31)28-13-10-18(26-21(30)16-8-9-16)20(28)24(14-29)11-5-12-24/h14-20H,3-13H2,1-2H3,(H,26,30)(H2,25,27,32)/t18-,19-,20-/m0/s1
InChIKeyGCDRFILPPBOJLM-UFYCRDLUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)[C@H](NC(=O)NC1CCCC1)C(=O)N2CC[C@H](NC(=O)C3CC3)[C@H]2C4(CCC4)C=O
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)N1CC[C@@H]([C@H]1C2(CCC2)C=O)NC(=O)C3CC3)NC(=O)NC4CCCC4
CACTVS 3.341CC(C)[CH](NC(=O)NC1CCCC1)C(=O)N2CC[CH](NC(=O)C3CC3)[CH]2C4(CCC4)C=O
ACDLabs 10.04O=C(N2C(C(NC(=O)C1CC1)CC2)C3(C=O)CCC3)C(NC(=O)NC4CCCC4)C(C)C
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)N1CCC(C1C2(CCC2)C=O)NC(=O)C3CC3)NC(=O)NC4CCCC4
FormulaC24 H38 N4 O4
NameN-[(2R,3S)-1-((2S)-2-{[(CYCLOPENTYLAMINO)CARBONYL]AMINO}-3-METHYLBUTANOYL)-2-(1-FORMYL-1-CYCLOBUTYL)PYRROLIDINYL]CYCLOPROPANECARBOXAMIDE
ChEMBL
DrugBankDB07582
ZINCZINC000033821260
PDB chain1rtl Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rtl Pyrrolidine-5,5-trans-lactams. 4. Incorporation of a P3/P4 urea leads to potent intracellular inhibitors of hepatitis C virus NS3/4A protease
Resolution2.75 Å
Binding residue
(original residue number in PDB)		Q41 H57 I132 S139 F154 A156 A157
Binding residue
(residue number reindexed from 1)		Q41 H57 I132 S139 F154 A156 A157
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.59,IC50=2.6uM
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 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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1rtl, PDBe:1rtl, PDBj:1rtl
PDBsum1rtl
PubMed14627400
UniProtP26664|POLG_HCV1 Genome polyprotein

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