Structure of PDB 3nf6 Chain A Binding Site BS03

Receptor Information
>3nf6 Chain A (length=149) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ
Ligand information
Ligand IDIMV
InChIInChI=1S/C17H13NO5/c19-14-7-10-3-1-2-4-12(10)18(14)8-11-5-6-13-16(23-9-22-13)15(11)17(20)21/h1-6H,7-9H2,(H,20,21)
InChIKeyWSADZPAZSYSTNO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2N(c1ccccc1C2)Cc3ccc4OCOc4c3C(=O)O
CACTVS 3.370OC(=O)c1c(CN2C(=O)Cc3ccccc23)ccc4OCOc14
OpenEye OEToolkits 1.7.0c1ccc2c(c1)CC(=O)N2Cc3ccc4c(c3C(=O)O)OCO4
FormulaC17 H13 N O5
Name5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
ChEMBLCHEMBL1738817
DrugBank
ZINCZINC000066156784
PDB chain3nf6 Chain B Residue 216 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nf6 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q95 L102 A128 A129 W132
Binding residue
(residue number reindexed from 1)		Q39 L46 A72 A73 W76
Annotation score1
Binding affinityMOAD: ic50=295uM
PDBbind-CN: -logKd/Ki=3.53,IC50=295uM
Enzymatic activity
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
Biological Process
GO:0015074 DNA integration

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Molecular Function
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Biological Process
External links
PDB RCSB:3nf6, PDBe:3nf6, PDBj:3nf6
PDBsum3nf6
PubMed21602613
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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