Structure of PDB 3nf8 Chain B Binding Site BS02

Receptor Information
>3nf8 Chain B (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 IDCDQ
InChIInChI=1S/C18H14ClNO5/c19-12-2-3-13-11(7-12)8-15(21)20(13)9-10-1-4-14-17(16(10)18(22)23)25-6-5-24-14/h1-4,7H,5-6,8-9H2,(H,22,23)
InChIKeyKBLBOZBAVQRJSU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c2c(ccc1OCCOc12)CN4c3ccc(Cl)cc3CC4=O
CACTVS 3.370OC(=O)c1c(CN2C(=O)Cc3cc(Cl)ccc23)ccc4OCCOc14
OpenEye OEToolkits 1.7.0c1cc2c(cc1Cl)CC(=O)N2Cc3ccc4c(c3C(=O)O)OCCO4
FormulaC18 H14 Cl N O5
Name6-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000066166930
PDB chain3nf8 Chain A Residue 267 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nf8 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 Y99 T125 A129 W132
Binding residue
(residue number reindexed from 1)		Q39 Y43 T69 A73 W76
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
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:3nf8, PDBe:3nf8, PDBj:3nf8
PDBsum3nf8
PubMed21602613
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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