Structure of PDB 3nf8 Chain B Binding Site BS05

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 B Residue 257 [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)		V79 G82 I84 V150 M154 E157 L158 H183
Binding residue
(residue number reindexed from 1)		V23 G26 I28 V94 M98 E101 L102 H127
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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