Structure of PDB 3nfa Chain A Binding Site BS03

Receptor Information
>3nfa 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 IDCBJ
InChIInChI=1S/C18H12BrNO6/c19-10-2-3-12-11(7-10)15(21)17(22)20(12)8-9-1-4-13-16(14(9)18(23)24)26-6-5-25-13/h1-4,7H,5-6,8H2,(H,23,24)
InChIKeyALXMSKACQCRMOE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c2c(ccc1OCCOc12)CN4c3ccc(Br)cc3C(=O)C4=O
OpenEye OEToolkits 1.7.0c1cc2c(cc1Br)C(=O)C(=O)N2Cc3ccc4c(c3C(=O)O)OCCO4
CACTVS 3.370OC(=O)c1c(CN2C(=O)C(=O)c3cc(Br)ccc23)ccc4OCCOc14
FormulaC18 H12 Br N O6
Name6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000066166928
PDB chain3nfa Chain B Residue 245 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nfa Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Q95 L102 A129 W132
Binding residue
(residue number reindexed from 1)		Q39 L46 A73 W76
Annotation score1
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:3nfa, PDBe:3nfa, PDBj:3nfa
PDBsum3nfa
PubMed21602613
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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