Structure of PDB 3nfa Chain B Binding Site BS02

Receptor Information
>3nfa 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 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 222 [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)		V79 A80 G82 I84 M154 E157 L158 H183
Binding residue
(residue number reindexed from 1)		V23 A24 G26 I28 M98 E101 L102 H127
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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