Structure of PDB 3nf6 Chain B Binding Site BS01

Receptor Information

>3nf6 Chain B (length=149) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: IMV
• InChI: InChI=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)
• InChIKey: WSADZPAZSYSTNO-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C2N(c1ccccc1C2)Cc3ccc4OCOc4c3C(=O)O
  CACTVS 3.370: OC(=O)c1c(CN2C(=O)Cc3ccccc23)ccc4OCOc14
  OpenEye OEToolkits 1.7.0: c1ccc2c(c1)CC(=O)N2Cc3ccc4c(c3C(=O)O)OCO4
• Formula: C17 H13 N O5
• Name: 5-[(2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
• ChEMBL: CHEMBL1738817
• ZINC: ZINC000066156784
• PDB chain: 3nf6 Chain A Residue 215

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nf6 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): Q95 T125 A128 A129 W132
• Binding residue (residue number reindexed from 1): Q39 T69 A72 A73 W76
• Annotation score: 1
• Binding affinity: MOAD: 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

External links

• PDB: RCSB:3nf6, PDBe:3nf6, PDBj:3nf6
• PDBsum: 3nf6
• PubMed: 21602613
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)