Structure of PDB 3nf9 Chain A Binding Site BS01

Receptor Information

>3nf9 Chain A (length=149) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: CD9
• InChI: InChI=1S/C17H12ClNO5/c18-11-3-1-9-5-14(20)19(12(9)6-11)7-10-2-4-13-16(24-8-23-13)15(10)17(21)22/h1-4,6H,5,7-8H2,(H,21,22)
• InChIKey: XVKFXTJLVSDWCE-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: Clc1ccc2c(c1)N(C(=O)C2)Cc3ccc4OCOc4c3C(=O)O
  OpenEye OEToolkits 1.7.0: c1cc2c(cc1Cl)N(C(=O)C2)Cc3ccc4c(c3C(=O)O)OCO4
  CACTVS 3.370: OC(=O)c1c(CN2C(=O)Cc3ccc(Cl)cc23)ccc4OCOc14
• Formula: C17 H12 Cl N O5
• Name: 5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
• ZINC: ZINC000066166929
• PDB chain: 3nf9 Chain A Residue 220

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nf9 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): V79 G82 V150 S153 M154 H183
• Binding residue (residue number reindexed from 1): V23 G26 V94 S97 M98 H127
• Annotation score: 1
• Binding affinity: MOAD: ic50=290uM
  PDBbind-CN: -logKd/Ki=3.54,IC50=290uM

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:3nf9, PDBe:3nf9, PDBj:3nf9
• PDBsum: 3nf9
• PubMed: 21602613
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)