Structure of PDB 3nf7 Chain A Binding Site BS01

Receptor Information

>3nf7 Chain A (length=149) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: CIW
• InChI: InChI=1S/C17H12ClNO5/c18-11-2-3-12-10(5-11)6-14(20)19(12)7-9-1-4-13-16(24-8-23-13)15(9)17(21)22/h1-5H,6-8H2,(H,21,22)
• InChIKey: ZWUIUQQUOGIKGU-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1cc2c(cc1Cl)CC(=O)N2Cc3ccc4c(c3C(=O)O)OCO4
  CACTVS 3.370: OC(=O)c1c(CN2C(=O)Cc3cc(Cl)ccc23)ccc4OCOc14
  ACDLabs 12.01: Clc1cc2c(cc1)N(C(=O)C2)Cc3ccc4OCOc4c3C(=O)O
• Formula: C17 H12 Cl N O5
• Name: 5-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
• ZINC: ZINC000066166931
• PDB chain: 3nf7 Chain A Residue 221

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nf7 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): V77 V79 G82 V150 M154 E157 L158 H183
• Binding residue (residue number reindexed from 1): V21 V23 G26 V94 M98 E101 L102 H127
• Annotation score: 1
• Binding affinity: MOAD: ic50=340uM
  PDBbind-CN: -logKd/Ki=3.47,IC50=340uM

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:3nf7, PDBe:3nf7, PDBj:3nf7
• PDBsum: 3nf7
• PubMed: 21602613
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)