Structure of PDB 3zsy Chain B Binding Site BS01

Receptor Information

>3zsy Chain B (length=149) Species: 12721 (Human immunodeficiency virus)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: OM3
• InChI: InChI=1S/C25H30N2O5/c1-27(15-19-11-12-21-23(32-16-31-21)22(19)25(29)30)14-18-9-5-6-10-20(18)24(28)26-13-17-7-3-2-4-8-17/h5-6,9-12,17H,2-4,7-8,13-16H2,1H3,(H,26,28)(H,29,30)/p+1
• InChIKey: STKSSLWZOAVRQS-UHFFFAOYSA-O
• SMILES:
  OpenEye OEToolkits 2.0.7: C[NH+](Cc1ccccc1C(=O)NCC2CCCCC2)Cc3ccc4c(c3C(=O)O)OCO4
  CACTVS 3.385: C[NH+](Cc1ccccc1C(=O)NCC2CCCCC2)Cc3ccc4OCOc4c3C(O)=O
• Formula: C25 H31 N2 O5
• Name: (R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM
• PDB chain: 3zsy Chain A Residue 1214

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3zsy Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Q95 Y99 A129
• Binding residue (residue number reindexed from 1): Q39 Y43 A73
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=3.23,Kd=595uM

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:3zsy, PDBe:3zsy, PDBj:3zsy
• PDBsum: 3zsy
• PubMed: 22808106
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)