Structure of PDB 3zsx Chain B Binding Site BS01

Receptor Information

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

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: N44
• InChI: InChI=1S/C27H26N2O5/c1-2-14-29(17-21-12-13-23-25(34-18-33-23)24(21)27(31)32)16-20-10-6-7-11-22(20)26(30)28-15-19-8-4-3-5-9-19/h2-13H,1,14-18H2,(H,28,30)(H,31,32)/p-1
• InChIKey: GNIJPYFYNUUVOY-UHFFFAOYSA-M
• SMILES:
  OpenEye OEToolkits 1.7.2: C=CCN(Cc1ccccc1C(=O)NCc2ccccc2)Cc3ccc4c(c3C(=O)[O-])OCO4
  CACTVS 3.370: [O-]C(=O)c1c(CN(CC=C)Cc2ccccc2C(=O)NCc3ccccc3)ccc4OCOc14
  ACDLabs 12.01: O=C(NCc1ccccc1)c2ccccc2CN(C\C=C)Cc3ccc4OCOc4c3C([O-])=O
• Formula: C27 H25 N2 O5
• Name: 5-({[2-(benzylcarbamoyl)benzyl](prop-2-en-1-yl)amino}methyl)-1,3-benzodioxole-4-carboxylate
• PDB chain: 3zsx Chain A Residue 1215

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3zsx Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): Q95 A129
• Binding residue (residue number reindexed from 1): Q39 A73
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=3.28,Kd=519uM

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