Structure of PDB 3zcm Chain B Binding Site BS01

Receptor Information

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

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ

Ligand information

• Ligand ID: PX3
• InChI: InChI=1S/C28H28N2O6/c1-3-14-30(17-21-10-13-24-26(36-18-35-24)25(21)28(32)33)16-20-6-4-5-7-23(20)27(31)29-15-19-8-11-22(34-2)12-9-19/h3-13H,1,14-18H2,2H3,(H,29,31)(H,32,33)
• InChIKey: WRLIFDLBMCTVHJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: COc1ccc(CNC(=O)c2ccccc2CN(CC=C)Cc3ccc4OCOc4c3C(O)=O)cc1
  ACDLabs 12.01: O=C(NCc1ccc(OC)cc1)c2ccccc2CN(C/C=C)Cc3ccc4OCOc4c3C(=O)O
  OpenEye OEToolkits 1.9.2: COc1ccc(cc1)CNC(=O)c2ccccc2CN(CC=C)Cc3ccc4c(c3C(=O)O)OCO4
• Formula: C28 H28 N2 O6
• Name: 5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-prop-2-enyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid
• ZINC: ZINC000095921328
• PDB chain: 3zcm Chain A Residue 1214

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3zcm Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Q95 A98 T125
• Binding residue (residue number reindexed from 1): Q39 A42 T69
• Annotation score: 1
• Binding affinity: MOAD: 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:3zcm, PDBe:3zcm, PDBj:3zcm
• PDBsum: 3zcm
• PubMed: 22808106
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)