3ZT2

Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.

Peat, T.S.Rhodes, D.I.Vandegraaff, N.Le, G.Smith, J.A.Clark, L.J.Jones, E.D.Coates, J.A.V.Thienthong, N.Newman, J.Dolezal, O.Mulder, R.Ryan, J.H.Savage, G.P.Francis, C.L.Deadman, J.J.

(2012) PLoS One 7: 40147

  • DOI: 10.1371/journal.pone.0040147
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the cr ...

    A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.


    Related Citations: 
    • Structural Basis for a New Mechanism of Inhibition of HIV-1 Integrase Identified by Fragment Screening and Structure-Based Design.
      Rhodes, D.I., Peat, T.S., Vandegraaff, N., Jeevarajah, D., Le, G., Jones, E.D., Smith, J.A., Coates, J.A., Winfield, L.J., Thienthong, N., Newman, J., Lucent, D., Ryan, J.H., Savage, G.P., Francis, C.L., Deadman, J.J.
      (2011) Antivir Chem Chemother 21: 155

    Organizational Affiliation

    CSIRO Materials, Science and Engineering, Parkville, Victoria, Australia. tom.peat@csiro.au



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTEGRASE
A, B
167Human immunodeficiency virusMutation(s): 3 
EC: 2.7.7
Find proteins for Q76353 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q76353
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZT2
Query on ZT2

Download CCD File 
A, B
5-[(E)-(2-OXO-2,3-DIHYDRO-1H-INDEN-1-YLIDENE)METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID
C18 H12 O5
WRNAEMYUELGDPO-NTUHNPAUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZT2Kd:  1375000   nM  PDBBind
ZT2Kd:  1375000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.331α = 90
b = 71.331β = 90
c = 66.979γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references, Structure summary