3ZCM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  3ZSO, 3ZSQ, 3ZSR, 3ZSV, 3ZSW, 3ZSX, 3ZSY, 3ZSZ, 3ZT0, 3ZT1, 3ZT2, 3ZT3, 3ZT4

  • 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.


    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
HIV INTEGRASE
A, B
167Human immunodeficiency virus 1N/A
Find proteins for Q76353 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q76353
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX3
Query on PX3

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Download CCD File 
A, B
5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-prop-2-enyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid
C28 H28 N2 O6
WRLIFDLBMCTVHJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PX3Kd: 519000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 70.855α = 90.00
b = 70.855β = 90.00
c = 67.132γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-21 
  • Released Date: 2012-12-05 
  • Deposition Author(s): Peat, T.S.

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release