3ZSO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3ZCM, 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 crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRASEA, B167Human immunodeficiency virusMutation(s): 3 
EC: 2.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O2N (Subject of Investigation/LOI)
Query on O2N

Download Ideal Coordinates CCD File 
K [auth A], R [auth B]5-{[(2-{[bis(4-methoxyphenyl)methyl]carbamoyl}benzyl)(prop-2-en-1-yl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid
C35 H34 N2 O7
BHZUDEPAXPIUNZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], P [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A], Q [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
O2N PDBBind:  3ZSO Kd: 7600 (nM) from 1 assay(s)
Binding MOAD:  3ZSO Kd: 7600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.063α = 90
b = 71.063β = 90
c = 67.027γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references, Structure summary
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation