4OJR

Crystal Structure of the HIV-1 Integrase catalytic domain with GSK1264


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allosteric Inhibition of Human Immunodeficiency Virus Integrase: LATE BLOCK DURING VIRAL REPLICATION AND ABNORMAL MULTIMERIZATION INVOLVING SPECIFIC PROTEIN DOMAINS.

Gupta, K.Brady, T.Dyer, B.M.Malani, N.Hwang, Y.Male, F.Nolte, R.T.Wang, L.Velthuisen, E.Jeffrey, J.Van Duyne, G.D.Bushman, F.D.

(2014) J.Biol.Chem. 289: 20477-20488

  • DOI: 10.1074/jbc.M114.551119

  • PubMed Abstract: 
  • HIV-1 replication in the presence of antiviral agents results in evolution of drug-resistant variants, motivating the search for additional drug classes. Here we report studies of GSK1264, which was identified as a compound that disrupts the interact ...

    HIV-1 replication in the presence of antiviral agents results in evolution of drug-resistant variants, motivating the search for additional drug classes. Here we report studies of GSK1264, which was identified as a compound that disrupts the interaction between HIV-1 integrase (IN) and the cellular factor lens epithelium-derived growth factor (LEDGF)/p75. GSK1264 displayed potent antiviral activity and was found to bind at the site occupied by LEDGF/p75 on IN by x-ray crystallography. Assays of HIV replication in the presence of GSK1264 showed only modest inhibition of the early infection steps and little effect on integration targeting, which is guided by the LEDGF/p75-IN interaction. In contrast, inhibition of late replication steps was more potent. Particle production was normal, but particles showed reduced infectivity. GSK1264 promoted aggregation of IN and preformed LEDGF/p75-IN complexes, suggesting a mechanism of inhibition. LEDGF/p75 was not displaced from IN during aggregation, indicating trapping of LEDGF/p75 in aggregates. Aggregation assays with truncated IN variants revealed that a construct with catalytic and C-terminal domains of IN only formed an open polymer associated with efficient drug-induced aggregation. These data suggest that the allosteric inhibitors of IN are promising antiviral agents and provide new information on their mechanism of action.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Integrase
A
164Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SQ
Query on 2SQ

Download SDF File 
Download CCD File 
A
(2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid
C26 H28 F N O5
LDALHHGVIZRJPA-QHCPKHFHSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CAC
Query on CAC

Download SDF File 
Download CCD File 
A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.664α = 90.00
b = 72.664β = 90.00
c = 65.453γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references