4DMN

HIV-1 Integrase Catalytical Core Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors.

Kessl, J.J.Jena, N.Koh, Y.Taskent-Sezgin, H.Slaughter, A.Feng, L.de Silva, S.Wu, L.Le Grice, S.F.Engelman, A.Fuchs, J.R.Kvaratskhelia, M.

(2012) J.Biol.Chem. 287: 16801-16811

  • DOI: 10.1074/jbc.M112.354373

  • PubMed Abstract: 
  • The multifunctional HIV-1 enzyme integrase interacts with viral DNA and its key cellular cofactor LEDGF to effectively integrate the reverse transcript into a host cell chromosome. These interactions are crucial for HIV-1 replication and present attr ...

    The multifunctional HIV-1 enzyme integrase interacts with viral DNA and its key cellular cofactor LEDGF to effectively integrate the reverse transcript into a host cell chromosome. These interactions are crucial for HIV-1 replication and present attractive targets for antiviral therapy. Recently, 2-(quinolin-3-yl) acetic acid derivatives were reported to selectively inhibit the integrase-LEDGF interaction in vitro and impair HIV-1 replication in infected cells. Here, we show that this class of compounds impairs both integrase-LEDGF binding and LEDGF-independent integrase catalytic activities with similar IC(50) values, defining them as bona fide allosteric inhibitors of integrase function. Furthermore, we show that 2-(quinolin-3-yl) acetic acid derivatives block the formation of the stable synaptic complex between integrase and viral DNA by allosterically stabilizing an inactive multimeric form of integrase. In addition, these compounds inhibit LEDGF binding to the stable synaptic complex. This multimode mechanism of action concordantly results in cooperative inhibition of the concerted integration of viral DNA ends in vitro and HIV-1 replication in cell culture. Our findings, coupled with the fact that high cooperativity of antiviral inhibitors correlates with their increased instantaneous inhibitory potential, an important clinical parameter, argue strongly that improved 2-(quinolin-3-yl) acetic acid derivatives could exhibit desirable clinical properties.


    Organizational Affiliation

    Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Integrase
A
163Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
0L9
Query on 0L9

Download SDF File 
Download CCD File 
A
(2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid
C19 H15 Br Cl N O3
BNDPDYQQAJUJPY-SFHVURJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0L9Kd: 4700 nM (98) BINDINGDB
0L9IC50: 28 - 261500 nM (98) BINDINGDB
0L9IC50: 2300 nM BINDINGMOAD
0L9IC50: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.082α = 90.00
b = 73.082β = 90.00
c = 64.808γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CrystalCleardata collection
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references
  • Version 1.2: 2012-07-18
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description