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 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4DMN

  • 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 attractive targets for antiviral therapy ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 IntegraseA163Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag-pol
EC: 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), 2.7.7 (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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0L9 (Subject of Investigation/LOI)
Query on 0L9

Download Ideal Coordinates CCD File 
F [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ARS
Query on ARS

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0L9 BindingDB:  4DMN Kd: 4700 (nM) from 1 assay(s)
IC50: min: 28, max: 2.62e+5 (nM) from 7 assay(s)
PDBBind:  4DMN IC50: 2300 (nM) from 1 assay(s)
Binding MOAD:  4DMN IC50: 2300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.082α = 90
b = 73.082β = 90
c = 64.808γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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