4E1M

Crystal Structure of HIV-1 Integrase with a non-catayltic site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

New Class of HIV-1 Integrase (IN) Inhibitors with a Dual Mode of Action.

Tsiang, M.Jones, G.S.Niedziela-Majka, A.Kan, E.Lansdon, E.B.Huang, W.Hung, M.Samuel, D.Novikov, N.Xu, Y.Mitchell, M.Guo, H.Babaoglu, K.Liu, X.Geleziunas, R.Sakowicz, R.

(2012) J Biol Chem 287: 21189-21203

  • DOI: https://doi.org/10.1074/jbc.M112.347534
  • Primary Citation of Related Structures:  
    4E1M, 4E1N

  • PubMed Abstract: 

    tert-Butoxy-(4-phenyl-quinolin-3-yl)-acetic acids (tBPQA) are a new class of HIV-1 integrase (IN) inhibitors that are structurally distinct from IN strand transfer inhibitors but analogous to LEDGINs. LEDGINs are a class of potent antiviral compounds that interacts with the lens epithelium-derived growth factor (LEDGF) binding pocket on IN and were identified through competition binding against LEDGF. LEDGF tethers IN to the host chromatin and enables targeted integration of viral DNA. The prevailing understanding of the antiviral mechanism of LEDGINs is that they inhibit LEDGF binding to IN, which prevents targeted integration of HIV-1. We showed that in addition to the properties already known for LEDGINs, the binding of tBPQAs to the IN dimer interface inhibits IN enzymatic activity in a LEDGF-independent manner. Using the analysis of two long terminal repeat junctions in HIV-infected cells, we showed that the inhibition by tBPQAs occurs at or prior to the viral DNA 3'-processing step. Biochemical studies revealed that this inhibition operates by compound-induced conformational changes in the IN dimer that prevent proper assembly of IN onto viral DNA. For the first time, tBPQAs were demonstrated to be allosteric inhibitors of HIV-1 IN displaying a dual mode of action: inhibition of IN-viral DNA assembly and inhibition of IN-LEDGF interaction.


  • Organizational Affiliation

    Gilead Sciences, Inc, Foster City, California 94404, USA. mtsiang@gilead.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Integrase166Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 1 
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TQ2
Query on TQ2

Download Ideal Coordinates CCD File 
B [auth A](2S)-tert-butoxy[4-(3,4-dimethylphenyl)-2-methylquinolin-3-yl]ethanoic acid
C24 H27 N O3
HGSMBBVZYWHGQB-QFIPXVFZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
TQ2 Binding MOAD:  4E1M IC50: 215 (nM) from 1 assay(s)
PDBBind:  4E1M IC50: 55 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.794α = 90
b = 71.794β = 90
c = 65.329γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 1.2: 2012-07-25
    Changes: Database references
  • Version 1.3: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description