4BE2

PFV intasome with inhibitor XZ-259


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase.

Metifiot, M.Maddali, K.Johnson, B.C.Hare, S.Smith, S.J.Zhao, X.Z.Marchand, C.Burke, T.R.Hughes, S.H.Cherepanov, P.Pommier, Y.

(2013) ACS Chem Biol 8: 209

  • DOI: 10.1021/cb300471n
  • Primary Citation of Related Structures:  
    4BDY, 4BDZ, 4BE0, 4BE1, 4BE2

  • PubMed Abstract: 
  • On the basis of a series of lactam and phthalimide derivatives that inhibit HIV-1 integrase, we developed a new molecule, XZ-259, with biochemical and antiviral activities comparable to raltegravir. We determined the crystal structures of XZ-259 and four other derivatives in complex with the prototype foamy virus intasome ...

    On the basis of a series of lactam and phthalimide derivatives that inhibit HIV-1 integrase, we developed a new molecule, XZ-259, with biochemical and antiviral activities comparable to raltegravir. We determined the crystal structures of XZ-259 and four other derivatives in complex with the prototype foamy virus intasome. The compounds bind at the integrase-Mg(2+)-DNA interface of the integrase active site. In biochemical and antiviral assays, XZ-259 inhibits raltegravir-resistant HIV-1 integrases harboring the Y143R mutation. Molecular modeling is also presented suggesting that XZ-259 can bind in the HIV-1 intasome with its dimethyl sulfonamide group adopting two opposite orientations. Molecular dynamics analyses of the HIV-1 intasome highlight the importance of the viral DNA in drug potency.


    Organizational Affiliation

    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health , 37 Convent Drive, Bethesda, Maryland 20892, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PFV INTEGRASEA, B395Human spumaretrovirusMutation(s): 2 
Gene Names: pol
EC: 2.7.7 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 3.4.23 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
Go to UniProtKB:  P14350
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)C19Human spumaretrovirus
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND) *AP*CP*A)-3'D17Human spumaretrovirus
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      XZ2 (Subject of Investigation/LOI)
      Query on XZ2

      Download Ideal Coordinates CCD File 
      Q [auth D]2-(3-chloro-4-fluorobenzyl)-6,7-dihydroxy-N,N-dimethyl-1-oxo-2,3-dihydro-1H-isoindole-4-sulfonamide
      C17 H16 Cl F N2 O5 S
      AUHJAAAKTCEGOJ-UHFFFAOYSA-N
       Ligand Interaction
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      F [auth A], L [auth A], N [auth B]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth A], I [auth A], M [auth A], O [auth B]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      J [auth A], K [auth A], P [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.38 Å
      • R-Value Free: 0.223 
      • R-Value Work: 0.195 
      • R-Value Observed: 0.196 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 159.42α = 90
      b = 159.42β = 90
      c = 123.68γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata 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: 2012-10-31
        Type: Initial release
      • Version 1.1: 2012-11-14
        Changes: Derived calculations
      • Version 1.2: 2013-01-30
        Changes: Database references
      • Version 1.3: 2019-01-30
        Changes: Data collection, Experimental preparation, Other
      • Version 1.4: 2019-02-06
        Changes: Data collection, Experimental preparation