3S3M

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and Dolutegravir (S/GSK1349572)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572).

Hare, S.Smith, S.J.Metifiot, M.Jaxa-Chamiec, A.Pommier, Y.Hughes, S.H.Cherepanov, P.

(2011) Mol Pharmacol 80: 565-572

  • DOI: 10.1124/mol.111.073189
  • Primary Citation of Related Structures:  
    3S3M, 3S3N, 3S3O

  • PubMed Abstract: 
  • Raltegravir (RAL) and related HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) efficiently block viral replication in vitro and suppress viremia in patients. These small molecules bind to the IN active site, causing it to disengage from the deoxyadenosine at the 3' end of viral DNA ...

    Raltegravir (RAL) and related HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) efficiently block viral replication in vitro and suppress viremia in patients. These small molecules bind to the IN active site, causing it to disengage from the deoxyadenosine at the 3' end of viral DNA. The emergence of viral strains that are highly resistant to RAL underscores the pressing need to develop INSTIs with improved resistance profiles. Herein, we show that the candidate second-generation drug dolutegravir (DTG, S/GSK1349572) effectively inhibits a panel of HIV-1 IN variants resistant to first-generation INSTIs. To elucidate the structural basis for the increased potency of DTG against RAL-resistant INs, we determined crystal structures of wild-type and mutant prototype foamy virus intasomes bound to this compound. The overall IN binding mode of DTG is strikingly similar to that of the tricyclic hydroxypyrrole MK-2048. Both second-generation INSTIs occupy almost the same physical space within the IN active site and make contacts with the β4-α2 loop of the catalytic core domain. The extended linker region connecting the metal chelating core and the halobenzyl group of DTG allows it to enter farther into the pocket vacated by the displaced viral DNA base and to make more intimate contacts with viral DNA, compared with those made by RAL and other INSTIs. In addition, our structures suggest that DTG has the ability to subtly readjust its position and conformation in response to structural changes in the active sites of RAL-resistant INs.


    Organizational Affiliation

    Division of Infectious Diseases, Imperial College London, London, United Kingdom.



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
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3'C19N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'D17N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 7 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DLU
      Query on DLU

      Download Ideal Coordinates CCD File 
      N [auth A](4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide
      C20 H19 F2 N3 O5
      RHWKPHLQXYSBKR-BMIGLBTASA-N
       Ligand Interaction
      HEZ
      Query on HEZ

      Download Ideal Coordinates CCD File 
      P [auth B]HEXANE-1,6-DIOL
      C6 H14 O2
      XXMIOPMDWAUFGU-UHFFFAOYSA-N
       Ligand Interaction
      SO4
      Query on SO4

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

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      G [auth A], H [auth A], I [auth A], J [auth A]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 
      L [auth A], M [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      NH4
      Query on NH4

      Download Ideal Coordinates CCD File 
      K [auth A]AMMONIUM ION
      H4 N
      QGZKDVFQNNGYKY-UHFFFAOYSA-O
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      DLUIC50 :  40   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.49 Å
      • R-Value Free: 0.232 
      • R-Value Work: 0.206 
      • R-Value Observed: 0.207 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 160.14α = 90
      b = 160.14β = 90
      c = 123.43γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      MAR345dtbdata collection
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-07-13
        Type: Initial release
      • Version 1.1: 2011-10-05
        Changes: Database references