5FRM

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ384 (compound 4a)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases.

Zhao, X.Z.Smith, S.J.Maskell, D.P.Metifiot, M.Pye, V.E.Fesen, K.Marchand, C.Pommier, Y.Cherepanov, P.Hughes, S.H.Burke, T.R.J.

(2016) ACS Chem Biol 11: 1074

  • DOI: 10.1021/acschembio.5b00948
  • Primary Citation of Related Structures:  
    5FRM, 5FRN, 5FRO

  • PubMed Abstract: 
  • HIV integrase (IN) strand transfer inhibitors (INSTIs) are among the newest anti-AIDS drugs; however, mutant forms of IN can confer resistance. We developed noncytotoxic naphthyridine-containing INSTIs that retain low nanomolar IC50 values against HIV-1 variants harboring all of the major INSTI-resistant mutations ...

    HIV integrase (IN) strand transfer inhibitors (INSTIs) are among the newest anti-AIDS drugs; however, mutant forms of IN can confer resistance. We developed noncytotoxic naphthyridine-containing INSTIs that retain low nanomolar IC50 values against HIV-1 variants harboring all of the major INSTI-resistant mutations. We found by analyzing crystal structures of inhibitors bound to the IN from the prototype foamy virus (PFV) that the most successful inhibitors show striking mimicry of the bound viral DNA prior to 3'-processing and the bound host DNA prior to strand transfer. Using this concept of "bi-substrate mimicry," we developed a new broadly effective inhibitor that not only mimics aspects of both the bound target and viral DNA but also more completely fills the space they would normally occupy. Maximizing shape complementarity and recapitulating structural components encompassing both of the IN DNA substrates could serve as a guiding principle for the development of new INSTIs.


    Organizational Affiliation

    Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health , 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: 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 3.4.23 (UniProt), 2.7.7 (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'C19synthetic construct
    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'D17synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      WA5 (Subject of Investigation/LOI)
      Query on WA5

      Download Ideal Coordinates CCD File 
      V [auth D]4-azanylidene-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide
      C16 H12 F2 N4 O3
      KQQAEMXQZXBXSU-MCMJHOFTSA-N
       Ligand Interaction
      MES
      Query on MES

      Download Ideal Coordinates CCD File 
      I [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
      C6 H13 N O4 S
      SXGZJKUKBWWHRA-UHFFFAOYSA-N
       Ligand Interaction
      SO4
      Query on SO4

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

      Download Ideal Coordinates CCD File 
      J [auth A], K [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth C]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 
      F [auth A], G [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.58 Å
      • R-Value Free: 0.203 
      • R-Value Work: 0.185 
      • R-Value Observed: 0.186 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 159.737α = 90
      b = 159.737β = 90
      c = 123.528γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      Aimlessdata scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2016-02-17
        Type: Initial release
      • Version 1.1: 2016-04-27
        Changes: Database references
      • Version 1.2: 2019-01-30
        Changes: Data collection, Experimental preparation, Other
      • Version 1.3: 2019-02-06
        Changes: Data collection, Experimental preparation
      • Version 1.4: 2019-04-10
        Changes: Data collection, Source and taxonomy