4ZTJ

Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors.

Raheem, I.T.Walji, A.M.Klein, D.Sanders, J.M.Powell, D.A.Abeywickrema, P.Barbe, G.Bennet, A.Clas, S.D.Dubost, D.Embrey, M.Grobler, J.Hafey, M.J.Hartingh, T.J.Hazuda, D.J.Miller, M.D.Moore, K.P.Pajkovic, N.Patel, S.Rada, V.Rearden, P.Schreier, J.D.Sisko, J.Steele, T.G.Truchon, J.F.Wai, J.Xu, M.Coleman, P.J.

(2015) J Med Chem 58: 8154-8165

  • DOI: 10.1021/acs.jmedchem.5b01037
  • Primary Citation of Related Structures:  
    4ZTF, 4ZTJ

  • PubMed Abstract: 
  • The search for new molecular constructs that resemble the critical two-metal binding pharmacophore required for HIV integrase strand transfer inhibition represents a vibrant area of research within drug discovery. Here we present the discovery of a new class of HIV integrase strand transfer inhibitors based on the 2-pyridinone core of MK-0536 ...

    The search for new molecular constructs that resemble the critical two-metal binding pharmacophore required for HIV integrase strand transfer inhibition represents a vibrant area of research within drug discovery. Here we present the discovery of a new class of HIV integrase strand transfer inhibitors based on the 2-pyridinone core of MK-0536. These efforts led to the identification of two lead compounds with excellent antiviral activity and preclinical pharmacokinetic profiles to support a once-daily human dose prediction. Dose escalating PK studies in dog revealed significant issues with limited oral absorption and required an innovative prodrug strategy to enhance the high-dose plasma exposures of the parent molecules.


    Organizational Affiliation

    Merck Frosst Centre for Therapeutic Research , Kirkland, QC Canada.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PFV INTEGRASEA, B395Human spumaretrovirusMutation(s): 0 
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
    DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')C19Human spumaretrovirus
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')D17Human spumaretrovirus
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      4RT (Subject of Investigation/LOI)
      Query on 4RT

      Download Ideal Coordinates CCD File 
      L [auth A](1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione
      C24 H23 Cl F N3 O5
      CMKPKOVJKYIZNW-DHTHFVMWSA-N
       Ligand Interaction
      SO4
      Query on SO4

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

      Download Ideal Coordinates CCD File 
      F [auth A], G [auth A], N [auth B], P [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 
      H [auth A], I [auth A], O [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.67 Å
      • R-Value Free: 0.221 
      • R-Value Work: 0.196 
      • R-Value Observed: 0.197 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 158.96α = 90
      b = 158.96β = 90
      c = 124.47γ = 90
      Software Package:
      Software NamePurpose
      Aimlessdata scaling
      BUSTER-TNTrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHASERphasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2015-05-14 
      • Released Date: 2015-10-07 
      • Deposition Author(s): Klein, D.J., Patel, S.

      Revision History  (Full details and data files)

      • Version 1.0: 2015-10-07
        Type: Initial release
      • Version 1.1: 2015-11-04
        Changes: Database references