6RP0

The crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights.

Rieux, C.Goffinont, S.Coste, F.Tber, Z.Cros, J.Roy, V.Guerin, M.Gaudon, V.Bourg, S.Biela, A.Aucagne, V.Agrofoglio, L.Garnier, N.Castaing, B.

(2020) Int J Mol Sci 21

  • DOI: 10.3390/ijms21062058
  • Primary Citation of Related Structures:  
    6RNM, 6RNO, 6RNR, 6RO2, 6ROK, 6RP0, 6RP7

  • PubMed Abstract: 
  • DNA glycosylases are emerging as relevant pharmacological targets in inflammation, cancer and neurodegenerative diseases. Consequently, the search for inhibitors of these enzymes has become a very active research field. As a continuation of previous work that showed that 2-thioxanthine (2TX) is an irreversible inhibitor of zinc finger (ZnF)-containing Fpg/Nei DNA glycosylases, we designed and synthesized a mini-library of 2TX-derivatives (TXn) and evaluated their ability to inhibit Fpg/Nei enzymes ...

    DNA glycosylases are emerging as relevant pharmacological targets in inflammation, cancer and neurodegenerative diseases. Consequently, the search for inhibitors of these enzymes has become a very active research field. As a continuation of previous work that showed that 2-thioxanthine (2TX) is an irreversible inhibitor of zinc finger (ZnF)-containing Fpg/Nei DNA glycosylases, we designed and synthesized a mini-library of 2TX-derivatives (TXn) and evaluated their ability to inhibit Fpg/Nei enzymes. Among forty compounds, four TXn were better inhibitors than 2TX for Fpg. Unexpectedly, but very interestingly, two dithiolated derivatives more selectively and efficiently inhibit the zincless finger (ZnLF)-containing enzymes (human and mimivirus Neil1 DNA glycosylases hNeil1 and MvNei1, respectively). By combining chemistry, biochemistry, mass spectrometry, blind and flexible docking and X-ray structure analysis, we localized new TXn binding sites on Fpg/Nei enzymes. This endeavor allowed us to decipher at the atomic level the mode of action for the best TXn inhibitors on the ZnF-containing enzymes. We discovered an original inhibition mechanism for the ZnLF-containing Fpg/Nei DNA glycosylases by disulfide cyclic trimeric forms of dithiopurines. This work paves the way for the design and synthesis of a new structural class of inhibitors for selective pharmacological targeting of hNeil1 in cancer and neurodegenerative diseases.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASEA271Lactococcus cremorisMutation(s): 0 
Gene Names: mutMfpg
EC: 3.2.2.23 (UniProt), 4.2.99.18 (UniProt)
UniProt
Find proteins for P42371 (Lactococcus lactis subsp. cremoris)
Explore P42371 
Go to UniProtKB:  P42371
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')B, D [auth F]14synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')C14synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      5JL (Subject of Investigation/LOI)
      Query on 5JL

      Download Ideal Coordinates CCD File 
      E [auth A]2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one
      C5 H4 N4 O S2
      NDSUZZIWNBVBKW-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      F [auth A]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.25 Å
      • R-Value Free: 0.202 
      • R-Value Work: 0.164 
      • R-Value Observed: 0.165 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.18α = 90
      b = 92.18β = 90
      c = 139.726γ = 90
      Software Package:
      Software NamePurpose
      XDSdata reduction
      SCALAdata scaling
      PHASERphasing
      PHENIXrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2020-04-15
        Type: Initial release