4IQW

Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target.

Costi, R., Cuzzucoli Crucitti, G., Pescatori, L., Messore, A., Scipione, L., Tortorella, S., Amoroso, A., Crespan, E., Campiglia, P., Maresca, B., Porta, A., Granata, I., Novellino, E., Gouge, J., Delarue, M., Maga, G., Di Santo, R.

(2013) J Med Chem 56: 7431-7441

  • DOI: 10.1021/jm4010187
  • Primary Citation of Related Structures:  
    4IQT, 4IQU, 4IQV, 4IQW

  • PubMed Abstract: 

    • Terminal deoxynucletidyl transferase (TdT) is overexpressed in some cancer types, where it might compete with pol μ during the mutagenic repair of double strand breaks (DSBs) through the nonhomologous end joining (NHEJ) pathway. Here we report the discov ...

    Terminal deoxynucletidyl transferase (TdT) is overexpressed in some cancer types, where it might compete with pol μ during the mutagenic repair of double strand breaks (DSBs) through the nonhomologous end joining (NHEJ) pathway. Here we report the discovery and characterization of pyrrolyl and indolyl diketo acids that specifically target TdT and behave as nucleotide-competitive inhibitors. These compounds show a selective toxicity toward MOLT-4 compared to HeLa cells that correlate well with in vitro selectivity for TdT. The binding site of two of these inhibitors was determined by cocrystallization with TdT, explaining why these compounds are competitive inhibitors of the deoxynucleotide triphosphate (dNTP). In addition, because of the observed dual localization of the phenyl substituent, these studies open the possibility of rationally designing more potent compounds.

    Organizational Affiliation: 

    Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma , P.le Aldo Moro 5, I-00185 Roma, Italy.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA nucleotidylexotransferase A381Mus musculusMutation(s): 1 
Gene Names: Dntt, Tdt
EC: 2.7.7.31 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P09838 (Mus musculus)
Explore P09838 
Go to UniProtKB:  P09838
NIH Common Fund Data Resources
IMPC:  MGI:98659
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*CP*G)-3'C4N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    1FQ
    Query on 1FQ
    Download Ideal Coordinates CCD File 
    A
    		(2Z,5E)-6-[4-(4-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid
    C17 H12 F N O5
    XOINLIFLBUUBGT-RSIRFQHMSA-N    		 Ligand Interaction
    NA
    Query on NA
    Download Ideal Coordinates CCD File 
    A
    		SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.229 
    • R-Value Work: 0.188 
    • R-Value Observed: 0.190 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 46.65α = 90
    b = 84.67β = 90
    c = 114.73γ = 90
    Software Package:
    Software NamePurpose
    ADSCdata collection
    PHASERphasing
    BUSTERrefinement
    XDSdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    • Deposited Date: 2013-01-13 
    • Released Date: 2013-09-04 
      • Deposition Author(s): Gouge, J., Delarue, M.

    Revision History 

    • Version 1.0: 2013-09-04
      Type: Initial release
    • Version 1.1: 2013-10-09
      Changes: Database references
    • Version 1.2: 2017-07-26
      Changes: Refinement description, Source and taxonomy