4IQU | pdb_00004iqu

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.225 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/jm4010187
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 46.06 kDa 
  • Atom Count: 3,185 
  • Modeled Residue Count: 358 
  • Deposited Residue Count: 400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA nucleotidylexotransferase400Mus musculusMutation(s): 0 
Gene Names: DnttTdt
EC: 2.7.7.31 (PDB Primary Data), 3.1.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09838 (Mus musculus)
Explore P09838 
Go to UniProtKB:  P09838
IMPC:  MGI:98659
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09838
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1FQ

Query on 1FQ



Download:Ideal Coordinates CCD File
C [auth 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
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.913α = 90
b = 84.804β = 90
c = 114.493γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy, Structure summary