8I68

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Uric acid, Form III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment.

Kesharwani, S.Raj, P.Paul, A.Roy, K.Bhanot, A.Mehta, A.Gopal, A.Varshney, U.Gopal, B.Sundriyal, S.

(2023) Eur J Med Chem 258: 115604-115604

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115604
  • Primary Citation of Related Structures:  
    8I61, 8I62, 8I63, 8I64, 8I65, 8I66, 8I67, 8I68, 8I69, 8I6A, 8I6B, 8I6C, 8I6D

  • PubMed Abstract: 

    Uracil DNA glycosylase (UDG or Ung) is a key enzyme involved in uracil excision from the DNA as a repair mechanism. Designing Ung inhibitors is thus a promising strategy to treat different cancers and infectious diseases. The uracil ring and its derivatives have been shown to inhibit Mycobacterium tuberculosis Ung (MtUng), resulting from specific and strong binding with the uracil-binding pocket (UBP). To design novel MtUng inhibitors, we screened several non-uracil ring fragments hypothesised to occupy MtUng UBP due to their high similarity to the uracil structural motif. These efforts have resulted in the discovery of novel MtUng ring inhibitors. Here we report the co-crystallised poses of these fragments, confirming their binding within the UBP, thus providing a robust structural framework for the design of novel lead compounds. We selected the barbituric acid (BA) ring as a case study for further derivatisation and SAR analysis. The modelling studies predicted the BA ring of the designed analogues to interact with the MtUng UBP much like the uracil ring. The synthesised compounds were screened in vitro using radioactivity and a fluorescence-based assay. These studies led to a novel BA-based MtUng inhibitor 18a (IC 50  = 300 μM) displaying ∼24-fold potency over the uracil ring.


  • Organizational Affiliation

    Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil-DNA glycosylase238Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ungRv2976cMTCY349.11
EC: 3.2.2.27
UniProt
Find proteins for P9WFQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFQ9 
Go to UniProtKB:  P9WFQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFQ9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.37α = 90
b = 60.02β = 90
c = 74.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references