9B2E | pdb_00009b2e

DHNA associated with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Crystal structure of dihydroneopterin aldolase from Mycobacterium tuberculosis associated with 8-mercaptoguanine, and development of novel S8-functionalized analogues as inhibitors: Synthesis, enzyme inhibition, in vitro toxicity and antitubercular activity.

Czeczot, A.M.Muniz, M.N.Perello, M.A.Silva, E.E.D.Timmers, L.F.S.M.Berger, A.Gonzalez, L.C.Arrache Goncalves, G.Moura, S.Machado, P.Bizarro, C.V.Basso, L.A.

(2024) J Enzyme Inhib Med Chem 39: 2388207-2388207

  • DOI: https://doi.org/10.1080/14756366.2024.2388207
  • Primary Citation of Related Structures:  
    9B2E

  • PubMed Abstract: 

    The crystallographic structure of the FolB enzyme from Mycobacterium tuberculosis ( Mt FolB), complexed with its inhibitor 8-mercaptoguanine (8-MG), was elucidated at a resolution of 1.95 Å. A novel series of S8-functionalized 8-MG derivatives were synthesised and evaluated as in vitro inhibitors of dihydroneopterin aldolase (DHNA, EC 4.1.2.25) activity of Mt FolB. These compounds exhibited IC 50 values in the submicromolar range. Evaluation of the activity for five compounds indicated their inhibition mode and inhibition constants. Molecular docking analyses were performed to determine the enzyme-inhibitor intermolecular interactions and ligand conformations upon complex formation. The inhibitory activities of all compounds against the M. tuberculosis H37Rv strain were evaluated. Compound 3e exhibited a minimum inhibitory concentration in the micromolar range. Finally, Compound 3e showed no apparent toxicity in both HepG2 and Vero cells. The findings presented herein will advance the quest for novel, specific inhibitors targeting Mt FolB, an attractive molecular target for TB drug development.


  • Organizational Affiliation

    Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-dihydroneopterin aldolase
A, B
121Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 4.1.2.25 (PDB Primary Data), 5.1.99.8 (UniProt), 1.13.11.81 (UniProt)
UniProt
Find proteins for P9WNC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNC5 
Go to UniProtKB:  P9WNC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNC5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.386α = 90
b = 81.386β = 90
c = 74.862γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil42170320172

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release