9CUN | pdb_00009cun

Crystal structure of Ami1 from M. tuberculosis in complex with a tetrazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Identification of Potential Inhibitors of Mycobacterium tuberculosis Amidases: An Integrated In Silico and Experimental Study.

Rosas-Cruz, M.Madariaga Mazon, A.Garcia-Mejia, C.D.Hernandez-Vazquez, E.Gomez-Velasco, H.Jimenez-Faraco, E.Farias-Gaytan, R.S.Hermoso, J.A.Martinez-Caballero, S.

(2024) ACS Omega 9: 46461-46471

  • DOI: https://doi.org/10.1021/acsomega.4c07964
  • Primary Citation of Related Structures:  
    9CUN

  • PubMed Abstract: 

    Virtual screening is a crucial tool in early stage drug discovery for identifying potential hit candidates. Here, we present an integrated approach that combines theoretical and experimental techniques to identify, for the first time, inhibitors of amidases (Ami1-Ami4) from Mycobacterium tuberculosis . Through computational methods, we proposed a set of potential inhibitors, which were subsequently evaluated experimentally using differential scanning fluorimetry. This led to the identification of two promising hits: a carbohydrazide core (hit 1 ) and a tetrazole core (hit 5 ). We further developed a small collection of compounds derived from hit 1 , which demonstrated improved affinity for Ami1. Additionally, we determined the crystallographic structure of the Ami1-hit 5 complex at a resolution of 1.45 Å, providing molecular-level insights into the interaction of this compound within the catalytic site. The findings of this study contribute to the advancement of drug discovery against tuberculosis and propose new targets for therapeutic development.


  • Organizational Affiliation
    • Instituto de Química, Universidad Nacional Autonóma de México, A. Universidad 3000, Ciudad Universitaria, CP 04510 Ciudad de México, Mexico.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylmuramoyl-L-alanine amidase Rv3717218Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3717
EC: 3.5.1.28
UniProt
Find proteins for I6Y4D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6Y4D2 
Go to UniProtKB:  I6Y4D2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6Y4D2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.353α = 90
b = 103.96β = 90
c = 130.143γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)MexicoIA205122

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references