8OTM

structure of InhA from mycobacterium tuberculosis in complex with N-((1-(3-hydroxy-4-phenoxybenzyl)-1H-1,2,3-triazol-4-yl)methyl)-2-oxo-2H-chromene-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of new diaryl ether inhibitors against Mycobacterium tuberculosis targeting the minor portal of InhA.

Chebaiki, M.Delfourne, E.Tamhaev, R.Danoun, S.Rodriguez, F.Hoffmann, P.Grosjean, E.Goncalves, F.Azema-Despeyroux, J.Pal, A.Kordulakova, J.Preuilh, N.Britton, S.Constant, P.Marrakchi, H.Maveyraud, L.Mourey, L.Lherbet, C.

(2023) Eur J Med Chem 259: 115646-115646

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115646
  • Primary Citation of Related Structures:  
    8OTM, 8OTN

  • PubMed Abstract: 

    Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) affects 10 million people each year and the emergence of resistant TB augurs for a growing incidence. In the last 60 years, only three new drugs were approved for TB treatment, for which resistances are already emerging. Therefore, there is a crucial need for new chemotherapeutic agents capable of eradicating TB. Enzymes belonging to the type II fatty acid synthase system (FAS-II) are involved in the biosynthesis of mycolic acids, cell envelope components essential for mycobacterial survival. Among them, InhA is the primary target of isoniazid (INH), one of the most effective compounds to treat TB. INH acts as a prodrug requiring activation by the catalase-peroxidase KatG, whose mutations are the major cause for INH resistance. Herein, a new series of direct InhA inhibitors were designed based on a molecular hybridization approach. They exhibit potent inhibitory activities of InhA and, for some of them, good antitubercular activities. Moreover, they display a low toxicity on human cells. A study of the mechanism of action of the most effective molecules shows that they inhibit the biosynthesis of mycolic acids. The X-ray structures of two InhA/NAD + /inhibitor complexes have been obtained showing a binding mode of a part of the molecule in the minor portal, rarely seen in the InhA structures reported so far.


  • Organizational Affiliation

    Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D
271Mycobacterium tuberculosisMutation(s): 0 
Gene Names: inhARv1484MTCY277.05
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
R [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
VZI (Subject of Investigation/LOI)
Query on VZI

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
S [auth D]
2-oxidanylidene-~{N}-[[1-[(3-oxidanyl-4-phenoxy-phenyl)methyl]-1,2,3-triazol-4-yl]methyl]chromene-3-carboxamide
C26 H20 N4 O5
VYCONRDQVKDCGH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
P [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
T [auth D],
U [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.588α = 90
b = 92.784β = 119.2
c = 90.751γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--
Universite de ToulouseFrance--
La Region OccitanieFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release