7K73 | pdb_00007k73

Structure of Enoyl-[acyl-carrier-protein] reductase [NADH] from Mycobacterium fortuitum bound to NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.147 (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 1.2 of the entry. See complete history

Literature

In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum.

Roquet-Baneres, F.Alcaraz, M.Hamela, C.Abendroth, J.Edwards, T.E.Kremer, L.

(2023) Antimicrob Agents Chemother : e0160722-e0160722

  • DOI: https://doi.org/10.1128/aac.01607-22
  • Primary Citation Related Structures: 
    7K73, 7U0O

  • PubMed Abstract: 

    Mycobacterium fortuitum represents one of the most clinically relevant rapid-growing mycobacterial species. Treatments are complex due to antibiotic resistance and to severe side effects of effective drugs, prolonged time of treatment, and co-infection with other pathogens. Herein, we explored the activity of NITD-916, a direct inhibitor of the enoyl-ACP reductase InhA of the type II fatty acid synthase in Mycobacterium tuberculosis. We found that this compound displayed very low MIC values against a panel of M. fortuitum clinical strains and exerted potent antimicrobial activity against M. fortuitum in macrophages. Remarkably, the compound was also highly efficacious in a zebrafish model of infection. Short duration treatments were sufficient to significantly protect the infected larvae from M. fortuitum-induced killing, which correlated with reduced bacterial burdens and abscesses. Biochemical analyses demonstrated an inhibition of de novo synthesis of mycolic acids. Resolving the crystal structure of the InhA MFO in complex with NAD and NITD-916 confirmed that NITD-916 is a direct inhibitor of InhA MFO . Importantly, single nucleotide polymorphism leading to a G96S substitution in InhA MFO conferred high resistance levels to NITD-916, thus resolving its target in M. fortuitum. Overall, these findings indicate that NITD-916 is highly active against M. fortuitum both in vitro and in vivo and should be considered in future preclinical evaluations for the treatment of M. fortuitum pulmonary diseases.


  • Organizational Affiliation
    • Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.

Macromolecule Content 

  • Total Structure Weight: 121.01 kDa 
  • Atom Count: 9,437 
  • Modeled Residue Count: 1,060 
  • Deposited Residue Count: 1,108 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]A,
B [auth C],
C [auth E],
D [auth G]
277Mycolicibacterium fortuitumMutation(s): 0 
Gene Names: fabIinhAA5637_21995A5751_12770FKW78_11710NCTC1542_01491XA26_29600
EC: 1.3.1.9
UniProt
Find proteins for A0A0N9XSE6 (Mycolicibacterium fortuitum)
Explore A0A0N9XSE6 
Go to UniProtKB:  A0A0N9XSE6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N9XSE6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
E [auth A],
I [auth C],
N [auth E],
R [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
H [auth A]
J [auth C]
K [auth C]
M [auth C]
F [auth A],
H [auth A],
J [auth C],
K [auth C],
M [auth C],
O [auth E],
Q [auth G],
S [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A],
L [auth C],
P [auth E],
T [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.94α = 90
b = 90.86β = 90.96
c = 91.91γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references, Refinement description
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description