4J4T

Crystal Structure of FabI from F. tularensis in complex with novel inhibitors based on the benzimidazole scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and biological evaluation of a novel series of benzimidazole inhibitors of Francisella tularensis enoyl-ACP reductase (FabI).

Mehboob, S.Song, J.Hevener, K.E.Su, P.C.Boci, T.Brubaker, L.Truong, L.Mistry, T.Deng, J.Cook, J.L.Santarsiero, B.D.Ghosh, A.K.Johnson, M.E.

(2015) Bioorg Med Chem Lett 25: 1292-1296

  • DOI: https://doi.org/10.1016/j.bmcl.2015.01.048
  • Primary Citation of Related Structures:  
    4J1N, 4J3F, 4J4T

  • PubMed Abstract: 

    Francisella tularensis, the causative agent of tularemia, presents a significant biological threat and is a Category A priority pathogen due to its potential for weaponization. The bacterial FASII pathway is a viable target for the development of novel antibacterial agents treating Gram-negative infections. Here we report the advancement of a promising series of benzimidazole FabI (enoyl-ACP reductase) inhibitors to a second-generation using a systematic, structure-guided lead optimization strategy, and the determination of several co-crystal structures that confirm the binding mode of designed inhibitors. These compounds display an improved low nanomolar enzymatic activity as well as promising low microgram/mL antibacterial activity against both F. tularensis and Staphylococcus aureus and its methicillin-resistant strain (MRSA). The improvements in activity accompanying structural modifications lead to a better understanding of the relationship between the chemical structure and biological activity that encompasses both enzymatic and whole-cell activity.


  • Organizational Affiliation

    Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States; Novalex Therapeutics, 2242 W. Harrison, Chicago, IL 60612, United States. Electronic address: shahila@uic.edu.


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, E
A, B, C, D, E, F, G, H
280Francisella tularensis subsp. tularensis SCHU S4Mutation(s): 0 
Gene Names: fabIFTT_0782
EC: 1.3.1.9
UniProt
Find proteins for Q5NGQ3 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4))
Explore Q5NGQ3 
Go to UniProtKB:  Q5NGQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NGQ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
FA [auth H]
I [auth A]
M [auth B]
AA [auth F],
DA [auth G],
FA [auth H],
I [auth A],
M [auth B],
R [auth C],
U [auth D],
Y [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
1JU
Query on 1JU

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
GA [auth H]
J [auth A]
N [auth B]
BA [auth F],
EA [auth G],
GA [auth H],
J [auth A],
N [auth B],
S [auth C],
V [auth D],
Z [auth E]
1-(1,3-benzodioxol-5-ylmethyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole
C19 H18 N2 O2
GFWJMMLPXBFICR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
IA [auth H]
JA [auth H]
K [auth A]
L [auth A]
P [auth B]
IA [auth H],
JA [auth H],
K [auth A],
L [auth A],
P [auth B],
T [auth C],
W [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
Q [auth B],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth F],
HA [auth H],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.398α = 90
b = 123.349β = 90
c = 202.653γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2015-03-18
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description