6P9L

Crystal structure of Mycobacterium tuberculosis KasA in complex with JFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA.

Inoyama, D.Awasthi, D.Capodagli, G.C.Tsotetsi, K.Sukheja, P.Zimmerman, M.Li, S.G.Jadhav, R.Russo, R.Wang, X.Grady, C.Richmann, T.Shrestha, R.Li, L.Ahn, Y.M.Ho Liang, H.P.Mina, M.Park, S.Perlin, D.S.Connell, N.Dartois, V.Alland, D.Neiditch, M.B.Kumar, P.Freundlich, J.S.

(2020) Cell Chem Biol 27: 560

  • DOI: https://doi.org/10.1016/j.chembiol.2020.02.007
  • Primary Citation of Related Structures:  
    6P9K, 6P9L, 6P9M

  • PubMed Abstract: 

    Published Mycobacterium tuberculosis β-ketoacyl-ACP synthase KasA inhibitors lack sufficient potency and/or pharmacokinetic properties. A structure-based approach was used to optimize existing KasA inhibitor DG167. This afforded indazole JSF-3285 with a 30-fold increase in mouse plasma exposure. Biochemical, genetic, and X-ray studies confirmed JSF-3285 targets KasA. JSF-3285 offers substantial activity in an acute mouse model of infection and in the corresponding chronic infection model, with efficacious reductions in colony-forming units at doses as low as 5 mg/kg once daily orally and improvement of the efficacy of front-line drugs isoniazid or rifampicin. JSF-3285 is a promising preclinical candidate for tuberculosis.


  • Organizational Affiliation

    Department of Pharmacology, Physiology, and Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 1414Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: kasARv2245MTCY427.26
EC: 2.3.1.41 (PDB Primary Data), 2.3.1.293 (UniProt)
UniProt
Find proteins for P9WQD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQD9 
Go to UniProtKB:  P9WQD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQD9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JFX (Subject of Investigation/LOI)
Query on JFX

Download Ideal Coordinates CCD File 
B [auth A]4-fluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide
C12 H16 F N3 O2 S
AHVAAGWAEHSRBU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.804α = 90
b = 77.804β = 90
c = 146.374γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109713

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description