6P9M | pdb_00006p9m

Crystal structure of Mycobacterium tuberculosis KasA in complex with O6J

• PDB DOI: https://doi.org/10.2210/pdb6P9M/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2019-06-10 Released: 2020-04-01 
• Deposition Author(s): Capodagli, G.C., Neiditch, M.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.232 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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

• PubMed: 32197094 
• DOI: https://doi.org/10.1016/j.chembiol.2020.02.007
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Pharmacology, Physiology, and Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, USA.
Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA.
Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, USA.
Public Health Research Institute, Rutgers University - New Jersey Medical School, Newark, NJ, USA.
Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, USA. Electronic address: [e-mail].
Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA. Electronic address: [e-mail].
Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, USA. Electronic address: [e-mail].
Department of Pharmacology, Physiology, and Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, USA; Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.83 kDa 
• Atom Count: 3,189 
• Modeled Residue Count: 414 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 1	A	414	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: kasA, Rv2245, MTCY427.26 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6J (Subject of Investigation/LOI)	C [auth A]	N-(2-cyano-3-methyl-1H-indol-5-yl)pentane-1-sulfonamide C15 H19 N3 O2 S YSEFPNYCRCSWGW-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	F [auth A], G [auth A], H [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.232 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.713	α = 90
b = 77.713	β = 90
c = 146.441	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Capodagli, G.C., Neiditch, M.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109713

Revision History  

• 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