9FOY | pdb_00009foy

Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b

• PDB DOI: https://doi.org/10.2210/pdb9FOY/pdb
• NAKB: 9FOY

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis H37Rv, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-12 Released: 2024-08-07 
• Deposition Author(s): Kokot, M., Hrast, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Minovski, N., Anderluh, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.304 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: experimental

Literature

Structural Aspects of Mycobacterium tuberculosis DNA Gyrase Targeted by Novel Bacterial Topoisomerase Inhibitors.

Kokot, M., Hrast Rambaher, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Parish, T., Minovski, N., Anderluh, M.

(2024) ACS Med Chem Lett 15: 2164-2170

• PubMed: 39691510 
• DOI: https://doi.org/10.1021/acsmedchemlett.4c00447
• Primary Citation Related Structures: 
  9FOY


• PubMed Abstract: 
  

  In this Letter, we present a small series of novel bacterial topoisomerase inhibitors (NTBIs) that exhibit both potent inhibition of Mycobacterium tuberculosis DNA gyrase and potent antimycobacterial activity. The disclosed crystal structure of M. tuberculosis DNA gyrase in complex with DNA and compound 5 from this NBTI series reveals the binding mode of an NBTI in the GyrA binding pocket and confirms the presence and importance of halogen bonding for the excellent on-target potency. In addition, we have shown that compound 5 is a promising M. tuberculosis DNA gyrase inhibitor, with an IC ₅₀ for M. tuberculosis gyrase of 0.096 μM, and it has potent activity against M. tuberculosis , with an IC ₅₀ of 0.165 μM.

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Organizational Affiliation: 
• Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
Department of Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
School of Medicine, University of Washington, Seattle, Washington 98195, United States.
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98105, United States.

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)

Macromolecule Content 

• Total Structure Weight: 181.96 kDa 
• Atom Count: 12,316 
• Modeled Residue Count: 1,500 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit A	A, B	756	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: gyrB, Rv0005, MTCY10H4.03, gyrA, Rv0006, MTCY10H4.04 EC: 5.6.2.2
UniProt
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG45  Go to UniProtKB:  P9WG45
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47
UniProt Groups	P9WG45P9WG47

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')	C [auth E], E [auth G]	8	Mycobacterium tuberculosis H37Rv

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')	D [auth F], F [auth H]	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ID9 (Subject of Investigation/LOI)	H	(1~{R})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol C24 H26 Br F2 N3 O2 RCLQISQKEHCDJQ-IUSZMWJPSA-N
A1ID8 (Subject of Investigation/LOI)	G [auth H]	(1~{S})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol C24 H26 Br F2 N3 O2 RCLQISQKEHCDJQ-HTZUNMPGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.304 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.041	α = 90
b = 131.703	β = 97.23
c = 96.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Kokot, M., Hrast, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Minovski, N., Anderluh, M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P012523/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V006983/1

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2025-02-19
  Changes: Database references, Structure summary