9FOY image
Deposition Date 2024-06-12
Release Date 2024-08-07
Last Version Date 2025-02-19
Entry Detail
PDB ID:
9FOY
Keywords:
ISOMERASE
Title:
Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b
Biological Source:
Source Organism:
Mycobacterium tuberculosis H37Rv (Taxon ID: 83332)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.80 Å
R-Value Free:
0.30
R-Value Work:
0.27
R-Value Observed:
0.28
Space Group:
P 1 21 1
9FOY validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA gyrase subunit B,DNA gyrase subunit A
Gene (Uniprot):gyrB, gyrA
Chain IDs:A, B
Chain Length:756
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv
UniProt ID:P9WG45,P9WG47 Pfam ID:PF01751, PF00986, PF00521 EC:5.6.2.2
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')
Chain IDs:C (auth: E), E (auth: G)
Chain Length:8
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
Chain IDs:D (auth: F), F (auth: H)
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
A1ID8
A1ID9
Primary Citation
Structural Aspects of Mycobacterium tuberculosis DNA Gyrase Targeted by Novel Bacterial Topoisomerase Inhibitors.
Acs Med.Chem.Lett. 15 2164 2170 (2024)
PMID: 39691510 DOI: 10.1021/acsmedchemlett.4c00447

Abstact

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 IC50 for M. tuberculosis gyrase of 0.096 μM, and it has potent activity against M. tuberculosis, with an IC50 of 0.165 μM.

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Disease

Primary Citation of related structures
9FOY