ISDA

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, synthetic construct

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2024-06-12

Release Date:

2024-08-07

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

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA gyrase subunit B,DNA gyrase subunit A
Chain IDs:A, B
Chain Length:756
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv

UniProt ID:P9WG45 Pfam ID:PF01751, PF00986 EC:5.6.2.2

Polymer Type:polydeoxyribonucleotide
Description: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
Description: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.

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

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures