7PQL | pdb_00007pql

Acinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain complexed with EBL2704

PDB DOI: https://doi.org/10.2210/pdb7PQL/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Acinetobacter baumannii 1419130
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-17 Released: 2022-09-28
Deposition Author(s): Cotman, A.E., Zega, A., Zidar, N., Ilas, J., Tomasic, T., Masic, L.P., Mundy, J.E.A., Stevenson, C.E.M., Burton, N., Lawson, D.M., Maxwell, A., Kikelj, D.
Funding Organization(s): European Communitys Seventh Framework Programme, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.219 (Depositor), 0.228 (DCC)
R-Value Work:
0.161 (Depositor), 0.172 (DCC)
R-Value Observed:
0.164 (Depositor)

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

Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.

Cotman, A.E., Durcik, M., Benedetto Tiz, D., Fulgheri, F., Secci, D., Sterle, M., Mozina, S., Skok, Z., Zidar, N., Zega, A., Ilas, J., Peterlin Masic, L., Tomasic, T., Hughes, D., Huseby, D.L., Cao, S., Garoff, L., Berruga Fernandez, T., Giachou, P., Crone, L., Simoff, I., Svensson, R., Birnir, B., Korol, S.V., Jin, Z., Vicente, F., Ramos, M.C., de la Cruz, M., Glinghammar, B., Lenhammar, L., Henderson, S.R., Mundy, J.E.A., Maxwell, A., Stevenson, C.E.M., Lawson, D.M., Janssen, G.V., Sterk, G.J., Kikelj, D.

(2023) J Med Chem 66: 1380-1425

PubMed: 36634346 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.2c01597
Primary Citation Related Structures:
7P2M, 7P2W, 7PQI, 7PQL, 7PQM, 7PTF, 7PTG

PubMed Abstract:
We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa , which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1 , we identified compound 27 , featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa , a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and ( S )- 27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.

Organizational Affiliation

Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 47.5 kDa
Atom Count: 3,361
Modeled Residue Count: 370
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	206	Acinetobacter baumannii 1419130	Mutation(s): 0 Gene Names: gyrB, J518_2757 EC: 5.6.2.2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
81N (Subject of Investigation/LOI) Query on 81N Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(1R)-1-phenylethoxy]-1,3-benzothiazole-6-carboxylic acid C₂₂ H₁₇ Cl₂ N₃ O₄ S LXTDDWSYQKHDKA-LLVKDONJSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
80S (Subject of Investigation/LOI) Query on 80S Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(1S)-1-phenylethoxy]-1,3-benzothiazole-6-carboxylic acid C₂₂ H₁₇ Cl₂ N₃ O₄ S LXTDDWSYQKHDKA-NSHDSACASA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.219 (Depositor), 0.228 (DCC)
R-Value Work: 0.161 (Depositor), 0.172 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.111	α = 90
b = 48.436	β = 124.17
c = 83.317	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-28

Deposition Author(s):

Funding Organization	Location	Grant Number
European Communitys Seventh Framework Programme	United Kingdom	115583
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P012523/1