3TTZ | pdb_00003ttz

Crystal structure of a topoisomerase ATPase inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3TTZ/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-15 Released: 2011-11-16 
• Deposition Author(s): Boriack-Sjodin, P.A., Read, J., Eakin, A.E., Sherer, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.194 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Pyrrolamide DNA gyrase inhibitors: Optimization of antibacterial activity and efficacy.

Sherer, B.A., Hull, K., Green, O., Basarab, G., Hauck, S., Hill, P., Loch, J.T., Mullen, G., Bist, S., Bryant, J., Boriack-Sjodin, A., Read, J., Degrace, N., Uria-Nickelsen, M., Illingworth, R.N., Eakin, A.E.

(2011) Bioorg Med Chem Lett 21: 7416-7420

• PubMed: 22041057 
• DOI: https://doi.org/10.1016/j.bmcl.2011.10.010
• Primary Citation Related Structures: 
  3TTZ


• PubMed Abstract: 
  

  The pyrrolamides are a new class of antibacterial agents targeting DNA gyrase, an essential enzyme across bacterial species and inhibition results in the disruption of DNA synthesis and subsequently, cell death. The optimization of biochemical activity and other drug-like properties through substitutions to the pyrrole, piperidine, and heterocycle portions of the molecule resulted in pyrrolamides with improved cellular activity and in vivo efficacy.

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Organizational Affiliation: 
• Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.05 kDa 
• Atom Count: 3,562 
• Modeled Residue Count: 379 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	198	Staphylococcus aureus	Mutation(s): 0  Gene Names: gyrB EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus) Explore P0A0K8  Go to UniProtKB:  P0A0K8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07N	C [auth A], F [auth B]	2-[(3S,4R)-4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}-3-fluoropiperidin-1-yl]-1,3-thiazole-5-carboxylic acid C15 H15 Cl2 F N4 O3 S BGDGHNSKANYMHF-JGVFFNPUSA-N
MG	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
07N	BindingDB:  3TTZ	IC50: min: 4, max: 10 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.194 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.178	α = 90
b = 55.629	β = 100.37
c = 51.216	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Boriack-Sjodin, P.A., Read, J., Eakin, A.E., Sherer, B.A.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations