4DUH

Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors.

Brvar, M.Perdih, A.Renko, M.Anderluh, G.Turk, D.Solmajer, T.

(2012) J.Med.Chem. 55: 6413-6426

  • DOI: 10.1021/jm300395d

  • PubMed Abstract: 
  • Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel ser ...

    Bacterial DNA gyrase is a well-established and validated target for the development of novel antibacterials. Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4'-methyl-N(2)-phenyl-[4,5'-bithiazole]-2,2'-diamine inhibitors of gyrase B with a low micromolar inhibitory activity by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques (differential scanning fluorimetry, surface plasmon resonance, and microscale thermophoresis). The binding mode of the potent inhibitor 18 was revealed by X-ray crystallography, confirming our initial in silico binding model. Furthermore, the high resolution of the complex structure allowed for the placement of the Gly97-Ser108 flexible loop, thus revealing its role in binding of this class of compounds. The crystal structure of the complex protein G24 and inhibitor 18 provides valuable information for further optimization of this novel class of DNA gyrase B inhibitors.


    Organizational Affiliation

    National Institute of Chemistry, Laboratory for Biocomputing and Bioinformatics, 1001 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
220Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gyrB (acrB, cou, himB, hisU, nalC, parA, pcbA)
EC: 5.6.2.3
Find proteins for P0AES6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RLI
Query on RLI

Download SDF File 
Download CCD File 
A, B
4-{[4'-methyl-2'-(propanoylamino)-4,5'-bi-1,3-thiazol-2-yl]amino}benzoic acid
C17 H16 N4 O3 S2
JOAXMWDTALNZFE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RLIKd: 6600 nM BINDINGMOAD
RLIKd: 6600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.236α = 90.00
b = 51.122β = 95.68
c = 79.130γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MxCuBEdata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-08-08
    Type: Database references