3TTZ

Crystal structure of a topoisomerase ATPase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2011.10.010

  • 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 activi ...

    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.


    Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. brian.sherer@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
198Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0A0K8 (Staphylococcus aureus)
Go to UniProtKB:  P0A0K8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
07N
Query on 07N

Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
07NIC50: 4 - <10 nM (89) BINDINGDB
07NIC50: 4 nM BINDINGMOAD
07NIC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.178α = 90.00
b = 55.629β = 100.37
c = 51.216γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
JDirectordata collection
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy