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 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA, B198Staphylococcus aureusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0K8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
07N
Query on 07N

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
07N Binding MOAD:  3TTZ IC50: 4 (nM) from 1 assay(s)
BindingDB:  3TTZ IC50: min: 4, max: 10 (nM) from 2 assay(s)
PDBBind:  3TTZ IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.178α = 90
b = 55.629β = 100.37
c = 51.216γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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