4NAU

S. aureus CoaD with Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Inhibitors of 4'-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy.

de Jonge, B.L.Walkup, G.K.Lahiri, S.D.Huynh, H.Neckermann, G.Utley, L.Nash, T.J.Brock, J.San Martin, M.Kutschke, A.Johnstone, M.Laganas, V.Hajec, L.Gu, R.F.Ni, H.Chen, B.Hutchings, K.Holt, E.McKinney, D.Gao, N.Livchak, S.Thresher, J.

(2013) Antimicrob.Agents Chemother. 57: 6005-6015

  • DOI: 10.1128/AAC.01661-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitors of 4'-phosphopantetheine adenylyltransferase (PPAT) were identified through high-throughput screening of the AstraZeneca compound library. One series, cycloalkyl pyrimidines, showed inhibition of PPAT isozymes from several species, with th ...

    Inhibitors of 4'-phosphopantetheine adenylyltransferase (PPAT) were identified through high-throughput screening of the AstraZeneca compound library. One series, cycloalkyl pyrimidines, showed inhibition of PPAT isozymes from several species, with the most potent inhibition of enzymes from Gram-positive species. Mode-of-inhibition studies with Streptococcus pneumoniae and Staphylococcus aureus PPAT demonstrated representatives of this series to be reversible inhibitors competitive with phosphopantetheine and uncompetitive with ATP, binding to the enzyme-ATP complex. The potency of this series was optimized using structure-based design, and inhibition of cell growth of Gram-positive species was achieved. Mode-of-action studies, using generation of resistant mutants with targeted sequencing as well as constructs that overexpress PPAT, demonstrated that growth suppression was due to inhibition of PPAT. An effect on bacterial burden was demonstrated in mouse lung and thigh infection models, but further optimization of dosing requirements and compound properties is needed before these compounds can be considered for progress into clinical development. These studies validated PPAT as a novel target for antibacterial therapy.


    Organizational Affiliation

    Infection Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A, B, C
160Staphylococcus aureus (strain MW2)Mutation(s): 0 
Gene Names: coaD
EC: 2.7.7.3
Find proteins for P63820 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  P63820
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2W3
Query on 2W3

Download SDF File 
Download CCD File 
A
2-[2-[(1S,2S)-2-[(3,4-dichlorophenyl)methylcarbamoyl]cyclohexyl]-6-ethyl-pyrimidin-4-yl]-4-oxidanyl-6-oxidanylidene-1H-pyrimidine-5-carboxamide
C25 H26 Cl2 N6 O4
SLGIPMWTTPZXTJ-GJZGRUSLSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A, B, C
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.256 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.095α = 90.00
b = 127.782β = 90.00
c = 127.123γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-22 
  • Released Date: 2014-03-12 
  • Deposition Author(s): Lahiri, S.D.

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description