4NAT

Inhibitors of 4-Phosphopanthetheine Adenylyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.0 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:  
    4NAT, 4NAU, 4NAH

  • 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 the most potent inhibition of enzymes from Gram-positive species ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphopantetheine adenylyltransferaseA, B, C160Staphylococcus aureus subsp. aureus MW2Mutation(s): 0 
Gene Names: coaDMW1007
EC: 2.7.7.3
Find proteins for P63820 (Staphylococcus aureus (strain MW2))
Explore P63820 
Go to UniProtKB:  P63820
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], K [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
2W5
Query on 2W5

Download Ideal Coordinates CCD File 
D [auth A], G [auth B], J [auth C](1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide
C20 H23 Cl2 N3 O3
WLATXSVSKGEBKX-ZIAGYGMSSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.157α = 90
b = 127.283β = 90
c = 126.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release