6OW7

X-ray Structure of Polypeptide Deformylase with a Piperazic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.

Spletstoser, J.T.Dreabit, J.Knox, A.N.Benowitz, A.Campobasso, N.Ward, P.Cui, G.Lewandowski, T.McCloskey, L.Aubart, K.M.

(2019) Bioorg Med Chem Lett 29: 2410-2414

  • DOI: 10.1016/j.bmcl.2019.05.028
  • Primary Citation of Related Structures:  
    6OW2, 6OW7

  • PubMed Abstract: 
  • The discovery of a novel series of peptide deformylase inhibitors incorporating a piperazic acid amino acid found in nature is described. These compounds demonstrated potent in vitro enzymatic potency and antimicrobial activity. Crystal structure analysis revealed the piperazic acid optimized a key contact with the PDF protein that accounted for the increased enzymatic potency of these compounds ...

    The discovery of a novel series of peptide deformylase inhibitors incorporating a piperazic acid amino acid found in nature is described. These compounds demonstrated potent in vitro enzymatic potency and antimicrobial activity. Crystal structure analysis revealed the piperazic acid optimized a key contact with the PDF protein that accounted for the increased enzymatic potency of these compounds. We describe lead optimization of the P3' region of the series that resulted in a compound with good potency against three target organisms. One molecule showed in vivo efficacy in a rat respiratory infection model but ultimately did not meet candidate progression criteria.


    Organizational Affiliation

    GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide deformylaseA [auth P], B [auth Q]202Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
EC: 3.5.1.88
UniProt
Find proteins for Q8DP79 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DP79 
Go to UniProtKB:  Q8DP79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N9Y (Subject of Investigation/LOI)
Query on N9Y

Download Ideal Coordinates CCD File 
E [auth P], H [auth Q](3S)-2-{(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl}-N-(pyridin-2-yl)hexahydropyridazine-3-carboxamide
C20 H29 N5 O4
IGYIJLMSSQSKHF-SJORKVTESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth P], G [auth Q]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth P], F [auth Q]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
N9Y Binding MOAD:  6OW7 IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.229α = 90
b = 69.229β = 90
c = 91.879γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references