4EOX

X-ray Structure of Polypeptide Deformylase Bound to a Acylprolinamide inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Acylprolinamides: a new class of peptide deformylase inhibitors with in vivo antibacterial activity.

Axten, J.M., Medina, J.R., Blackledge, C.W., Duquenne, C., Grant, S.W., Bobko, M.A., Peng, T., Miller, W.H., Pinckney, T., Gallagher, T.F., Kulkarni, S., Lewandowski, T., Van Aller, G.S., Zonis, R., Ward, P., Campobasso, N.

(2012) Bioorg Med Chem Lett 22: 4028-4032

  • DOI: https://doi.org/10.1016/j.bmcl.2012.04.086
  • Primary Citation of Related Structures:  
    4EOX

  • PubMed Abstract: 

    A new class of PDF inhibitor with potent, broad spectrum antibacterial activity is described. Optimization of blood stability and potency provided compounds with improved pharmacokinetics that were suitable for in vivo experiments. Compound 5c, which has robust antibacterial activity, demonstrated efficacy in two respiratory tract infection models.

    • Organizational Affiliation: 

    Infectious Diseases Center of Excellence for Drug Discovery, Antibacterial Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426, USA. jeffrey.m.axten@gsk.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylaseA [auth P]203Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: def, spr1310
EC: 3.5.1.88
UniProt
Find proteins for Q8DP79 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DP79 
Go to UniProtKB:  Q8DP79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DP79
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0S5
Query on 0S5
Download Ideal Coordinates CCD File 
C [auth P]N-benzoyl-1-[(2R)-3-cyclopentyl-2-{[formyl(hydroxy)amino]methyl}propanoyl]-L-prolinamide
C22 H29 N3 O5
JPSWIPZHYDYDLN-MOPGFXCFSA-N
NI
Query on NI
Download Ideal Coordinates CCD File 
B [auth P]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0S5 Binding MOAD:  4EOX IC50: 0.28 (nM) from 1 assay(s)
PDBBind:  4EOX IC50: 0.28 (nM) from 1 assay(s)
BindingDB:  4EOX IC50: 0.28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.681α = 90
b = 49.681β = 90
c = 92.748γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations