4EOX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.783 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2012.04.086

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
P
203Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: def
EC: 3.5.1.88
Find proteins for Q8DP79 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DP79
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0S5
Query on 0S5

Download SDF File 
Download CCD File 
P
N-benzoyl-1-[(2R)-3-cyclopentyl-2-{[formyl(hydroxy)amino]methyl}propanoyl]-L-prolinamide
C22 H29 N3 O5
JPSWIPZHYDYDLN-MOPGFXCFSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
P
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0S5IC50: 0.3 nM (99) BINDINGDB
0S5IC50: 0.28 nM BINDINGMOAD
0S5IC50: 0.28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.783 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 49.681α = 90.00
b = 49.681β = 90.00
c = 92.748γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
MAR345dtbdata collection
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references