4EOX | pdb_00004eox

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

• PDB DOI: https://doi.org/10.2210/pdb4EOX/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-16 Released: 2012-05-30 
• Deposition Author(s): Ward, P., Campobasso, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.230 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

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

• PubMed: 22579486 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.086
• Primary Citation 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.

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Organizational Affiliation: 
• Infectious Diseases Center of Excellence for Drug Discovery, Antibacterial Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.2 kDa 
• Atom Count: 1,688 
• Modeled Residue Count: 192 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A [auth P]	203	Streptococcus pneumoniae R6	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0S5	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	B [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0S5	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 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.681	α = 90
b = 49.681	β = 90
c = 92.748	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Ward, P., Campobasso, N.

Revision History  

• 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