6OW2

X-ray Structure of Polypeptide Deformylase

• PDB DOI: https://doi.org/10.2210/pdb6OW2/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-09 Released: 2019-06-26 
• Deposition Author(s): Campobasso, N., Spletstoser, J., Ward, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

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

• PubMed: 31160176 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA. Electronic address: [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: 23.13 kDa 
• Atom Count: 1,617 
• Modelled Residue Count: 191 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A [auth P]	202	Streptococcus pneumoniae	Mutation(s): 0  Gene Names:  defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_01588, ERS409327_03241, ERS409593_03947, KK0981_34260, NCTC12140_00964 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
NB4 (Subject of Investigation/LOI)	C [auth P]	(2R)-2-(cyclopentylmethyl)-N'-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide C22 H36 F N7 O4 ZUQCOBLJLUYLKK-MSOLQXFVSA-N
NI	B [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NB4	Binding MOAD:  6OW2	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.334	α = 90
b = 50.334	β = 90
c = 91.482	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Campobasso, N., Spletstoser, J., Ward, P.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references