1S17

Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb1S17/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-05 Released: 2004-03-30 
• Deposition Author(s): Molteni, V., He, X., Nabakka, J., Yang, K., Kreusch, A., Gordon, P., Bursulaya, B., Ryder, N.S., Goldberg, R., He, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.233 (Depositor) 
• R-Value Work: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Identification of novel potent bicyclic peptide deformylase inhibitors

Molteni, V., He, X., Nabakka, J., Yang, K., Kreusch, A., Gordon, P., Bursulaya, B., Warner, I., Shin, T., Biorac, T., Ryder, N.S., Goldberg, R., Doughty, J., He, Y.

(2004) Bioorg Med Chem Lett 14: 1477-1481

• PubMed: 15006385 
• DOI: https://doi.org/10.1016/j.bmcl.2004.01.014
• Primary Citation of Related Structures:  
  1S17


• PubMed Abstract: 
  

  Screening of our compound collection using Staphylococcus aureus Ni-Peptide deformylase (PDF) afforded a very potent PDF inhibitor with an IC(50) in the low nanomolar range but with poor antibacterial activity (MIC). Three-dimensional structural information obtained from Pseudomonas aeruginosa Ni-PDF complexed with the inhibitor suggested the synthesis of a variety of analogues that would maintain high binding affinity while attempting to improve antibacterial activity. Many of the compounds synthesized proved to be excellent PDF-Ni inhibitors and some showed increased antibacterial activity in selected strains.

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Organizational Affiliation: 

Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 2,918 
• Modelled Residue Count: 330 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	180	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: DEF, PA0019 EC: 3.5.1.88
UniProt
Find proteins for Q9I7A8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7A8  Go to UniProtKB:  Q9I7A8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNR	D [auth A], G [auth B]	2-(3,4-DIHYDRO-3-OXO-2H-BENZO[B][1,4]THIAZIN-2-YL)-N-HYDROXYACETAMIDE C10 H10 N2 O3 S UKDWCJNGBPZOBU-MRVPVSSYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.233 (Depositor) 
• R-Value Work:  0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.009	α = 90
b = 73.994	β = 90
c = 76.864	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Molteni, V., He, X., Nabakka, J., Yang, K., Kreusch, A., Gordon, P., Bursulaya, B., Ryder, N.S., Goldberg, R., He, Y.

Revision History  

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description