5JF3

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A unique peptide deformylase platform to rationally design and challenge novel active compounds.

Fieulaine, S.Alves de Sousa, R.Maigre, L.Hamiche, K.Alimi, M.Bolla, J.M.Taleb, A.Denis, A.Pages, J.M.Artaud, I.Meinnel, T.Giglione, C.

(2016) Sci Rep 6: 35429-35429

  • DOI: 10.1038/srep35429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae ...

    Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.


    Organizational Affiliation

    UMR8601, LCBPT, CNRS Université Paris Descartes, PRES Paris Cité, 45 rue des Sts Pères 75270 Paris Cedex 06, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.,GlaxoSmithKline, ZA Courtaboeuf, 25 Avenue du Québec, 91140 Villebon-sur-Yvette, France.,UMR_MD1, Aix-Marseille Univ, IRBA, Facultés de Médecine et de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A
204Streptococcus agalactiae serotype III (strain NEM316)Mutation(s): 1 
Gene Names: def
EC: 3.5.1.88
Find proteins for Q8E378 (Streptococcus agalactiae serotype III (strain NEM316))
Go to UniProtKB:  Q8E378
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
SF5
Query on SF5

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Download CCD File 
A
methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate
C18 H23 N3 O5
PKBQPXFVXNPVJM-CQSZACIVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SF5Ki: 38 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.070α = 90.00
b = 65.490β = 90.00
c = 88.790γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
FRODOmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-MIME 2006

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence