5JF7

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor SMP289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


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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:  
    5JF0, 5JEY, 5JEX, 5JEZ, 5JF2, 5JF1, 5JF4, 5JF3, 5JF6, 5JF5, 5JF8, 5JF7

  • 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 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 ...

    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

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide deformylaseA204Streptococcus agalactiaeMutation(s): 1 
Gene Names: defgbs1883
EC: 3.5.1.88
UniProt
Find proteins for Q8E378 (Streptococcus agalactiae serotype III (strain NEM316))
Explore Q8E378 
Go to UniProtKB:  Q8E378
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6JU (Subject of Investigation/LOI)
Query on 6JU

Download Ideal Coordinates CCD File 
B [auth A]2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
C17 H15 Br N2 O2
UALZWYXMMCSOBJ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
AL-PEPTIDE LINKINGC3 H7 N O5 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
6JU Binding MOAD:  5JF7 Ki: 909 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.47α = 90
b = 65.97β = 90
c = 89.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
FRODOmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-MIME 2006

Revision History  (Full details and data files)

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