3E3U

Crystal structure of Mycobacterium tuberculosis peptide deformylase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results.

Pichota, A.Duraiswamy, J.Yin, Z.Keller, T.H.Alam, J.Liung, S.Lee, G.Ding, M.Wang, G.Chan, W.L.Schreiber, M.Ma, I.Beer, D.Ngew, X.Mukherjee, K.Nanjundappa, M.Teo, J.W.Thayalan, P.Yap, A.Dick, T.Meng, W.Xu, M.Koehn, J.Pan, S.H.Clark, K.Xie, X.Shoen, C.Cynamon, M.

(2008) Bioorg Med Chem Lett 18: 6568-6572

  • DOI: 10.1016/j.bmcl.2008.10.040
  • Primary Citation of Related Structures:  
    3E3U

  • PubMed Abstract: 
  • Bacterial peptide deformylase (PDF) belongs to a subfamily of metalloproteases catalyzing the removal of the N-terminal formyl group from newly synthesized proteins. We report the synthesis and biological activity of highly potent inhibitors of Mycobacterium tuberculosis (Mtb) PDF enzyme as well as the first X-ray crystal structure of Mtb PDF ...

    Bacterial peptide deformylase (PDF) belongs to a subfamily of metalloproteases catalyzing the removal of the N-terminal formyl group from newly synthesized proteins. We report the synthesis and biological activity of highly potent inhibitors of Mycobacterium tuberculosis (Mtb) PDF enzyme as well as the first X-ray crystal structure of Mtb PDF. Structure-activity relationship and crystallographic data clarified the structural requirements for high enzyme potency and cell based potency. Activities against single and multi-drug-resistant Mtb strains are also reported.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore. arkadius.pichota@novartis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide deformylaseA197Mycobacterium tuberculosisMutation(s): 0 
Gene Names: def
EC: 3.5.1.88
UniProt
Find proteins for P9WIJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIJ3 
Go to UniProtKB:  P9WIJ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVC (Subject of Investigation/LOI)
Query on NVC

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]N-[(2R)-2-{[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl}hexyl]-N-hydroxyformamide
C19 H25 N3 O4
QDDZLTVSNABZIK-ZBFHGGJFSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NVC PDBBind:  3E3U IC50: 13 (nM) from 1 assay(s)
Binding MOAD:  3E3U IC50: 13 (nM) from 1 assay(s)
BindingDB:  3E3U IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.87α = 90
b = 54.765β = 94.39
c = 40.215γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance