3E3U

Crystal structure of Mycobacterium tuberculosis peptide deformylase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3E3U/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-08 Released: 2009-01-20 
• Deposition Author(s): Meng, W., Xu, M., Pan, S., Koehn, J.

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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 

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

• PubMed: 19008098 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore. [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: 22.1 kDa 
• Atom Count: 1,799 
• Modelled Residue Count: 196 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	197	Mycobacterium tuberculosis	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NVC	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
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NVC	PDBBind:  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 = 100.87	α = 90
b = 54.765	β = 94.39
c = 40.215	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Meng, W., Xu, M., Pan, S., Koehn, J.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations