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Literature summary extracted from

  • 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.
    Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results (2008), Bioorg. Med. Chem. Lett., 18, 6568-6572.
    View publication on PubMed

Application

EC Number Application Comment Organism
3.5.1.88 medicine peptide deformylase is a target for the design of novel antibiotics Mycobacterium tuberculosis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.88 structures of several complexes of Mycobacterium tuberculosis peptide deformylase with the inhibitors are determined at 2.0 to 1.4 A Mycobacterium tuberculosis

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 (3R)-3-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]-N-hydroxyheptanamide
-
 Mycobacterium tuberculosis
3.5.1.88 (3R)-3-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]heptanoic acid
-
 Mycobacterium tuberculosis
3.5.1.88 (3R)-3-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]-N-hydroxyheptanamide
-
 Mycobacterium tuberculosis
3.5.1.88 (3R)-3-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]heptanoic acid
-
 Mycobacterium tuberculosis
3.5.1.88 actinonin
-
 Mycobacterium tuberculosis
3.5.1.88 LBK-611
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]heptyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]hexyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]pentyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]heptyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]hexyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]pentyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-3-[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-3-[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]-2-benzyl-3-oxopropyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-3-[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis
3.5.1.88 N-[(2R)-3-[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]-2-benzyl-3-oxopropyl]-N-hydroxyformamide
-
 Mycobacterium tuberculosis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 Ni2+
-
 Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.88 additional information Mycobacterium tuberculosis catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized proteins ?
-
 ?
3.5.1.88 additional information Mycobacterium tuberculosis H37Rv catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized proteins ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Mycobacterium tuberculosis P9WIJ3
-
-
3.5.1.88 Mycobacterium tuberculosis H37Rv P9WIJ3
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 additional information catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized proteins Mycobacterium tuberculosis ?
-
 ?
3.5.1.88 additional information catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized proteins Mycobacterium tuberculosis H37Rv ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 peptide deformylase
-
 Mycobacterium tuberculosis

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
3.5.1.88 0.000008
-
-
 Mycobacterium tuberculosis N-[(2R)-3-[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
3.5.1.88 0.00001
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]hexyl]-N-hydroxyformamide
3.5.1.88 0.000013
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]heptyl]-N-hydroxyformamide
3.5.1.88 0.000013
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]hexyl]-N-hydroxyformamide
3.5.1.88 0.000015
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]heptyl]-N-hydroxyformamide
3.5.1.88 0.000018
-
-
 Mycobacterium tuberculosis (3R)-3-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]-N-hydroxyheptanamide
3.5.1.88 0.000021
-
-
 Mycobacterium tuberculosis N-[(2R)-3-[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
3.5.1.88 0.000024
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]pentyl]-N-hydroxyformamide
3.5.1.88 0.000028
-
-
 Mycobacterium tuberculosis N-[(2R)-2-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]pentyl]-N-hydroxyformamide
3.5.1.88 0.000049
-
-
 Mycobacterium tuberculosis (3R)-3-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]-N-hydroxyheptanamide
3.5.1.88 0.000068
-
-
 Mycobacterium tuberculosis N-[(2R)-3-[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]-2-benzyl-3-oxopropyl]-N-hydroxyformamide
3.5.1.88 0.000161
-
-
 Mycobacterium tuberculosis N-[(2R)-3-[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]-2-benzyl-3-oxopropyl]-N-hydroxyformamide
3.5.1.88 0.000202
-
-
 Mycobacterium tuberculosis (3R)-3-[[(2S)-2-(1H-benzimidazol-2-yl)pyrrolidin-1-yl]carbonyl]heptanoic acid
3.5.1.88 0.000803
-
-
 Mycobacterium tuberculosis (3R)-3-[[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl]heptanoic acid