Literature summary for 3.5.1.88 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.

Application

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

Crystallization (Commentary)

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

Inhibitors

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

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Ni2+	-	Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

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

Organism

Organism	UniProt	Comment	Textmining
Mycobacterium tuberculosis	P9WIJ3	-	-
Mycobacterium tuberculosis H37Rv	P9WIJ3	-	-

Substrates and Products (Substrate)

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

Synonyms

Synonyms	Comment	Organism
peptide deformylase	-	Mycobacterium tuberculosis

IC50 Value

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