Detailed information for compound 1654977

Basic information

Technical information
  • TDR Targets ID: 1654977
  • Name: methyl N-[(2S)-1-[(2R)-2-(cyclopentylmethyl)- 3-(formyl-hydroxyamino)propanoyl]pyrrolidine- 2-carbonyl]carbamate
  • MW: 369.413 | Formula: C17H27N3O6
  • H donors: 2 H acceptors: 5 LogP: 1.87 Rotable bonds: 11
    Rule of 5 violations (Lipinski): 1
  • SMILES: O=CN(C[C@H](C(=O)N1CCC[C@H]1C(=O)NC(=O)OC)CC1CCCC1)O
  • InChi: 1S/C17H27N3O6/c1-26-17(24)18-15(22)14-7-4-8-20(14)16(23)13(10-19(25)11-21)9-12-5-2-3-6-12/h11-14,25H,2-10H2,1H3,(H,18,22,24)/t13-,14+/m1/s1
  • InChiKey: LODHUVNBDRQVHZ-KGLIPLIRSA-N  


Substructure search Similarity search

Network

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Synonyms

  • methyl N-[(2S)-1-[(2R)-2-(cyclopentylmethyl)-3-(formyl-hydroxy-amino)propanoyl]pyrrolidine-2-carbonyl]carbamate
  • N-[[(2S)-1-[(2R)-2-(cyclopentylmethyl)-3-(formyl-hydroxyamino)-1-oxopropyl]-2-pyrrolidinyl]-oxomethyl]carbamic acid methyl ester
  • N-[(2S)-1-[(2R)-2-(cyclopentylmethyl)-3-(formyl-hydroxy-amino)propanoyl]pyrrolidine-2-carbonyl]carbamic acid methyl ester
  • methyl N-[(2S)-1-[(2R)-2-(cyclopentylmethyl)-3-(hydroxy-methanoyl-amino)propanoyl]pyrrolidin-2-yl]carbonylcarbamate

Targets

Known targets for this compound

Species Target name Source Bibliographic reference
Staphylococcus aureus Peptide deformylase Starlite/ChEMBL References
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) Peptide deformylase Starlite/ChEMBL References

Predicted pathogen targets for this compound

By orthology
Species Potential target Known druggable target/s Ortholog Group
Mycobacterium tuberculosis Probable polypeptide deformylase Def (PDF) (formylmethionine deformylase) Get druggable targets OG5_128237 All targets in OG5_128237
Plasmodium vivax peptide deformylase, putative Get druggable targets OG5_128237 All targets in OG5_128237
Treponema pallidum polypeptide deformylase (def) Get druggable targets OG5_128237 All targets in OG5_128237
Chlamydia trachomatis peptide deformylase Get druggable targets OG5_128237 All targets in OG5_128237
Plasmodium yoelii polypeptide deformylase, putative Get druggable targets OG5_128237 All targets in OG5_128237
Wolbachia endosymbiont of Brugia malayi peptide deformylase Get druggable targets OG5_128237 All targets in OG5_128237
Toxoplasma gondii hypothetical protein Get druggable targets OG5_128237 All targets in OG5_128237
Mycobacterium ulcerans peptide deformylase Get druggable targets OG5_128237 All targets in OG5_128237
Plasmodium berghei peptide deformylase, putative Get druggable targets OG5_128237 All targets in OG5_128237
Plasmodium falciparum peptide deformylase Get druggable targets OG5_128237 All targets in OG5_128237
Neospora caninum Peptide deformylase, related Get druggable targets OG5_128237 All targets in OG5_128237
Mycobacterium leprae PROBABLE POLYPEPTIDE DEFORMYLASE DEF (PDF) (FORMYLMETHIONINE DEFORMYLASE) Get druggable targets OG5_128237 All targets in OG5_128237
Plasmodium knowlesi peptide deformylase, putative Get druggable targets OG5_128237 All targets in OG5_128237
By sequence similarity to non orthologous known druggable targets
Species Potential target Known druggable target Length Alignment span Identity
Trypanosoma cruzi hypothetical protein Peptide deformylase   183 aa 155 aa 22.6 %
Trichomonas vaginalis abca6, putative Peptide deformylase   183 aa 162 aa 25.3 %
Loa Loa (eye worm) adipor-like receptor Peptide deformylase   203 aa 163 aa 23.9 %
Obtained from network model

Ranking Plot

Putative Targets List

Species Potential target Raw Global Species
Trypanosoma cruzi polypeptide deformylase-like protein, putative 0.0213 0.0194 0.0391
Trypanosoma cruzi Peptide deformylase 2, putative 0.0213 0.0194 0.0391
Trypanosoma brucei DNA topoisomerase ii 0.0689 0.4963 1
Toxoplasma gondii hypothetical protein 0.0558 0.3646 0.6796
Brugia malayi Probable DNA topoisomerase II 0.0279 0.0853 0.5
Brugia malayi DNA topoisomerase II, alpha isozyme 0.0279 0.0853 0.5
Trypanosoma brucei Peptide deformylase 2 0.0213 0.0194 0.0391
Schistosoma mansoni DNA topoisomerase II 0.0279 0.0853 0.5
Chlamydia trachomatis DNA gyrase subunit B 0.0782 0.5891 0.3533
Onchocerca volvulus DNA topoisomerase 2 homolog 0.0279 0.0853 0.5
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative 0.0689 0.4963 1
Onchocerca volvulus DNA topoisomerase 2 homolog 0.0279 0.0853 0.5
Trypanosoma cruzi polypeptide deformylase-like protein, putative 0.0213 0.0194 0.0391
Echinococcus multilocularis DNA topoisomerase 2 alpha 0.0279 0.0853 0.5
Plasmodium vivax DNA gyrase subunit B, putative 0.1192 1 1
Leishmania major polypeptide deformylase-like protein, putative 0.0213 0.0194 0.0391
Echinococcus granulosus DNA topoisomerase 2 alpha 0.0279 0.0853 0.5
Brugia malayi DNA gyrase/topoisomerase IV, A subunit family protein 0.0279 0.0853 0.5
Loa Loa (eye worm) TOPoisomerase family member 0.0279 0.0853 1
Trichomonas vaginalis DNA topoisomerase II, putative 0.0279 0.0853 0.5
Trypanosoma brucei Polypeptide deformylase 1 0.0213 0.0194 0.0391
Plasmodium falciparum DNA gyrase subunit B 0.1192 1 1
Entamoeba histolytica DNA topoisomerase II, putative 0.0279 0.0853 0.5
Leishmania major mitochondrial DNA topoisomerase II 0.0689 0.4963 1
Onchocerca volvulus Putative DNA topoisomerase 2, mitochondrial 0.0279 0.0853 0.5
Treponema pallidum DNA gyrase, subunit B (gyrB) 0.1192 1 1
Trypanosoma cruzi Peptide deformylase 2, putative 0.0213 0.0194 0.0391
Mycobacterium leprae PROBABLE POLYPEPTIDE DEFORMYLASE DEF (PDF) (FORMYLMETHIONINE DEFORMYLASE) 0.0558 0.3646 1
Giardia lamblia DNA topoisomerase II 0.0241 0.0479 0.5
Plasmodium falciparum peptide deformylase 0.0558 0.3646 0.3053
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative 0.0689 0.4963 1
Plasmodium vivax peptide deformylase, putative 0.0558 0.3646 0.3053
Toxoplasma gondii ATPase/histidine kinase/DNA gyrase B/HSP90 domain-containing protein 0.0689 0.4963 1
Mycobacterium tuberculosis DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) 0.1192 1 1
Wolbachia endosymbiont of Brugia malayi DNA gyrase, topoisomerase II, B subunit, GyrB 0.1192 1 1
Mycobacterium ulcerans DNA gyrase subunit B 0.1192 1 1

Activities

Activity type Activity value Assay description Source Reference
IC50 (binding) = 1.9 nM Inhibition of Streptococcus pneumoniae PDF assessed as formate release from fMAS peptide substrate after 20 mins by formate dehydrogenase coupled assay ChEMBL. 22579486
IC50 (binding) = 4.5 nM Inhibition of Staphylococcus aureus PDF assessed as formate release from fMAS peptide substrate after 20 mins by formate dehydrogenase coupled assay ChEMBL. 22579486

Phenotypes

Whole-cell/tissue/organism interactions

We have no records of whole-cell/tissue assays done with this compound What does this mean?

Many chemical entities in TDR Targets come from high-throughput screenings with whole cells or tissue samples, and not all assayed compounds have been tested against a single a single target protein, probably because they get ruled out during screening process. Even if these compounds may have not been of interest in the original screening, they may come as interesting leads for other screening assays. Furthermore, we may be able to propose drug-target associations using chemical similarities and network patterns.

Annotated phenotypes:

We have no manually annotated phenotypes for this drug. What does this mean? / Care to help?
In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.
 
In any case, if you have information about papers containing relevant validation data for this target, please log in using your TDR Targets username and password and send them to us using the corresponding form in this page (only visible to registered users) or contact us.

External resources for this compound

Bibliographic References

No literature references available for this target.

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