Detailed information for compound 1404784

Basic information

Technical information
  • TDR Targets ID: 1404784
  • Name: 5-[2-hydroxy-3-[4-(phenylmethyl)piperazin-1-y l]propyl]-3-methyl-1-oxopyrido[2,1-b]benzimid azole-4-carbonitrile
  • MW: 455.551 | Formula: C27H29N5O2
  • H donors: 1 H acceptors: 3 LogP: 1.99 Rotable bonds: 6
    Rule of 5 violations (Lipinski): 1
  • SMILES: N#Cc1c(C)cc(=O)n2c1n(CC(CN1CCN(CC1)Cc1ccccc1)O)c1c2cccc1
  • InChi: 1S/C27H29N5O2/c1-20-15-26(34)32-25-10-6-5-9-24(25)31(27(32)23(20)16-28)19-22(33)18-30-13-11-29(12-14-30)17-21-7-3-2-4-8-21/h2-10,15,22,33H,11-14,17-19H2,1H3
  • InChiKey: JZMZJELIIXNAIZ-UHFFFAOYSA-N  


Substructure search Similarity search

Network

Hover on a compound node to display the structore

Synonyms

  • 5-[2-hydroxy-3-[4-(phenylmethyl)piperazin-1-yl]propyl]-3-methyl-1-oxo-pyrido[2,1-b]benzimidazole-4-carbonitrile
  • 5-[2-hydroxy-3-[4-(phenylmethyl)-1-piperazinyl]propyl]-3-methyl-1-oxo-4-pyrido[2,1-b]benzimidazolecarbonitrile
  • 5-[3-[4-(benzyl)piperazin-1-yl]-2-hydroxy-propyl]-1-keto-3-methyl-pyrido[2,1-b]benzimidazole-4-carbonitrile
  • SMR000438292
  • 5-[3-(4-Benzyl-piperazin-1-yl)-2-hydroxy-propyl]-3-methyl-1-oxo-1,5-dihydro-benzo[4,5]imidazo[1,2-a]py ridine-4-carbonitrile
  • MLS000763054
  • STOCK5S-09893

Targets

Known targets for this compound

Species Target name Source Bibliographic reference
Homo sapiens ATPase family, AAA domain containing 5 Starlite/ChEMBL No references
Homo sapiens ataxin 2 Starlite/ChEMBL No references
Homo sapiens SMAD family member 2 Starlite/ChEMBL No references

Predicted pathogen targets for this compound

By orthology
Species Potential target Known druggable target/s Ortholog Group
Loa Loa (eye worm) transcription factor SMAD2 Get druggable targets OG5_131716 All targets in OG5_131716
Echinococcus multilocularis atpase aaa+ type core atpase aaa type core Get druggable targets OG5_139225 All targets in OG5_139225
Loa Loa (eye worm) MH2 domain-containing protein Get druggable targets OG5_131716 All targets in OG5_131716
Brugia malayi MH2 domain containing protein Get druggable targets OG5_131716 All targets in OG5_131716
By sequence similarity to non orthologous known druggable targets
Species Potential target Known druggable target Length Alignment span Identity
Brugia malayi MH2 domain containing protein SMAD family member 2 467 aa 405 aa 31.6 %
Obtained from network model

Ranking Plot

Putative Targets List

Species Potential target Raw Global Species
Loa Loa (eye worm) hypothetical protein 0.0552 0.5593 1
Echinococcus granulosus para nitrobenzyl esterase 0.0093 0.0861 0.1539
Schistosoma mansoni histone deacetylase 0.0257 0.2552 0.4563
Brugia malayi hypothetical protein 0.003 0.0213 0.038
Loa Loa (eye worm) transcription factor SMAD2 0.0144 0.1386 0.2478
Echinococcus multilocularis histone deacetylase 7 0.0073 0.0656 0.0656
Schistosoma mansoni histone deacetylase 4 5 0.0073 0.0656 0.1172
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Toxoplasma gondii histone deacetylase HDAC1 0.0073 0.0656 0.1893
Plasmodium vivax histone deacetylase 1, putative 0.0257 0.2552 1
Brugia malayi Histone deacetylase 1 0.0257 0.2552 0.4563
Echinococcus granulosus acetylcholinesterase 0.0552 0.5593 1
Trypanosoma cruzi histone deacetylase 1, putative 0.0257 0.2552 1
Schistosoma mansoni family S9 non-peptidase homologue (S09 family) 0.0093 0.0861 0.1539
Loa Loa (eye worm) hypothetical protein 0.0257 0.2552 0.4563
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Trypanosoma brucei histone deacetylase, putative 0.0073 0.0656 0.1893
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Brugia malayi Histone deacetylase family protein 0.0073 0.0656 0.1172
Echinococcus granulosus BC026374 protein S09 family 0.0093 0.0861 0.1539
Trypanosoma brucei histone deacetylase 3 0.0073 0.0656 0.1893
Echinococcus multilocularis carboxylesterase 5A 0.0552 0.5593 0.5593
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Trypanosoma cruzi histone deacetylase 1, putative 0.0257 0.2552 1
Onchocerca volvulus 0.0093 0.0861 1
Schistosoma mansoni neuroligin 3 (S09 family) 0.0093 0.0861 0.1539
Echinococcus multilocularis histone deacetylase 6 0.0073 0.0656 0.0656
Echinococcus multilocularis neuroligin 0.0093 0.0861 0.0861
Onchocerca volvulus 0.0093 0.0861 1
Echinococcus granulosus histone deacetylase 6 0.0073 0.0656 0.1172
Onchocerca volvulus 0.0093 0.0861 1
Schistosoma mansoni histone deacetylase hda2 0.0073 0.0656 0.1172
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Echinococcus granulosus carboxylesterase 5A 0.0552 0.5593 1
Trichomonas vaginalis histone deacetylase 1, 2 ,3, putative 0.0257 0.2552 1
Trichomonas vaginalis histone deacetylase 1, 2 ,3, putative 0.0257 0.2552 1
Echinococcus granulosus acetylcholinesterase 0.0552 0.5593 1
Echinococcus granulosus histone deacetylase 6 0.0073 0.0656 0.1172
Toxoplasma gondii histone deacetylase HDAC4 0.0073 0.0656 0.1893
Echinococcus granulosus histone deacetylase 0.0073 0.0656 0.1172
Echinococcus granulosus histone deacetylase 6 0.0073 0.0656 0.1172
Loa Loa (eye worm) MH2 domain-containing protein 0.0144 0.1386 0.2478
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Onchocerca volvulus 0.0093 0.0861 1
Echinococcus multilocularis histone deacetylase 8 0.0073 0.0656 0.0656
Echinococcus granulosus histone deacetylase 1 0.0257 0.2552 0.4563
Brugia malayi hypothetical protein 0.0093 0.0861 0.1539
Trypanosoma cruzi histone deacetylase, putative 0.0073 0.0656 0.1893
Schistosoma mansoni acetylcholinesterase 0.0093 0.0861 0.1539
Entamoeba histolytica histone deacetylase, putative 0.0257 0.2552 0.5
Echinococcus multilocularis histone deacetylase 6 0.0073 0.0656 0.0656
Echinococcus granulosus Ataxin 2 N terminaldomain containing protein 0.0014 0.004 0.0071
Brugia malayi Carboxylesterase family protein 0.0093 0.0861 0.1539
Toxoplasma gondii histone deacetylase HDAC3 0.0257 0.2552 1
Loa Loa (eye worm) histone deacetylase 1 0.0257 0.2552 0.4563
Echinococcus multilocularis acetylcholinesterase 0.0552 0.5593 0.5593
Mycobacterium tuberculosis POSSIBLE PARA-NITROBENZYL ESTERASE (FRAGMENT) 0.0093 0.0861 0.5
Onchocerca volvulus 0.0093 0.0861 1
Trypanosoma brucei histone deacetylase 1 0.0257 0.2552 1
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Echinococcus granulosus histone deacetylase 7 0.0073 0.0656 0.1172
Brugia malayi Carboxylesterase family protein 0.0552 0.5593 1
Plasmodium vivax histone deacetylase 2, putative 0.0073 0.0656 0.1893
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Schistosoma mansoni family S9 non-peptidase homologue (S09 family) 0.0552 0.5593 1
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Mycobacterium ulcerans carboxylesterase, LipT 0.0093 0.0861 0.5
Echinococcus multilocularis Ataxin 2, N terminal,domain containing protein 0.0014 0.004 0.004
Loa Loa (eye worm) carboxylesterase 0.0093 0.0861 0.1539
Loa Loa (eye worm) carboxylesterase 0.0552 0.5593 1
Leishmania major histone deacetylase, putative 0.0073 0.0656 0.1893
Brugia malayi histone deacetylase 3 (HD3) 0.0257 0.2552 0.4563
Schistosoma mansoni hypothetical protein 0.0014 0.004 0.0071
Plasmodium vivax histone deacetylase, putative 0.0073 0.0656 0.1893
Schistosoma mansoni BC026374 protein (S09 family) 0.0093 0.0861 0.1539
Echinococcus granulosus neuroligin 0.0093 0.0861 0.1539
Loa Loa (eye worm) histone deacetylase 3 0.0257 0.2552 0.4563
Brugia malayi Carboxylesterase family protein 0.0093 0.0861 0.1539
Trichomonas vaginalis histone deacetylase 1, 2 ,3, putative 0.0257 0.2552 1
Loa Loa (eye worm) acetylcholinesterase 1 0.0552 0.5593 1
Loa Loa (eye worm) hypothetical protein 0.0552 0.5593 1
Loa Loa (eye worm) histone deacetylase 7A 0.0073 0.0656 0.1172
Trypanosoma cruzi histone deacetylase, putative 0.0073 0.0656 0.1893
Trypanosoma cruzi histone deacetylase, putative 0.0073 0.0656 0.1893
Loa Loa (eye worm) hypothetical protein 0.0073 0.0656 0.1172
Echinococcus granulosus histone deacetylase 8 0.0073 0.0656 0.1172
Leishmania major histone deacetylase, putative 0.0257 0.2552 1
Toxoplasma gondii histone deacetylase HDAC5 0.0074 0.0658 0.1906
Brugia malayi MH2 domain containing protein 0.0144 0.1386 0.2478
Schistosoma mansoni histone deacetylase 4 5 0.0073 0.0656 0.1172
Trypanosoma cruzi histone deacetylase, putative 0.0073 0.0656 0.1893
Plasmodium vivax histone deacetylase, putative 0.0073 0.0656 0.1893
Echinococcus granulosus family S9 non peptidase ue S09 family 0.0093 0.0861 0.1539
Schistosoma mansoni histone deacetylase 0.0257 0.2552 0.4563
Trypanosoma brucei histone deacetylase 2 0.0073 0.0656 0.1893
Schistosoma mansoni family S9 non-peptidase homologue (S09 family) 0.0093 0.0861 0.1539
Echinococcus multilocularis acetylcholinesterase 0.0552 0.5593 0.5593
Trichomonas vaginalis histone deacetylase, putative 0.0257 0.2552 1
Loa Loa (eye worm) histone deacetylase 0.0073 0.0656 0.1172
Echinococcus multilocularis BC026374 protein (S09 family) 0.0093 0.0861 0.0861
Brugia malayi Carboxylesterase family protein 0.0093 0.0861 0.1539
Plasmodium falciparum histone deacetylase 1 0.0257 0.2552 1
Schistosoma mansoni histone deacetylase 1 2 3 0.0073 0.0656 0.1172
Brugia malayi Carboxylesterase family protein 0.0552 0.5593 1
Brugia malayi Histone deacetylase family protein 0.0073 0.0656 0.1172
Toxoplasma gondii histone deacetylase HDAC2 0.0257 0.2552 1
Brugia malayi histone deacetylase 1 (HD1) 0.0257 0.2552 0.4563
Brugia malayi histone deacetylase 11 0.0073 0.0656 0.1172
Mycobacterium tuberculosis Carboxylesterase LipT 0.0093 0.0861 0.5
Echinococcus multilocularis histone deacetylase 6 0.0073 0.0656 0.0656
Plasmodium falciparum histone deacetylase, putative 0.0073 0.0656 0.1893
Mycobacterium tuberculosis POSSIBLE PARA-NITROBENZYL ESTERASE (FRAGMENT) 0.0093 0.0861 0.5
Echinococcus multilocularis histone deacetylase 3 0.0257 0.2552 0.2552
Echinococcus multilocularis histone deacetylase 0.0073 0.0656 0.0656
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Loa Loa (eye worm) histone deacetylase 11 0.0073 0.0656 0.1172
Schistosoma mansoni gliotactin 0.0093 0.0861 0.1539
Trypanosoma cruzi histone deacetylase, putative 0.0073 0.0656 0.1893
Loa Loa (eye worm) hypothetical protein 0.0093 0.0861 0.1539
Loa Loa (eye worm) hypothetical protein 0.003 0.0213 0.038
Echinococcus multilocularis family S9 non peptidase ue (S09 family) 0.0093 0.0861 0.0861
Loa Loa (eye worm) carboxylesterase 0.0093 0.0861 0.1539
Plasmodium falciparum histone deacetylase 2 0.0073 0.0656 0.1893
Leishmania major histone deacetylase, putative 0.0073 0.0656 0.1893
Schistosoma mansoni family S9 non-peptidase homologue (S09 family) 0.0093 0.0861 0.1539
Echinococcus multilocularis para nitrobenzyl esterase 0.0093 0.0861 0.0861
Giardia lamblia Histone deacetylase 0.0257 0.2552 0.5
Brugia malayi Carboxylesterase family protein 0.0093 0.0861 0.1539
Brugia malayi hypothetical protein 0.002 0.0101 0.0181
Echinococcus multilocularis histone deacetylase 1 0.0257 0.2552 0.2552
Echinococcus granulosus histone deacetylase 3 0.0257 0.2552 0.4563
Trypanosoma brucei histone deacetylase 4 0.0073 0.0656 0.1893
Leishmania major histone deacetylase, putative 0.0257 0.2552 1
Schistosoma mansoni histone deacetylase hda2 0.0073 0.0656 0.1172

Activities

Activity type Activity value Assay description Source Reference
Potency (functional) 1.3115 uM PUBCHEM_BIOASSAY: Primary qHTS for delayed death inhibitors of the malarial parasite plastid, 96 hour incubation. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID488745, AID488752, AID488774, AID504848, AID504850] ChEMBL. No reference
Potency (functional) 1.3115 uM PUBCHEM_BIOASSAY: Primary qHTS for delayed death inhibitors of the malarial parasite plastid, 48 hour incubation. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID488752, AID488774, AID504848, AID504850] ChEMBL. No reference
Potency (functional) 10 uM PUBCHEM_BIOASSAY: qHTS for Inhibitors of TGF-b. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID588856, AID588860] ChEMBL. No reference
Potency (functional) 14.575 uM PUBCHEM_BIOASSAY: qHTS screen for small molecules that inhibit ELG1-dependent DNA repair in human embryonic kidney (HEK293T) cells expressing luciferase-tagged ELG1. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID493107, AID493125] ChEMBL. No reference
Potency (functional) 19.9526 uM PubChem BioAssay. qHTS for Inhibitors of ATXN expression. (Class of assay: confirmatory) ChEMBL. No reference
Potency (functional) 29.0929 uM PubChem BioAssay. A quantitative high throughput screen for small molecules that induce DNA re-replication in MCF 10a normal breast cells. (Class of assay: confirmatory) ChEMBL. No reference
Potency (functional) = 35.4813 um PUBCHEM_BIOASSAY: qHTS Assay for Inhibitors of Human Jumonji Domain Containing 2E (JMJD2E). (Class of assay: confirmatory) ChEMBL. No reference
Potency (binding) 39.8107 uM PubChem BioAssay. qHTS Assay for Inhibitors of MBNL1-poly(CUG) RNA binding. (Class of assay: confirmatory) ChEMBL. No reference
Potency (functional) 70.7946 uM PUBCHEM_BIOASSAY: qHTS Assay for the Inhibitors of Human Flap endonuclease 1 (FEN1). (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID488813] ChEMBL. No reference
Potency (functional) = 89.1251 um PUBCHEM_BIOASSAY: qHTS Assay for Inhibitors of DNA Polymerase Beta. (Class of assay: confirmatory) ChEMBL. No reference

Phenotypes

Whole-cell/tissue/organism interactions

Species name Source Reference Is orphan
Plasmodium falciparum ChEMBL23

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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