TDR Targets

Basic information

Technical information

TDR Targets ID: 433506
Name: N-[4-chloro-3-[(4-methylpiperazin-1-yl)methyl ]phenyl]-6-(2-methylsulfanylpyrimidin-4-yl)ox y-1H-benzimidazol-2-amine
MW: 496.028 | Formula: C24H26ClN7OS
H donors: 2 H acceptors: 3 LogP: 4.63 Rotable bonds: 7
Rule of 5 violations (Lipinski): 1
SMILES: CSc1nccc(n1)Oc1ccc2c(c1)nc([nH]2)Nc1ccc(c(c1)CN1CCN(CC1)C)Cl
InChi: 1S/C24H26ClN7OS/c1-31-9-11-32(12-10-31)15-16-13-17(3-5-19(16)25)27-23-28-20-6-4-18(14-21(20)29-23)33-22-7-8-26-24(30-22)34-2/h3-8,13-14H,9-12,15H2,1-2H3,(H2,27,28,29)
InChiKey: JGMRAEWVFZTZRS-UHFFFAOYSA-N

Network

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Target Layer

Model Organisms

Species	Viewmode
Arabidopsis thaliana
Caenorhabditis elegans
Dictyostelium discoideum
Drosophila melanogaster
Escherichia coli
Homo sapiens
Mus musculus
Oryza sativa
Saccharomyces cerevisiae
Schmidtea mediterranea
Other organisms

TDR Pathogens:

Species	Viewmode
Brugia malayi
Chlamydia trachomatis
Echinococcus granulosus
Entamoeba histolytica
Echinococcus multilocularis
Giardia lamblia
Leishmania major
Loa Loa (eye worm)
Mycobacterium leprae
Mycobacterium tuberculosis
Mycobacterium ulcerans
Onchocerca volvulus
Plasmodium falciparum
Plasmodium vivax
Schistosoma mansoni
Trypanosoma brucei
Trypanosoma cruzi
Toxoplasma gondii
Treponema pallidum
Trichomonas vaginalis
Wolbachia endosymbiont of Brugia malayi

Other Pathogens:

Species	Viewmode
Babesia bovis
Candida albicans
Cryptosporidium hominis
Cryptosporidium parvum
Leishmania braziliensis
Leishmania donovani
Leishmania infantum
Leishmania mexicana
Neospora caninum
Plasmodium berghei
Plasmodium knowlesi
Plasmodium yoelii
Schistosoma japonicum
Trypanosoma brucei gambiense
Trypanosoma congolense
Theileria parva

Compound Layer

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Clustering layers

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Synonyms

N-[4-chloro-3-[(4-methyl-1-piperazinyl)methyl]phenyl]-6-[[2-(methylthio)-4-pyrimidinyl]oxy]-1H-benzimidazol-2-amine
[4-chloro-3-[(4-methylpiperazino)methyl]phenyl]-[6-[2-(methylthio)pyrimidin-4-yl]oxy-1H-benzimidazol-2-yl]amine

Targets

Known targets for this compound

Species	Target name	Source	Bibliographic reference
Homo sapiens	kinase insert domain receptor	Starlite/ChEMBL	References

Predicted pathogen targets for this compound

By orthology

Species	Potential target	Known druggable target/s	Ortholog Group
Brugia malayi	Immunoglobulin I-set domain containing protein	Get druggable targets OG5_130320	All targets in OG5_130320
Loa Loa (eye worm)	TK/KIN16 protein kinase	Get druggable targets OG5_130320	All targets in OG5_130320
Onchocerca volvulus		Get druggable targets OG5_130320	All targets in OG5_130320
Onchocerca volvulus	Tyrosine kinase homolog	Get druggable targets OG5_130320	All targets in OG5_130320

By sequence similarity to non orthologous known druggable targets

No druggable targets predicted by sequence similarity

Ranking Plot

Putative Targets List

Species	Potential target	Raw	Global	Species
Loa Loa (eye worm)	hypothetical protein	0.0029	0.0572	0.082
Trypanosoma brucei	phosphatidylinositol 4-kinase, putative	0.0037	0.0896	1
Schistosoma mansoni	hypothetical protein	0.0016	0.0078	0.087
Trypanosoma cruzi	phosphatidylinositol kinase related protein, putative	0.0029	0.0572	0.1091
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Loa Loa (eye worm)	TK/KIN16 protein kinase	0.0183	0.6627	1
Trypanosoma brucei	phosphatidylinositol kinase related protein, putative	0.0036	0.0851	0.9159
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Schistosoma mansoni	ataxia telangiectasia mutated (atm)-related	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0036	0.0851	0.9446
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Echinococcus multilocularis	PIK kinase, FAT and Armadillo domain containing protein	0.0016	0.0078	0.0078
Echinococcus granulosus	serine protein kinase ATM	0.0036	0.0851	0.0851
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Toxoplasma gondii	target of rapamycin (TOR), putative	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Echinococcus multilocularis	FKBP12 rapamycin complex associated protein	0.0037	0.0896	0.0896
Leishmania major	target of rapamycin (TOR) kinase 1, putative	0.0037	0.0896	0.1913
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0023	0.0357	0.3411
Loa Loa (eye worm)	phosphatidylinositol 3	0.0037	0.0896	0.1312
Brugia malayi	Phosphatidylinositol 3- and 4-kinase family protein	0.0036	0.0851	0.1181
Leishmania major	hypothetical protein, conserved	0.01	0.3367	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Echinococcus multilocularis	phosphatidylinositol 3 and 4 kinase	0.0037	0.0896	0.0896
Schistosoma mansoni	cell adhesion molecule	0.0015	0.0031	0.0348
Echinococcus granulosus	serine:threonine protein kinase SMG1	0.0021	0.0264	0.0264
Echinococcus multilocularis	roundabout 2	0.0018	0.0144	0.0144
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trypanosoma brucei	Phosphatidylinositol 3-kinase tor1	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Leishmania major	phosphatidylinositol 3-related kinase, putative	0.0037	0.0896	0.1913
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Schistosoma mansoni	fkbp-rapamycin associated protein	0.0021	0.0264	0.2941
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Loa Loa (eye worm)	hypothetical protein	0.0021	0.0264	0.0352
Trypanosoma brucei	phosphatidylinositol 3-kinase, putative	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trypanosoma cruzi	hypothetical protein, conserved	0.0093	0.3088	1
Entamoeba histolytica	hypothetical protein	0.0036	0.0851	0.9283
Toxoplasma gondii	FATC domain-containing protein	0.0036	0.0851	0.9159
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Entamoeba histolytica	FKBP-rapamycin associated protein (FRAP), putative	0.0037	0.0896	1
Trypanosoma cruzi	phosphatidylinositol 3-related kinase, putative	0.0037	0.0896	0.224
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trypanosoma cruzi	phosphatidylinositol kinase related protein, putative	0.0036	0.0851	0.208
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Brugia malayi	Phosphatidylinositol 3- and 4-kinase family protein	0.0021	0.0264	0.0284
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Leishmania major	target of rapamycin kinase (TOR) kinase 3	0.0037	0.0896	0.1913
Echinococcus granulosus	PIK kinase FAT and Armadillo domain containing protein	0.0016	0.0078	0.0078
Loa Loa (eye worm)	hypothetical protein	0.0018	0.0144	0.0171
Trypanosoma cruzi	Phosphatidylinositol 3-kinase tor2	0.0037	0.0896	0.224
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trypanosoma brucei	target of rapamycin kinase 3, putative	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Echinococcus granulosus	neurotracting:lsamp:neurotrimin:obcam	0.0015	0.0031	0.0031
Trichomonas vaginalis	conserved hypothetical protein	0.0023	0.0357	0.3411
Echinococcus multilocularis	serine:threonine protein kinase SMG1	0.0021	0.0264	0.0264
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Loa Loa (eye worm)	phosphatidylinositol 3	0.0037	0.0896	0.1312
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Entamoeba histolytica	phosphatidylinositol3-kinaseTor2, putative	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Giardia lamblia	GTOR	0.0037	0.0896	0.5
Trypanosoma cruzi	target of rapamycin kinase 3	0.0037	0.0896	0.224
Loa Loa (eye worm)	hypothetical protein	0.0023	0.0357	0.0494
Loa Loa (eye worm)	hypothetical protein	0.0016	0.0078	0.0071
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Brugia malayi	Phosphatidylinositol 3- and 4-kinase family protein	0.0037	0.0896	0.125
Onchocerca volvulus	Tyrosine kinase homolog	0.0171	0.6154	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0021	0.0264	0.2269
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Schistosoma mansoni	phosphatidylinositol 3-and 4-kinase	0.0037	0.0896	1
Leishmania major	target of rapamycin (TOR) kinase 2, putative	0.0037	0.0896	0.1913
Leishmania major	phosphatidylinositol 3-kinase, putative	0.0037	0.0896	0.1913
Brugia malayi	Phosphatidylinositol 3- and 4-kinase family protein	0.0037	0.0896	0.125
Echinococcus granulosus	roundabout 2	0.0018	0.0144	0.0144
Trypanosoma cruzi	Phosphatidylinositol 3-kinase tor1	0.0037	0.0896	0.224
Echinococcus multilocularis	DNA dependent protein kinase catalytic subunit	0.0268	1	1
Schistosoma mansoni	ataxia telangiectasia mutated (atm)	0.0036	0.0851	0.9494
Loa Loa (eye worm)	hypothetical protein	0.0018	0.0144	0.0171
Echinococcus granulosus	phosphatidylinositol 3 and 4 kinase	0.0037	0.0896	0.0896
Echinococcus multilocularis	serine protein kinase ATM	0.0036	0.0851	0.0851
Echinococcus granulosus	FKBP12 rapamycin complex associated protein	0.0037	0.0896	0.0896
Trypanosoma brucei	phosphatidylinositol 3-related kinase, putative	0.0037	0.0896	1
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Trypanosoma cruzi	phosphatidylinositol 3-related kinase, putative	0.0037	0.0896	0.224
Trichomonas vaginalis	PIKK family atypical protein kinase	0.0037	0.0896	1
Brugia malayi	Immunoglobulin I-set domain containing protein	0.0183	0.6627	1
Trypanosoma cruzi	phosphatidylinositol kinase related protein, putative	0.0022	0.0312	0.017

Activities

Activity type	Activity value	Assay description	Source	Reference
IC50 (functional)	0	Inhibition of VEGF-stimulated HUVEC cell proliferation after 72 hrs	ChEMBL.	17696416
Ki (functional)	= 128 nM	Inhibition of KDR phosphorylation	ChEMBL.	17696416
Ki (functional)	= 128 nM	Inhibition of KDR phosphorylation	ChEMBL.	17696416

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

ChEMBL: CHEMBL231468
PubChem: 17755216

Bibliographic References

1 literature reference was collected for this gene.

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Detailed information for compound 433506