Detailed information for compound 418103

Basic information

Technical information
  • TDR Targets ID: 418103
  • Name: 1-ethyl-3-[5-methoxy-6-(2-methoxypyrimidin-5- yl)-1H-benzimidazol-2-yl]urea
  • MW: 342.353 | Formula: C16H18N6O3
  • H donors: 3 H acceptors: 4 LogP: 1.38 Rotable bonds: 7
    Rule of 5 violations (Lipinski): 1
  • SMILES: CCNC(=O)Nc1[nH]c2c(n1)cc(c(c2)OC)c1cnc(nc1)OC
  • InChi: 1S/C16H18N6O3/c1-4-17-15(23)22-14-20-11-5-10(13(24-2)6-12(11)21-14)9-7-18-16(25-3)19-8-9/h5-8H,4H2,1-3H3,(H3,17,20,21,22,23)
  • InChiKey: ADASGIIHCQJGMX-UHFFFAOYSA-N  


Substructure search Similarity search

Network

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Synonyms

  • 1-ethyl-3-[5-methoxy-6-(2-methoxy-5-pyrimidinyl)-1H-benzimidazol-2-yl]urea
  • 3-ethyl-1-[5-methoxy-6-(2-methoxypyrimidin-5-yl)-1H-benzimidazol-2-yl]urea
  • 3-ethyl-1-[5-methoxy-6-(2-methoxy-5-pyrimidinyl)-1H-benzimidazol-2-yl]urea

Targets

Known targets for this compound

Species Target name Source Bibliographic reference
Staphylococcus aureus DNA gyrase Starlite/ChEMBL References

Predicted pathogen targets for this compound

By orthology
Species Potential target Known druggable target/s Ortholog Group
Wolbachia endosymbiont of Brugia malayi DNA gyrase subunit A Get druggable targets OG5_129568 All targets in OG5_129568
Plasmodium knowlesi DNA gyrase subunit A, putative Get druggable targets OG5_129568 All targets in OG5_129568
Babesia bovis DNA gyrase A subunit, putative Get druggable targets OG5_129568 All targets in OG5_129568
Theileria parva DNA gyrase subunit A, putative Get druggable targets OG5_129568 All targets in OG5_129568
Plasmodium vivax DNA gyrase subunit A, putative Get druggable targets OG5_129568 All targets in OG5_129568
Toxoplasma gondii DNA gyrase/topoisomerase IV, A subunit domain-containing protein Get druggable targets OG5_129568 All targets in OG5_129568
Mycobacterium leprae Probable DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (Type II DNA topoisomerase) Get druggable targets OG5_129568 All targets in OG5_129568
Chlamydia trachomatis DNA gyrase subunit A Get druggable targets OG5_129568 All targets in OG5_129568
Mycobacterium ulcerans DNA gyrase subunit A Get druggable targets OG5_129568 All targets in OG5_129568
Plasmodium falciparum DNA gyrase subunit A Get druggable targets OG5_129568 All targets in OG5_129568
Mycobacterium tuberculosis DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) Get druggable targets OG5_129568 All targets in OG5_129568
Neospora caninum DNA gyrase subunit A, putative Get druggable targets OG5_129568 All targets in OG5_129568
Plasmodium berghei DNA gyrase subunit A, putative Get druggable targets OG5_129568 All targets in OG5_129568
Plasmodium yoelii DNA gyrase subunit a-related Get druggable targets OG5_129568 All targets in OG5_129568
Treponema pallidum DNA gyrase, subunit A (gyrA) Get druggable targets OG5_129568 All targets in OG5_129568
By sequence similarity to non orthologous known druggable targets
Species Potential target Known druggable target Length Alignment span Identity
Plasmodium berghei DNA gyrase subunit B, putative DNA gyrase   644 aa 662 aa 36.3 %
Plasmodium falciparum DNA topoisomerase 2 DNA gyrase   644 aa 647 aa 23.2 %
Entamoeba histolytica DNA topoisomerase II, putative DNA gyrase   644 aa 544 aa 25.0 %
Leishmania infantum mitochondrial DNA topoisomerase II DNA gyrase   644 aa 624 aa 23.2 %
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative DNA gyrase   644 aa 615 aa 22.6 %
Candida albicans DNA topoisomerase II similar to S. cerevisiae TOP2 (YNL088W) DNA gyrase   644 aa 625 aa 25.6 %
Brugia malayi DNA gyrase/topoisomerase IV, A subunit family protein DNA gyrase   644 aa 548 aa 25.7 %
Brugia malayi DNA topoisomerase II, alpha isozyme DNA gyrase   644 aa 659 aa 24.3 %
Schistosoma mansoni DNA topoisomerase II DNA gyrase   644 aa 633 aa 24.3 %
Trypanosoma brucei DNA topoisomerase II beta, putative DNA gyrase   644 aa 570 aa 24.0 %
Toxoplasma gondii DNA topoisomerase 2, putative DNA gyrase   644 aa 664 aa 24.1 %
Leishmania major mitochondrial DNA topoisomerase II DNA gyrase   644 aa 624 aa 23.1 %
Trypanosoma cruzi DNA topoisomerase II, putative DNA gyrase   644 aa 674 aa 23.0 %
Theileria parva DNA topoisomerase II, putative DNA gyrase   644 aa 683 aa 23.9 %
Leishmania braziliensis DNA topoisomerase ii DNA gyrase   644 aa 675 aa 23.0 %
Loa Loa (eye worm) TOPoisomerase family member DNA gyrase   644 aa 668 aa 26.2 %
Trypanosoma brucei gambiense DNA topoisomerase II, putative DNA gyrase   644 aa 619 aa 25.7 %
Leishmania mexicana mitochondrial DNA topoisomerase II DNA gyrase   644 aa 620 aa 23.4 %
Trypanosoma brucei DNA topoisomerase II alpha, putative DNA gyrase   644 aa 676 aa 23.4 %
Leishmania donovani DNA topoisomerase ii DNA gyrase   644 aa 666 aa 23.4 %
Wolbachia endosymbiont of Brugia malayi DNA gyrase, topoisomerase II, B subunit, GyrB DNA gyrase   644 aa 561 aa 50.4 %
Neospora caninum hypothetical protein DNA gyrase   644 aa 693 aa 24.1 %
Leishmania donovani mitochondrial DNA topoisomerase II DNA gyrase   644 aa 624 aa 23.2 %
Trypanosoma brucei gambiense DNA topoisomerase II, putative DNA gyrase   644 aa 666 aa 23.4 %
Onchocerca volvulus DNA gyrase   644 aa 624 aa 25.8 %
Trypanosoma congolense DNA topoisomerase II, putative DNA gyrase   644 aa 617 aa 24.8 %
Trypanosoma brucei gambiense DNA topoisomerase II, putative DNA gyrase   644 aa 676 aa 23.4 %
Babesia bovis DNA topoisomerase II, putative DNA gyrase   644 aa 587 aa 22.7 %
Mycobacterium ulcerans DNA gyrase subunit B DNA gyrase   644 aa 663 aa 54.0 %
Brugia malayi Probable DNA topoisomerase II DNA gyrase   644 aa 672 aa 25.9 %
Trypanosoma congolense DNA topoisomerase II, putative DNA gyrase   644 aa 678 aa 22.9 %
Echinococcus multilocularis DNA topoisomerase 2 alpha DNA gyrase   644 aa 612 aa 25.8 %
Trypanosoma congolense DNA topoisomerase II, putative DNA gyrase   644 aa 678 aa 22.7 %
Leishmania braziliensis mitochondrial DNA topoisomerase II DNA gyrase   644 aa 622 aa 23.8 %
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative DNA gyrase   644 aa 615 aa 22.6 %
Echinococcus granulosus DNA topoisomerase 2 alpha DNA gyrase   644 aa 613 aa 25.9 %
Leishmania infantum DNA topoisomerase ii DNA gyrase   644 aa 666 aa 23.6 %
Leishmania major DNA topoisomerase ii DNA gyrase   644 aa 672 aa 23.4 %
Mycobacterium leprae Probable DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (Type II DNA topoisomerase) DNA gyrase   644 aa 667 aa 53.1 %
Theileria parva DNA gyrase subunit B, putative DNA gyrase   644 aa 638 aa 37.1 %
Chlamydia trachomatis DNA gyrase subunit B DNA gyrase   644 aa 561 aa 55.3 %
Mycobacterium tuberculosis DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) DNA gyrase   644 aa 661 aa 53.0 %
Plasmodium knowlesi DNA gyrase subunit B, putative DNA gyrase   644 aa 517 aa 36.0 %
Candida albicans DNA topoisomerase II similar to S. cerevisiae TOP2 (YNL088W) DNA gyrase   644 aa 625 aa 25.6 %
Trypanosoma brucei DNA topoisomerase ii DNA gyrase   644 aa 619 aa 25.7 %
Trypanosoma cruzi DNA topoisomerase II, putative DNA gyrase   644 aa 674 aa 23.0 %
Dictyostelium discoideum DNA topoisomerase II DNA gyrase   644 aa 655 aa 23.8 %
Onchocerca volvulus DNA gyrase   644 aa 618 aa 26.5 %
Leishmania mexicana DNA topoisomerase ii DNA gyrase   644 aa 668 aa 23.1 %
Onchocerca volvulus Ectoderm-expressed 4 homolog DNA gyrase   644 aa 673 aa 24.1 %
Obtained from network model

Ranking Plot

Putative Targets List

Species Potential target Raw Global Species
Loa Loa (eye worm) hypothetical protein 0.073 0.4102 1
Treponema pallidum DNA gyrase, subunit A (gyrA) 0.0136 0.0614 1
Trypanosoma cruzi cytochrome p450-like protein, putative 0.0036 0.0022 0.4736
Loa Loa (eye worm) DOMON domain-containing protein 0.014 0.0634 0.15
Mycobacterium leprae Probable DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (Type II DNA topoisomerase) 0.0065 0.0195 1
Trypanosoma cruzi Lanosterol 14-alpha demethylase 0.0036 0.0022 0.4736
Plasmodium falciparum DNA gyrase subunit A 0.0136 0.0614 1
Brugia malayi DOMON domain containing protein 0.014 0.0634 0.15
Brugia malayi DOMON domain containing protein 0.014 0.0634 0.15
Loa Loa (eye worm) cytochrome P450 family protein 0.0057 0.0146 0.0304
Brugia malayi Cytochrome P450 family protein 0.0057 0.0146 0.0304
Trypanosoma brucei Lanosterol 14-alpha demethylase 0.0036 0.0022 0.4736
Trypanosoma cruzi Lanosterol 14-alpha demethylase 0.0036 0.0022 0.4736
Loa Loa (eye worm) TOPoisomerase family member 0.004 0.0046 0.0059
Mycobacterium ulcerans DNA gyrase subunit A 0.0136 0.0614 1
Trypanosoma cruzi cytochrome P450, putative 0.0036 0.0022 0.4736
Plasmodium falciparum DNA gyrase subunit B 0.0072 0.0234 0.3308
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative 0.004 0.0046 1
Mycobacterium tuberculosis DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) 0.0072 0.0234 0.3581
Brugia malayi Copper type II ascorbate-dependent monooxygenase, N-terminal domain containing protein 0.037 0.199 0.4822
Leishmania major lanosterol 14-alpha-demethylase, putative 0.0036 0.0022 0.4736
Onchocerca volvulus 0.014 0.0634 1
Schistosoma mansoni peptidyl-glycine monooxygenase 0.073 0.4102 0.5157
Brugia malayi DNA topoisomerase II, alpha isozyme 0.004 0.0046 0.0059
Trichomonas vaginalis DNA topoisomerase II, putative 0.004 0.0046 0.5
Trypanosoma brucei DNA topoisomerase ii 0.004 0.0046 1
Onchocerca volvulus 0.014 0.0634 1
Schistosoma mansoni DNA topoisomerase II 0.004 0.0046 0.0031
Brugia malayi DNA gyrase/topoisomerase IV, A subunit family protein 0.004 0.0046 0.0059
Brugia malayi Copper type II ascorbate-dependent monooxygenase, C-terminal domain containing protein 0.0359 0.1925 0.4665
Mycobacterium tuberculosis DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase) 0.0136 0.0614 1
Schistosoma mansoni dopamine-beta-monooxygenase 0.1381 0.7935 1
Leishmania major mitochondrial DNA topoisomerase II 0.004 0.0046 1
Mycobacterium ulcerans DNA gyrase subunit B 0.0072 0.0234 0.3581
Leishmania major cytochrome p450-like protein 0.0036 0.0022 0.4736
Leishmania major cytochrome p450-like protein 0.0036 0.0022 0.4736
Chlamydia trachomatis DNA gyrase subunit A 0.0136 0.0614 1
Toxoplasma gondii DNA gyrase/topoisomerase IV, A subunit domain-containing protein 0.0136 0.0614 0.057
Brugia malayi Probable DNA topoisomerase II 0.004 0.0046 0.0059
Trypanosoma cruzi mitochondrial DNA topoisomerase II, putative 0.004 0.0046 1
Wolbachia endosymbiont of Brugia malayi DNA gyrase subunit A 0.0136 0.0614 1
Plasmodium vivax DNA gyrase subunit A, putative 0.0136 0.0614 1
Entamoeba histolytica DNA topoisomerase II, putative 0.004 0.0046 0.5
Trypanosoma cruzi cytochrome P450, putative 0.0036 0.0022 0.4736
Echinococcus multilocularis DNA topoisomerase 2 alpha 0.004 0.0046 0.0059
Schistosoma mansoni peptidylglycine monooxygenase 0.073 0.4102 0.5157
Brugia malayi Copper type II ascorbate-dependent monooxygenase, C-terminal domain containing protein 0.073 0.4102 1
Echinococcus granulosus peptidyl glycine alpha amidating monooxygenase 0.073 0.4102 1
Brugia malayi Copper type II ascorbate-dependent monooxygenase, C-terminal domain containing protein 0.073 0.4102 1
Trypanosoma brucei cytochrome P450, putative 0.0036 0.0022 0.4736
Echinococcus multilocularis peptidyl glycine alpha amidating monooxygenase 0.073 0.4102 1
Brugia malayi DOMON domain containing protein 0.014 0.0634 0.15
Loa Loa (eye worm) hypothetical protein 0.073 0.4102 1
Loa Loa (eye worm) DOMON domain-containing protein 0.014 0.0634 0.15
Giardia lamblia DNA topoisomerase II 0.0036 0.0026 0.5
Plasmodium vivax DNA gyrase subunit B, putative 0.0072 0.0234 0.3308
Echinococcus granulosus DNA topoisomerase 2 alpha 0.004 0.0046 0.0059
Leishmania major cytochrome p450-like protein 0.0036 0.0022 0.4736
Loa Loa (eye worm) DOMON domain-containing protein 0.014 0.0634 0.15

Activities

Activity type Activity value Assay description Source Reference
Activity (functional) Reduction in steady-state levels of supercoiled pUC18 in Escherichia coli CAG12184 tolC mutant ChEMBL. 17116675
Activity (functional) 0 Reduction in steady-state levels of supercoiled pUC18 in Escherichia coli CAG12184 tolC mutant ChEMBL. 17116675
Inhibition (functional) = 20 % Inhibition of RNA synthesis in Staphylococcus aureus ATCC 29213 assessed as [3H]uridine incorporation ChEMBL. 17116675
Inhibition (functional) = 20 % Inhibition of protein synthesis in Staphylococcus aureus ATCC 29213 assessed as [3H]aminoacid incorporation ChEMBL. 17116675
Inhibition (functional) = 80 % Inhibition of DNA synthesis in Staphylococcus aureus ATCC 29213 assessed as [3H]thymidine incorporation ChEMBL. 17116675
Ki (binding) = 0.044 uM Inhibition of Staphylococcus aureus DNA gyrase ChEMBL. 18690678
MIC (functional) = 0.5 ug ml-1 Antibacterial activity against Streptococcus pneumoniae ATCC BAA-255 after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 0.5 ug ml-1 Antibacterial activity against novobiocin-resistant Streptococcus pneumoniae ATCC BAA-255 with GyrB S127L mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 0.5 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 with GyrB T167A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 1 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 1 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 with GyrB T167I mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against novobiocin-resistant Haemophilus influenzae ATCC 51907 with GyrB R140C mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against novobiocin-resistant Haemophilus influenzae ATCC 51907 with GyrB R140H mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 carrying plasmid expressing wild type GyrB ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 carrying plasmid expressing GyrB R144I mutant ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 without plasmid ChEMBL. 17116675
MIC (functional) = 2 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB R144I mutation without plasmid ChEMBL. 17116675
MIC (functional) = 4 ug ml-1 Antibacterial activity against novobiocin-resistant Staphylococcus aureus ATCC 29213 with GyrB R144I mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 4 ug ml-1 Antibacterial activity against Streptococcus pneumoniae ATCC BAA-255 with ParE T172I mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 4 ug ml-1 Antibacterial activity against Haemophilus influenzae ATCC 51907 after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 4 ug ml-1 Antibacterial activity against novobiocin-resistant Haemophilus influenzae ATCC 51907 with GyrB R140L mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Streptococcus pneumoniae ATCC BAA-255 with ParE T172A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 with ParE T169A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 carrying plasmid expressing GyrB T173N mutant ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 carrying plasmid expressing GyrB T173I mutant ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173N mutation without plasmid ChEMBL. 17116675
MIC (functional) = 8 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173I mutation without plasmid ChEMBL. 17116675
MIC (functional) = 16 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173N mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 16 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173I mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) > 64 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173N and GrlB T166A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) > 64 ug ml-1 Antibacterial activity against Staphylococcus aureus ATCC 29213 with GyrB T173I and GrlB T166A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) = 64 ug ml-1 Antibacterial activity against Streptococcus pneumoniae ATCC BAA-255 with GyrB T172A and ParE T172A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) > 64 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 with GyrB T167I and ParE T169A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) > 64 ug ml-1 Antibacterial activity against Enterococcus faecalis ATCC 29212 with GyrB T167A and ParE T169A mutation after 18 to 20 hrs ChEMBL. 17116675
MIC (functional) > 64 ug ml-1 Antibacterial activity against Haemophilus influenzae ATCC 51907 with GyrB T169I mutation after 18 to 20 hrs ChEMBL. 17116675

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

1 literature reference was collected for this gene.

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