Detailed information for compound 1053379

Basic information

Technical information
  • TDR Targets ID: 1053379
  • Name: (2S,3R,4R,5S,6R)-2-(1H-benzimidazol-2-yl)-6-( hydroxymethyl)oxane-3,4,5-triol
  • MW: 280.277 | Formula: C13H16N2O5
  • H donors: 5 H acceptors: 5 LogP: -0.94 Rotable bonds: 2
    Rule of 5 violations (Lipinski): 1
  • SMILES: OC[C@H]1O[C@@H](c2nc3c([nH]2)cccc3)[C@@H]([C@H]([C@@H]1O)O)O
  • InChi: 1S/C13H16N2O5/c16-5-8-9(17)10(18)11(19)12(20-8)13-14-6-3-1-2-4-7(6)15-13/h1-4,8-12,16-19H,5H2,(H,14,15)/t8-,9-,10+,11-,12-/m1/s1
  • InChiKey: XEMMGXXVANKOFH-RMPHRYRLSA-N  


Substructure search Similarity search

Network

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Synonyms

  • (2S,3R,4R,5S,6R)-2-(1H-benzimidazol-2-yl)-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
  • (2S,3R,4R,5S,6R)-2-(1H-benzimidazol-2-yl)-6-methylol-tetrahydropyran-3,4,5-triol
  • CHEBI:43513
  • 2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,2,3-BENZIMIDAZOLE
  • 2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1-BENZIMIDAZOLE
  • IMK
  • (1S)-1,5-anhydro-1-(1H-benzimidazol-2-yl)-D-glucitol
  • 2-(beta-D-glucosyl)benzimidazole

Targets

Known targets for this compound

Species Target name Source Bibliographic reference
Oryctolagus cuniculus Glycogen phosphorylase, muscle form Starlite/ChEMBL References

Predicted pathogen targets for this compound

By orthology
Species Potential target Known druggable target/s Ortholog Group
Neospora caninum hypothetical protein Get druggable targets OG5_126999 All targets in OG5_126999
Onchocerca volvulus Glycogen phosphorylase homolog Get druggable targets OG5_126999 All targets in OG5_126999
Schistosoma mansoni glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus multilocularis glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Giardia lamblia Glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Trichomonas vaginalis glycogen phosphorylase, putative Get druggable targets OG5_126999 All targets in OG5_126999
Schistosoma japonicum ko:K00688 starch phosphorylase [EC2.4.1.1], putative Get druggable targets OG5_126999 All targets in OG5_126999
Schistosoma japonicum ko:K00688 starch phosphorylase [EC2.4.1.1], putative Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus granulosus Glycosyl transferase family 35 Get druggable targets OG5_126999 All targets in OG5_126999
Trichomonas vaginalis glycogen phosphorylase, putative Get druggable targets OG5_126999 All targets in OG5_126999
Candida albicans glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Loa Loa (eye worm) glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Schistosoma mansoni glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus multilocularis glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Brugia malayi carbohydrate phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus granulosus glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Cryptosporidium hominis glycogen phosphorylase 1 Get druggable targets OG5_126999 All targets in OG5_126999
Chlamydia trachomatis glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Entamoeba histolytica glycogen phosphorylase, putative Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus granulosus glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Candida albicans hypothetical protein Get druggable targets OG5_126999 All targets in OG5_126999
Cryptosporidium parvum glycogen phosphorylase Get druggable targets OG5_126999 All targets in OG5_126999
Echinococcus multilocularis Glycosyl transferase, family 35 Get druggable targets OG5_126999 All targets in OG5_126999
Schistosoma japonicum Glycogen phosphorylase, brain form, putative Get druggable targets OG5_126999 All targets in OG5_126999
Entamoeba histolytica glycogen phosphorylase, putative Get druggable targets OG5_126999 All targets in OG5_126999
By sequence similarity to non orthologous known druggable targets
Species Potential target Known druggable target Length Alignment span Identity
Onchocerca volvulus Glycogen phosphorylase, muscle form   843 aa 840 aa 70.2 %
Obtained from network model

Ranking Plot

Putative Targets List

Species Potential target Raw Global Species
Entamoeba histolytica glycogenphosphorylase, putative 0.0056 0.185 0.3063
Loa Loa (eye worm) hypothetical protein 0.0024 0.0286 0.0286
Schistosoma mansoni hypothetical protein 0.0063 0.2144 0.0781
Mycobacterium ulcerans hypothetical protein 0.0024 0.0286 0.1548
Echinococcus granulosus glycogen phosphorylase 0.013 0.5389 1
Brugia malayi Latrophilin receptor protein 2 0.0063 0.2144 0.1912
Entamoeba histolytica glycogen phosphorylase, putative 0.0056 0.185 0.3063
Entamoeba histolytica glycogen phosphorylase, putative 0.013 0.5389 1
Schistosoma mansoni hypothetical protein 0.0063 0.2144 0.0781
Schistosoma mansoni hypothetical protein 0.0063 0.2144 0.0781
Leishmania major 4-coumarate:coa ligase-like protein 0.0024 0.0286 0.5
Mycobacterium ulcerans long-chain-fatty-acid-CoA ligase 0.0024 0.0286 0.1548
Mycobacterium leprae PROBABLE FATTY-ACID-CoA LIGASE FADD7 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 0.0024 0.0286 0.5
Plasmodium falciparum acyl-CoA synthetase 0.0018 0 0.5
Brugia malayi latrophilin 2 splice variant baaae 0.0135 0.5614 0.5485
Mycobacterium tuberculosis Probable glycogen phosphorylase GlgP 0.0056 0.185 1
Echinococcus multilocularis glycogen phosphorylase 0.013 0.5389 1
Entamoeba histolytica glycogen phosphorylase, putative 0.013 0.5389 1
Mycobacterium ulcerans long-chain fatty-acid CoA ligase 0.0024 0.0286 0.1548
Mycobacterium ulcerans acyl-CoA synthetase 0.0024 0.0286 0.1548
Trichomonas vaginalis glycogen phosphorylase, putative 0.013 0.5389 0.5
Echinococcus multilocularis Glycosyl transferase, family 35 0.013 0.5389 1
Leishmania major 4-coumarate:coa ligase-like protein 0.0024 0.0286 0.5
Mycobacterium ulcerans acyl-CoA synthetase 0.0024 0.0286 0.1548
Loa Loa (eye worm) hypothetical protein 0.0024 0.0286 0.0286
Schistosoma mansoni glycogen phosphorylase 0.013 0.5389 0.9404
Chlamydia trachomatis glycogen phosphorylase 0.013 0.5389 1
Mycobacterium ulcerans long-chain-fatty-acid--CoA ligase 0.0024 0.0286 0.1548
Echinococcus multilocularis glycogen phosphorylase 0.013 0.5389 1
Loa Loa (eye worm) hypothetical protein 0.0024 0.0286 0.0286
Brugia malayi Calcitonin receptor-like protein seb-1 0.0198 0.8604 0.8563
Schistosoma mansoni hypothetical protein 0.0135 0.5614 1
Brugia malayi Corticotropin releasing factor receptor 2 precursor, putative 0.0198 0.8604 0.8563
Loa Loa (eye worm) pigment dispersing factor receptor c 0.0198 0.8604 0.8604
Mycobacterium ulcerans fatty-acid-CoA ligase 0.0024 0.0286 0.1548
Entamoeba histolytica glycogen phosphorylase, putative 0.0056 0.185 0.3063
Mycobacterium ulcerans acyl-CoA synthetase 0.0024 0.0286 0.1548
Loa Loa (eye worm) latrophilin receptor protein 2 0.0063 0.2144 0.2144
Mycobacterium tuberculosis Probable fatty-acid-CoA ligase FadD2 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase) 0.0024 0.0286 0.1548
Echinococcus granulosus glycogen phosphorylase 0.013 0.5389 1
Mycobacterium tuberculosis Probable chain -fatty-acid-CoA ligase FadD13 (fatty-acyl-CoA synthetase) 0.0024 0.0286 0.1548
Plasmodium vivax acyl-CoA synthetase, putative 0.0018 0 0.5
Leishmania major 4-coumarate:coa ligase-like protein 0.0024 0.0286 0.5
Giardia lamblia Glycogen phosphorylase 0.013 0.5389 0.5
Onchocerca volvulus Glycogen phosphorylase homolog 0.013 0.5389 1
Schistosoma mansoni hypothetical protein 0.0063 0.2144 0.0781
Mycobacterium leprae PROBABLE FATTY-ACID-CoA LIGASE FADD2 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 0.0024 0.0286 0.5
Echinococcus granulosus Glycosyl transferase family 35 0.013 0.5389 1
Brugia malayi calcium-independent alpha-latrotoxin receptor 2, putative 0.0063 0.2144 0.1912
Mycobacterium ulcerans glycogen phosphorylase GlgP 0.0056 0.185 1
Brugia malayi carbohydrate phosphorylase 0.013 0.5389 0.5253
Loa Loa (eye worm) hypothetical protein 0.0063 0.2144 0.2144
Loa Loa (eye worm) follicle stimulating hormone receptor 0.0227 1 1
Schistosoma mansoni glycogen phosphorylase 0.013 0.5389 0.9404
Loa Loa (eye worm) glycogen phosphorylase 0.013 0.5389 0.5389
Trichomonas vaginalis glycogen phosphorylase, putative 0.013 0.5389 0.5
Loa Loa (eye worm) hypothetical protein 0.0135 0.5614 0.5614
Loa Loa (eye worm) hypothetical protein 0.0198 0.8604 0.8604

Activities

Activity type Activity value Assay description Source Reference
IC50 (binding) = 8.6 uM Binding affinity to rabbit muscular GPb by NMR binding assay ChEMBL. 22229710
Ki (binding) = 9 uM Inhibition of rabbit muscle glycogen phosphorylase b ChEMBL. 19450985
Ki (binding) = 9 uM Inhibition of rabbit muscle glycogen phosphorylase b ChEMBL. 24900719
Ki (binding) = 9 uM Inhibition of rabbit muscle glycogen phosphorylase b ChEMBL. 24608000
Ki (binding) = 9 uM Competitive inhibition of rabbit muscle glycogen phosphorylase-b using glucose-1-phosphate as substrate preincubated with glycogen for 15 mins followed by substrate addition measured every 1 min for 5 mins ChEMBL. 26713107
Ki (binding) = 9 uM Competitive inhibition of rabbit muscle glycogen phosphorylase-b in presence of varying levels of glucose-1-phosphate and constant concentration of glycogen and AMP by double reciprocal plot method LITERATURE. 27522507
Ki (binding) = 9 uM Inhibition of rabbit skeletal muscle glycogen phosphorylase b assessed as inorganic phosphate release using glucose-1-phosphate as substrate by double-reciprocal plot analysis LITERATURE. 27624527
Ki (binding) = 11 uM Inhibition of rabbit muscle glycogen phosphorylase-b ChEMBL. 26713107
Ki (binding) = 11 uM Inhibition of rabbit muscle glycogen phosphorylase-b LITERATURE. 27522507
Ki (binding) = 11 uM Inhibition of rabbit muscle glycogen phosphorylase b using alpha-D-glucose-1-phosphate as substrate LITERATURE. 27624527

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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