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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-11 21:45:03 UTC
Update Date2018-03-12 21:57:09 UTC
HMDB IDHMDB0036592
Secondary Accession Numbers
  • HMDB36592
Metabolite Identification
Common NameValidamycin A
DescriptionValidamycin a, also known as mycin or rhizocin, belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Validamycin a exists as a solid, soluble (in water), and a very weakly acidic compound (based on its pKa). Within the cell, validamycin a is primarily located in the cytoplasm.
Structure
Thumb
Synonyms
ValueSource
Antibiotic T 7545aHMDB
MycinHMDB
RhizocinHMDB
SolacolHMDB
T 7545aHMDB
ValidacinHMDB
ValidamycinHMDB
Validamycin, jmafHMDB
ValimonHMDB
Chemical FormulaC20H35NO13
Average Molecular Weight497.4908
Monoisotopic Molecular Weight497.210840211
IUPAC Name2-(hydroxymethyl)-6-[(2,3,5-trihydroxy-6-methyl-4-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)oxy]oxane-3,4,5-triol
Traditional Name2-(hydroxymethyl)-6-[(2,3,5-trihydroxy-6-methyl-4-{[4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl)oxy]oxane-3,4,5-triol
CAS Registry Number37248-47-8
SMILES
CC1C(O)C(NC2C=C(CO)C(O)C(O)C2O)C(O)C(O)C1OC1OC(CO)C(O)C(O)C1O
InChI Identifier
InChI=1S/C20H35NO13/c1-5-10(24)9(21-7-2-6(3-22)11(25)15(29)12(7)26)14(28)17(31)19(5)34-20-18(32)16(30)13(27)8(4-23)33-20/h2,5,7-32H,3-4H2,1H3
InChI KeyPJASXVPPJJZEIB-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentO-glycosyl compounds
Alternative Parents
Substituents
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Aminocyclitol
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Organoheterocyclic compound
  • Polyol
  • Secondary amine
  • Oxacycle
  • Acetal
  • Secondary aliphatic amine
  • Primary alcohol
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Amine
  • Organonitrogen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Biological location:

Role

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point130 - 135 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility140 g/LALOGPS
logP-2.7ALOGPS
logP-6.6ChemAxon
logS-0.55ALOGPS
pKa (Strongest Acidic)12.08ChemAxon
pKa (Strongest Basic)7.19ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area253.02 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity109.9 m³·mol⁻¹ChemAxon
Polarizability48.02 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-017r-0131900000-8c595e997ca033d45e35View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-024i-3123029000-cb798084edba2d0072a4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-02ai-0008900000-93d867ebdbc9625d7ecdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-0109200000-dce044a374d3d8561f02View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-0649000000-1083ec5ab997c26b4b38View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00mk-0135900000-28cee34cdf6f571393b9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-0119500000-c2c72bf7c0acb1076ec6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0f8c-3359000000-8ae0bb4fcac21c10e6dfView in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB015504
KNApSAcK IDC00018797
Chemspider IDNot Available
KEGG Compound IDC12112
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .