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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:22:33 UTC
HMDB IDHMDB0000739
Secondary Accession Numbers
  • HMDB00739
Metabolite Identification
Common NameIsodesmosine
DescriptionIsodesmosine, also known as Ide, belongs to the class of organic compounds known as tetracarboxylic acids and derivatives. These are carboxylic acids containing exactly four carboxyl groups. Isodesmosine is a very strong basic compound (based on its pKa). A rare amino acid found in elastin, formed by condensation of four molecules of lysine into a pyridinium ring.
Structure
Data?1582752153
Synonyms
ValueSource
2-(4-Amino-4-carboxybutyl)-1-(5-amino-5-carboxypentyl)-3,5-bis(3-amino-3-carboxypropyl)pyridiniumChEBI
2-Amino-6-[3,5-bis(3-amino-4-hydroxy-4-oxobutyl)-2-(4-amino-5-hydroxy-5-oxopentyl)pyridin-1-ium-1-yl]hexanoic acidChEBI
IdeChEBI
2-Amino-6-[3,5-bis(3-amino-4-hydroxy-4-oxobutyl)-2-(4-amino-5-hydroxy-5-oxopentyl)pyridin-1-ium-1-yl]hexanoateGenerator
2-(4-Amino-4-carboxybutyl)-1-(5-amino-5-carboxypentyl)-3,5-bis(3-amino-3-carboxypropyl)-pyridiniumHMDB
Iso-desmosinHMDB
Chemical FormulaC24H40N5O8
Average Molecular Weight526.6031
Monoisotopic Molecular Weight526.287688281
IUPAC Name3,5-bis(3-amino-3-carboxypropyl)-2-(4-amino-4-carboxybutyl)-1-(5-amino-5-carboxypentyl)pyridin-1-ium
Traditional Nameisodesmosine
CAS Registry Number991-01-5
SMILES
NC(CCCC[N+]1=CC(CCC(N)C(O)=O)=CC(CCC(N)C(O)=O)=C1CCCC(N)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C24H39N5O8/c25-16(21(30)31)4-1-2-11-29-13-14(7-9-18(27)23(34)35)12-15(8-10-19(28)24(36)37)20(29)6-3-5-17(26)22(32)33/h12-13,16-19H,1-11,25-28H2,(H3-,30,31,32,33,34,35,36,37)/p+1
InChI KeyRGXCTRIQQODGIZ-UHFFFAOYSA-O
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetracarboxylic acids and derivatives. These are carboxylic acids containing exactly four carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTetracarboxylic acids and derivatives
Direct ParentTetracarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tetracarboxylic acid or derivatives
  • Alpha-amino acid
  • Alpha-amino acid or derivatives
  • Aralkylamine
  • Pyridine
  • Pyridinium
  • Heteroaromatic compound
  • Amino acid or derivatives
  • Amino acid
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Hydrocarbon derivative
  • Amine
  • Organic cation
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.012 g/LALOGPS
logP-4.6ALOGPS
logP-14ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)1.04ChemAxon
pKa (Strongest Basic)10.12ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area257.16 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity133.35 m³·mol⁻¹ChemAxon
Polarizability56.3 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0019-0000900000-78ef29d9446bcb2f1511Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00di-1000059000-f1c087858d1fc630f361Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0000190000-808de3e96eaf83168632Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0095-0000910000-97e503d6c21442da41c7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-2300900000-99327764dbc9812bcc34Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000090000-62b53001eb9cde723507Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-1000090000-7d10eeb30c8bc5581672Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00dl-9200540000-2bad06401982c266a8c7Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
UrineDetected and Quantified0.00029 +/- 0.00022 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.0014 +/- 0.000077 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.002 +/- 0.0002 umol/mmol creatinineAdult (>18 years old)BothLiver fibrosis details
Associated Disorders and Diseases
Disease References
Cirrhosis
  1. Afdhal NH, Keaveny AP, Cohen SB, Nunes DP, Maldonado N, O'Brien M, Stone PJ: Urinary assays for desmosine and hydroxylysylpyridinoline in the detection of cirrhosis. J Hepatol. 1997 Dec;27(6):993-1002. [PubMed:9453424 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000467
KNApSAcK IDNot Available
Chemspider ID13214
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIsodesmosine
METLIN ID5707
PubChem Compound13811
PDB IDNot Available
ChEBI ID64366
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceThomas, J.; Elsden, D. F.; Partridge, S. M. Partial structure of two major degradation products from the cross-linkages in elastin. Nature (London, United Kingdom) (1963), 200(4907), 651-2.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Cumiskey WR, Pagani ED, Bode DC: Enrichment and analysis of desmosine and isodesmosine in biological fluids. J Chromatogr B Biomed Appl. 1995 Jun 23;668(2):199-207. [PubMed:7581855 ]
  2. Viglio S, Iadarola P, Lupi A, Trisolini R, Tinelli C, Balbi B, Grassi V, Worlitzsch D, Doring G, Meloni F, Meyer KC, Dowson L, Hill SL, Stockley RA, Luisetti M: MEKC of desmosine and isodesmosine in urine of chronic destructive lung disease patients. Eur Respir J. 2000 Jun;15(6):1039-45. [PubMed:10885422 ]
  3. Ma S, Lieberman S, Turino GM, Lin YY: The detection and quantitation of free desmosine and isodesmosine in human urine and their peptide-bound forms in sputum. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12941-3. Epub 2003 Oct 16. [PubMed:14563926 ]