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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2018-05-19 22:06:15 UTC
HMDB IDHMDB0000572
Secondary Accession Numbers
  • HMDB00572
Metabolite Identification
Common NameDesmosine
DescriptionDesmosine is formed by condensation of four molecules of lysine into a pyridinium ring. Elastin molecules aggregate in the extracellular space where they are crosslinked by stable desmosine bridges. The resulting polymer is structurally organized as branched fibers and lamellae, which, in skin, are wider (a few microns) in the deep dermis and become progressively thinner (fraction of a micron) towards the papillary dermis. Several general and local factors seem to regulate elastin gene expression, deposition and degradation. (PMID: 9297692 ). Desmosines are crosslinking amino acids unique to mature elastin in humans. Owing to this unicity, they have been discussed as potentially indicators of connective tissue disorders whose clinical manifestations are mostly the result of elastin degradation. (PMID: 17390614 ). Emphysema (Pulmonary emphysema is a devastating disease for which there is no effective treatment) is associated with degradation of elastic fibers (PMID: 14704646 ). It has been shown that the urinary concentration of elastin specific crosslinks, desmosine correlates well with liver fibrosis score in biopsy specimens from patients with liver disease secondary to hepatitis C virus and alcohol. (PMID: 10996125 ).
Structure
Thumb
Synonyms
ValueSource
4-(4-amino-4-Carboxybutyl)-1-(5-amino-5-carboxypentyl)-3,5-bis(3-amino-3-carboxypropyl)pyridiniumHMDB
Chemical FormulaC24H40N5O8
Average Molecular Weight526.6031
Monoisotopic Molecular Weight526.287688281
IUPAC Name3,5-bis[(3S)-3-amino-3-carboxypropyl]-4-[(4S)-4-amino-4-carboxybutyl]-1-(5-amino-5-carboxypentyl)pyridin-1-ium
Traditional Name3,5-bis[(3S)-3-amino-3-carboxypropyl]-4-[(4S)-4-amino-4-carboxybutyl]-1-(5-amino-5-carboxypentyl)pyridin-1-ium
CAS Registry Number11003-57-9
SMILES
NC(CCCC[N+]1=CC(CC[C@H](N)C(O)=O)=C(CCC[C@H](N)C(O)=O)C(CC[C@H](N)C(O)=O)=C1)C(O)=O
InChI Identifier
InChI=1S/C24H39N5O8/c25-17(21(30)31)5-1-2-11-29-12-14(7-9-19(27)23(34)35)16(4-3-6-18(26)22(32)33)15(13-29)8-10-20(28)24(36)37/h12-13,17-20H,1-11,25-28H2,(H3-,30,31,32,33,34,35,36,37)/p+1/t17?,18-,19-,20-/m0/s1
InChI KeyVEVRNHHLCPGNDU-NIVVRJPPSA-O
Chemical Taxonomy
DescriptionThis compound 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
  • L-alpha-amino acid
  • Aralkylamine
  • Pyridine
  • Pyridinium
  • Heteroaromatic compound
  • Amino acid
  • Amino acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Hydrocarbon derivative
  • Amine
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Organic oxide
  • Organic cation
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
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-4.5ALOGPS
logP-13ChemAxon
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
Refractivity133.53 m³·mol⁻¹ChemAxon
Polarizability56.4 ųChemAxon
Number of Rings1ChemAxon
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, Positivesplash10-0019-0000900000-64c725d85f44d0ade63aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-05g0-8100098000-49762d050753246255e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0000190000-760a274d2ce59871397cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0097-0000920000-e995b52b9c9010ed39e0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0i01-2100900000-bc52bbe1e56f6c011adcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000090000-d1853206aef8d4c91afbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-1000090000-b59aa402259987bdbb50View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00dl-9200320000-e8dc575b5c38c51817b8View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Urine
Tissue Locations
  • Kidney
  • Skin
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.0003 +/- 0.0002 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.0015 +/- 0.000064 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.0025 +/- 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
FoodDB IDFDB000516
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDesmosine
METLIN ID5554
PubChem Compound53477704
PDB IDNot Available
ChEBI ID37628
References
Synthesis ReferenceRencher, William Franklin, Jr. Design and synthesis of desmosine-like peptidyl carbamates as novel inhibitors of human leukocyte elastase. (1988), 164 pp. CAN 111:233627 AN 1989:633627
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Luisetti M, Sturani C, Sella D, Madonini E, Galavotti V, Bruno G, Peona V, Kucich U, Dagnino G, Rosenbloom J, Starcher B, Grassi C: MR889, a neutrophil elastase inhibitor, in patients with chronic obstructive pulmonary disease: a double-blind, randomized, placebo-controlled clinical trial. Eur Respir J. 1996 Jul;9(7):1482-6. [PubMed:8836663 ]
  2. Ono S, Yamauchi M: Elastin cross-linking in the skin from patients with amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry. 1994 Jan;57(1):94-6. [PubMed:8301312 ]
  3. Uitto J, Santa Cruz DJ, Starcher BC, Whyte MP, Murphy WA: Biochemical and ultrastructural demonstration of elastin accumulation in the skin lesions of the Buschke-Ollendorff syndrome. J Invest Dermatol. 1981 Apr;76(4):284-7. [PubMed:7205030 ]
  4. Tenholder MF, Rajagopal KR, Phillips YY, Dillard TA, Bennett LL, Mundie TG, Tellis CJ: Urinary desmosine excretion as a marker of lung injury in the adult respiratory distress syndrome. Chest. 1991 Nov;100(5):1385-90. [PubMed:1935298 ]
  5. Fill JA, Brandt JT, Wiedemann HP, Rinehart BL, Lindemann CF, Komara JJ, Bowsher RR, Spence MC, Zeiher BG: Urinary desmosine as a biomarker in acute lung injury. Biomarkers. 2006 Jan-Feb;11(1):85-96. [PubMed:16484139 ]
  6. 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 ]
  7. 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 ]
  8. Oikarinen AI, Palatsi R, Adomian GE, Oikarinen H, Clark JG, Uitto J: Anetoderma: biochemical and ultrastructural demonstration of an elastin defect in the skin of three patients. J Am Acad Dermatol. 1984 Jul;11(1):64-72. [PubMed:6736354 ]
  9. Wondrak GT, Roberts MJ, Jacobson MK, Jacobson EL: 3-hydroxypyridine chromophores are endogenous sensitizers of photooxidative stress in human skin cells. J Biol Chem. 2004 Jul 16;279(29):30009-20. Epub 2004 May 7. [PubMed:15133022 ]
  10. Pasquali-Ronchetti I, Baccarani-Contri M: Elastic fiber during development and aging. Microsc Res Tech. 1997 Aug 15;38(4):428-35. [PubMed:9297692 ]
  11. Viglio S, Annovazzi L, Luisetti M, Stolk J, Casado B, Iadarola P: Progress in the methodological strategies for the detection in real samples of desmosine and isodesmosine, two biological markers of elastin degradation. J Sep Sci. 2007 Feb;30(2):202-13. [PubMed:17390614 ]
  12. Cantor JO, Shteyngart B: How a test for elastic fiber breakdown products in sputum could speed development of a treatment for pulmonary emphysema. Med Sci Monit. 2004 Jan;10(1):RA1-4. [PubMed:14704646 ]
  13. Stone PJ: Potential use of collagen and elastin degradation markers for monitoring liver fibrosis in schistosomiasis. Acta Trop. 2000 Oct 23;77(1):97-9. [PubMed:10996125 ]