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Human Metabolome Database Version 3.5

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Showing metabocard for Pyridinoline (HMDB00851)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:09:26 -0700
HMDB ID HMDB00851
Secondary Accession Numbers None
Metabolite Identification
Common Name Pyridinoline
Description Pyridinoline is a breakdown product of bone collagen. It can be used as a bone marker to measure osteoclastic activity.
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (+)-pyridinoline
  2. 1-(2S)-(+)-Pyridinoline
  3. 4-((2S)-2-Amino-2-carboxyethyl)-1-((2R,5S)-5-amino-5-carboxy-2-hydroxypentyl)-3-((3S)-3-amino-3-carboxypropyl)-5-hydroxy-Pyridinium inner salt
  4. Hydroxylysylpyridinoline
  5. Pyridinoline
Chemical Formula C18H28N4O8
Average Molecular Weight 428.4369
Monoisotopic Molecular Weight 428.190713892
IUPAC Name 4-[(2S)-2-amino-2-carboxyethyl]-3-[(3S)-3-amino-3-carboxypropyl]-1-[(2R,5S)-5-amino-5-carboxylato-2-hydroxypentyl]-5-hydroxypyridin-1-ium
Traditional IUPAC Name 4-[(2S)-2-amino-2-carboxyethyl]-3-[(3S)-3-amino-3-carboxypropyl]-1-[(2R,5S)-5-amino-5-carboxylato-2-hydroxypentyl]-5-hydroxypyridin-1-ium
CAS Registry Number 63800-01-1
SMILES N[C@@H](CCC1=C[N+](C[C@H](O)CC[C@H](N)C([O-])=O)=CC(O)=C1C[C@H](N)C(O)=O)C(O)=O
InChI Identifier InChI=1S/C18H28N4O8/c19-12(16(25)26)3-1-9-6-22(7-10(23)2-4-13(20)17(27)28)8-15(24)11(9)5-14(21)18(29)30/h6,8,10,12-14,23H,1-5,7,19-21H2,(H3-,24,25,26,27,28,29,30)/t10-,12+,13+,14+/m1/s1
InChI Key LCYXYLLJXMAEMT-SAXRGWBVSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Amino Acids, Peptides, and Analogues
Class Amino Acids and Derivatives
Sub Class Alpha Amino Acids and Derivatives
Other Descriptors
  • Aromatic Heteromonocyclic Compounds
  • Heterocyclic Fatty Acids
  • Organic Compounds
Substituents
  • Carboxylic Acid
  • Carboxylic Acid Salt
  • Polyamine
  • Primary Aliphatic Amine (Alkylamine)
  • Pyridine
  • Pyridinium
  • Secondary Alcohol
  • Tricarboxylic Acid Derivative
Direct Parent Alpha Amino Acids and Derivatives
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Protein synthesis, amino acid biosynthesis
Application Not Available
Cellular locations Not Available
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 0.45 g/L ALOGPS
LogP -3.94 ALOGPS
LogP -13 ChemAxon
LogS -3.03 ALOGPS
pKa (strongest acidic) 0.73 ChemAxon
pKa (strongest basic) 9.8 ChemAxon
Hydrogen Acceptor Count 11 ChemAxon
Hydrogen Donor Count 7 ChemAxon
Polar Surface Area 237.13 A2 ChemAxon
Rotatable Bond Count 13 ChemAxon
Refractivity 114.84 ChemAxon
Polarizability 43.12 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations Not Available
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Bladder
  • Fibroblasts
  • Prostate
  • Skin
  • Cartilage
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Urine Detected and Quantified
Article_icon
0.033 (0.0045-0.062) umol/mmol creatinine Adult (>18 years old) Female Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
0.0016 (0.0010-0.0039) uM Adult (>18 years old) Both Rheumatoid arthritis Not Available
Urine Detected and Quantified
Article_icon
0.075 +/- 0.012 umol/mmol creatinine Adult (>18 years old) Female Congestive heart failure Not Available
Associated Disorders and Diseases
Disease References
Rheumatoid arthritis
  • Jensen T, Klarlund M, Hansen M, Jensen KE, Skjodt H, Hyldstrup L: Connective tissue metabolism in patients with unclassified polyarthritis and early rheumatoid arthritis. Relationship to disease activity, bone mineral density, and radiographic outcome. J Rheumatol. 2004 Sep;31(9):1698-708. Pubmed: 15338487 Link_out
    Associated OMIM IDs
    DrugBank ID Not Available
    Phenol Explorer Compound ID Not Available
    Phenol Explorer Metabolite ID Not Available
    FoodDB ID FDB010805
    KNApSAcK ID Not Available
    Chemspider ID 94798 Link_out
    KEGG Compound ID Not Available
    BioCyc ID Not Available
    BiGG ID Not Available
    Wikipedia Link Not Available
    NuGOwiki Link HMDB00851 Link_out
    Metagene Link HMDB00851 Link_out
    METLIN ID 5814 Link_out
    PubChem Compound 105068 Link_out
    PDB ID Not Available
    ChEBI ID Not Available
    References
    Synthesis Reference Allevi, Pietro; Cribiu, Riccardo; Giannini, Elios; Anastasia, Mario. Practical syntheses of pyridinolines, important amino acidic biomarkers of collagen health. Journal of Organic Chemistry (2007), 72(9), 3478-3483.
    Material Safety Data Sheet (MSDS) Not Available
    General References
    1. Fujimoto D, Moriguchi T: Pyridinoline, a non-reducible crosslink of collagen. Quantitative determination, distribution, and isolation of a crosslinked peptide. J Biochem (Tokyo). 1978 Mar;83(3):863-7. Pubmed: 641035 Link_out
    2. Ricard-Blum S, Esterre P, Grimaud JA: Collagen cross-linking by pyridinoline occurs in non-reversible skin fibrosis. Cell Mol Biol (Noisy-le-grand). 1993 Nov;39(7):723-7. Pubmed: 8268758 Link_out
    3. Ueda M, Inaba M, Okuno S, Maeno Y, Ishimura E, Yamakawa T, Nishizawa Y: Serum BAP as the clinically useful marker for predicting BMD reduction in diabetic hemodialysis patients with low PTH. Life Sci. 2005 Jul 22;77(10):1130-9. Pubmed: 15978265 Link_out
    4. Okamura T, Akita H, Tatsura H, Kawai N, Nagata D, Azemoto M, Iwase Y, Kohri K: The efficacy of a serum carboxyterminal pyridinoline cross-linked telopeptide of type I collagen as a quantitative screening marker for bone metastases in patients with urological malignancies. Cancer Detect Prev. 2003;27(1):14-8. Pubmed: 12600412 Link_out
    5. Bank RA, Verzijl N, Lafeber FP, Tekoppele JM: Putative role of lysyl hydroxylation and pyridinoline cross-linking during adolescence in the occurrence of osteoarthritis at old age. Osteoarthritis Cartilage. 2002 Feb;10(2):127-34. Pubmed: 11869072 Link_out
    6. van der Slot AJ, van Dura EA, de Wit EC, De Groot J, Huizinga TW, Bank RA, Zuurmond AM: Elevated formation of pyridinoline cross-links by profibrotic cytokines is associated with enhanced lysyl hydroxylase 2b levels. Biochim Biophys Acta. 2005 Jun 30;1741(1-2):95-102. Epub 2004 Oct 5. Pubmed: 15955452 Link_out
    7. Istok R, Bely M, Stancikova M, Rovensky J: Evidence for increased pyridinoline concentration in fibrotic tissues in diffuse systemic sclerosis. Clin Exp Dermatol. 2001 Sep;26(6):545-7. Pubmed: 11678886 Link_out
    8. Teichmann J, Lange U, Stracke H, Federlin K, Bretzel RG: Bone metabolism and bone mineral density of systemic lupus erythematosus at the time of diagnosis. Rheumatol Int. 1999;18(4):137-40. Pubmed: 10220833 Link_out
    9. Vesper HW, Audain C, Woolfitt A, Ospina M, Barr J, Robins SP, Myers GL: High-performance liquid chromatography method to analyze free and total urinary pyridinoline and deoxypyridinoline. Anal Biochem. 2003 Jul 15;318(2):204-11. Pubmed: 12814623 Link_out
    10. Wan KC, Wu HT, Chan HP, Hung LK: Effects of antioxidants on pyridinoline cross-link formation in culture supernatants of fibroblasts from normal skin and hypertrophic scars. Clin Exp Dermatol. 2002 Sep;27(6):507-12. Pubmed: 12372096 Link_out
    11. Ricard-Blum S, Bresson-Hadni S, Grenard P, Humbert P, Carbillet JP, Risteli L, Vuitton DA: The level of the collagen cross-link pyridinoline reflects the improvement of cutaneous lesions in one case of skin alveolar echinococcosis. Parasitol Res. 1998 Sep;84(9):715-9. Pubmed: 9766899 Link_out
    12. Wan KC, Chow TC: Age-related changes in the concentration of pyridinoline cross-links in human skin. Ann Clin Biochem. 1999 Sep;36 ( Pt 5):666-8. Pubmed: 10505220 Link_out
    13. Muller A, Stein G, Lehmann G, Hein G: Investigations of bone turnover in renal osteopathy. Eur J Med Res. 1999 Feb 25;4(2):78-84. Pubmed: 10066644 Link_out
    14. Miyamoto KK, McSherry SA, Robins SP, Besterman JM, Mohler JL: Collagen cross-link metabolites in urine as markers of bone metastases in prostatic carcinoma. J Urol. 1994 Apr;151(4):909-13. Pubmed: 7510346 Link_out
    15. Takahashi M, Kushida K, Ohishi T, Kawana K, Hoshino H, Uchiyama A, Inoue T: Quantitative analysis of crosslinks pyridinoline and pentosidine in articular cartilage of patients with bone and joint disorders. Arthritis Rheum. 1994 May;37(5):724-8. Pubmed: 8185700 Link_out
    16. Tilson MD, Davis G: Deficiencies of copper and a compound with ion-exchange characteristics of pyridinoline in skin from patients with abdominal aortic aneurysms. Surgery. 1983 Aug;94(2):134-41. Pubmed: 6879435 Link_out
    17. Fernandes RJ, Eyre DR: The elastin-like protein matrix of lamprey branchial cartilage is cross-linked by lysyl pyridinoline. Biochem Biophys Res Commun. 1999 Aug 11;261(3):635-40. Pubmed: 10441478 Link_out