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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-04-22 23:32:52 UTC
HMDB IDHMDB0000851
Secondary Accession Numbers
  • HMDB00851
Metabolite Identification
Common NamePyridinoline
DescriptionPyridinoline is a breakdown product of bone collagen. It can be used as a bone marker to measure osteoclastic activity.
Structure
Data?1582752160
Synonyms
ValueSource
(+)-PyridinolineHMDB
1-(2S)-(+)-PyridinolineHMDB
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 saltHMDB
HydroxylysylpyridinolineHMDB
Hydroxylysyl pyridinolineHMDB
PyridinolineMeSH
Chemical FormulaC18H28N4O8
Average Molecular Weight428.4369
Monoisotopic Molecular Weight428.190713892
IUPAC Name4-[(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 Name4-[(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 Number63800-01-1
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 KeyLCYXYLLJXMAEMT-SAXRGWBVSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Hydroxypyridine
  • Aralkylamine
  • Pyridine
  • Pyridinium
  • Heteroaromatic compound
  • Carboxylic acid salt
  • Amino acid
  • Secondary alcohol
  • Carboxylic acid
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic zwitterion
  • Organic salt
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

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 Solubility0.45 g/LALOGPS
logP-3.9ALOGPS
logP-13ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)0.73ChemAxon
pKa (Strongest Basic)9.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area237.13 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity114.84 m³·mol⁻¹ChemAxon
Polarizability43.12 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, Positivesplash10-001i-1139100000-5d8fc20ccc7b98532363Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-001u-3200292000-91125c23cde5753b8015Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0001900000-1071214d48bc921584a2Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00ba-0009400000-b7f8b4454b46b9b588a6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-054t-1429200000-e0435f18dbbf7dca10c3Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000900000-843d31dfa041aff3e01eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-1100900000-c38c200cd8e6b732fd69Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-7921000000-79aa7de87908b35ae0f5Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Bladder
  • Cartilage
  • Epidermis
  • Fibroblasts
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.033 (0.0045-0.062) umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0016 (0.0010-0.0039) uMAdult (>18 years old)BothRheumatoid arthritis details
UrineDetected and Quantified0.075 +/- 0.012 umol/mmol creatinineAdult (>18 years old)FemaleCongestive heart failure details
Associated Disorders and Diseases
Disease References
Rheumatoid arthritis
  1. 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 ]
Congestive heart failure
  1. Shane E, Mancini D, Aaronson K, Silverberg SJ, Seibel MJ, Addesso V, McMahon DJ: Bone mass, vitamin D deficiency, and hyperparathyroidism in congestive heart failure. Am J Med. 1997 Sep;103(3):197-207. [PubMed:9316552 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB010805
KNApSAcK IDNot Available
Chemspider ID94798
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyridinoline
METLIN ID5814
PubChem Compound105068
PDB IDNot Available
ChEBI ID88539
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceAllevi, 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. 1978 Mar;83(3):863-7. [PubMed:641035 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]
  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 ]