Deoxypyridinoline (CHEM021696)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-05-25 18:10:17 UTC
Update Date2016-11-09 01:17:20 UTC
Accession NumberCHEM021696
Identification
Common NameDeoxypyridinoline
ClassSmall Molecule
DescriptionDeoxypyridinoline (DPD) is a breakdown product of type I fibrillar collagen, it occurs mainly in Type I collagen of bone. DPD shows a high specificity for bone, and the measurement of urinary DPD is not influenced by newly collagens and dietary intake. DPD cross-links of type 1 collagen are excreted in urine either as free or peptide-bound moieties. It is the peptide-bound cross-links that decrease by the greatest amount in response to bisphosphonate therapy. DPD is one of the most extensively characterized biochemical bone markers, but the interpretation of results is hampered by biologic and other preanalytical variability. Biochemical bone markers can provide a valuable tool in the management of metabolic bone diseases. Their most recognized application in clinical practice is for monitoring treatment for osteoporosis as an adjunct to bone mineral density measurements. Other applications that have been investigated include their use as a diagnostic tool for bone diseases other than osteoporosis and as predictive markers for bone loss and the risk of bone fracture. DPD measured in urine follow a circadian or diurnal cycle with a peak in the early morning and nadir in the late afternoon to early evening. The magnitude of the diurnal change, i.e., nadir concentration divided by peak concentration, expressed as a percentage is around 70% (range, 53-75%). (PMID: 11805003, 17229003, 16751696).
Contaminant Sources
  • FooDB Chemicals
  • HMDB Contaminants - Urine
Contaminant TypeNot Available
Chemical Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
4-(2-Amino-2-carboxyethyl)-1-(5-amino-5-carboxypentyl)-3-(3-amino-3-carboxypropyl)-5-hydroxy-pyridinium inner salt stereoisomerHMDB
DeoxipyridinolineHMDB
Deoxy-pyridinolineHMDB
DeoxypiridinolineHMDB
DeoxypirydynolineHMDB
DeoxypyridinoloneHMDB
DeoxypyridolineHMDB
DesoxypyridinolineHMDB
LysylpyridinolineHMDB
N-(5-Amino-5-carboxypentyl)-3-hydroxy-4-(2-amino-2-carboxyethyl)-5-(3-amino-3-carboxypropyl)pyridineHMDB
Chemical FormulaC18H28N4O7
Average Molecular Mass412.438 g/mol
Monoisotopic Mass412.196 g/mol
CAS Registry Number83462-55-9
IUPAC Name4-[(2S)-2-amino-2-carboxyethyl]-3-[(3S)-3-amino-3-carboxypropyl]-1-[(5S)-5-amino-5-carboxypentyl]-5-hydroxypyridin-1-ium
Traditional Name4-[(2S)-2-amino-2-carboxyethyl]-3-[(3S)-3-amino-3-carboxypropyl]-1-[(5S)-5-amino-5-carboxypentyl]-5-hydroxypyridin-1-ium
SMILESN[C@@H](CCCC[N+]1=CC(CC[C@H](N)C([O-])=O)=C(C[C@H](N)C(O)=O)C(O)=C1)C(O)=O
InChI IdentifierInChI=1S/C18H28N4O7/c19-12(16(24)25)3-1-2-6-22-8-10(4-5-13(20)17(26)27)11(15(23)9-22)7-14(21)18(28)29/h8-9,12-14H,1-7,19-21H2,(H3-,23,24,25,26,27,28,29)/t12-,13-,14-/m0/s1
InChI KeyZAHDXEIQWWLQQL-IHRRRGAJSA-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
  • Pyridinolate
  • Aralkylamine
  • Pyridine
  • Pyridinium
  • Heteroaromatic compound
  • Amino acid
  • Carboxylic acid
  • Organoheterocyclic compound
  • Azacycle
  • Organic zwitterion
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Organic oxide
  • Carbonyl group
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.15 g/LALOGPS
logP-4.1ALOGPS
logP-12ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)0.83ChemAxon
pKa (Strongest Basic)9.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area216.9 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity113.48 m³·mol⁻¹ChemAxon
Polarizability42.08 ųChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-2029000000-bd1b37cf42f6ca53e3faSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-014i-5212591000-a631876ab8a721ce23e2Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_16) - 70eV, PositiveNot AvailableSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0001900000-635243e94b1bde7fa2f8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08ir-0009200000-5b2e6b764362837842fcSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0uyi-2609000000-85238060df1e37341e99Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0000900000-fb17bf7ac61b15c5529bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-1000900000-953b3f1eb159e9fd568cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00fr-9321000000-2dd743934a01f1623082Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03xr-0009400000-306c023ce519cc90c386Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5019000000-a5356bd2aed0616a5553Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-4091000000-382e57452c8ebe13e257Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03xu-1009400000-ad7e7a69d65e5cce2658Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0300-2009100000-132db17dd2c4331eca76Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0596-2192000000-45a922c56b2c7be849c6Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)Not Available
Uses/SourcesNot Available
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB0000569
FooDB IDFDB013750
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG IDNot Available
BioCyc IDNot Available
METLIN ID5552
PDB IDNot Available
Wikipedia LinkDeoxypyridinoline
Chemspider ID9479456
ChEBI ID89510
PubChem Compound ID11304480
Kegg Compound IDNot Available
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. Hatch, Robert P. Method for the synthesis of deoxypyridinoline. U.S. (1998), 7 pp.
2. Haderslev KV, Tjellesen L, Sorensen HA, Staun M: Alendronate increases lumbar spine bone mineral density in patients with Crohn's disease. Gastroenterology. 2000 Sep;119(3):639-46.
3. Tanaka K, Inaba M, Goto H, Nagata-Sakurai M, Sakai S, Yamada S, Ueda M, Ishimura E, Nishizawa Y: Paraarticular trabecular bone loss at the ultradistal radius and increased arterial stiffening in postmenopausal patients with rheumatoid arthritis. J Rheumatol. 2006 Apr;33(4):652-8.
4. Romanello M, Noris Suarez K, Bettica P, Moro L: Detection of pyridinium cross-links in human bile. Calcif Tissue Int. 1995 Dec;57(6):415-8.
5. Hoff AO, Catala-Lehnen P, Thomas PM, Priemel M, Rueger JM, Nasonkin I, Bradley A, Hughes MR, Ordonez N, Cote GJ, Amling M, Gagel RF: Increased bone mass is an unexpected phenotype associated with deletion of the calcitonin gene. J Clin Invest. 2002 Dec;110(12):1849-57.
6. Hodsman AB, Fraher LJ, Ostbye T, Adachi JD, Steer BM: An evaluation of several biochemical markers for bone formation and resorption in a protocol utilizing cyclical parathyroid hormone and calcitonin therapy for osteoporosis. J Clin Invest. 1993 Mar;91(3):1138-48.
7. Kaufmann J, Mueller A, Voigt A, Carl HD, Gursche A, Zacher J, Stein G, Hein G: Hydroxypyridinium collagen crosslinks in serum, urine, synovial fluid and synovial tissue in patients with rheumatoid arthritis compared with osteoarthritis. Rheumatology (Oxford). 2003 Feb;42(2):314-20.
8. Giangregorio LM, Hicks AL, Webber CE, Phillips SM, Craven BC, Bugaresti JM, McCartney N: Body weight supported treadmill training in acute spinal cord injury: impact on muscle and bone. Spinal Cord. 2005 Nov;43(11):649-57.
9. Pronchenko IA, Buzulina VP, Tomolina NA, Vedernikova RN, Ermakova IP: [Biochemical markers of bone metabolism and bone tissue losses after allotransplantation of the cadaveric kidney: a cross-sectional]. Klin Lab Diagn. 2005 Nov;(11):3-8.
10. Yoshihara Y, Tsukazaki T, Osaki M, Nakashima M, Hasui K, Shindo H: Altered expression of inflammatory cytokines in primary osteoarthritis by human T lymphotropic virus type I retrovirus infection: a cross-sectional study. Arthritis Res Ther. 2004;6(4):R347-54. Epub 2004 Jun 7.
11. Vesper HW, Demers LM, Eastell R, Garnero P, Kleerekoper M, Robins SP, Srivastava AK, Warnick GR, Watts NB, Myers GL: Assessment and recommendations on factors contributing to preanalytical variability of urinary pyridinoline and deoxypyridinoline. Clin Chem. 2002 Feb;48(2):220-35.
12. Shankar S, Hosking DJ: Biochemical assessment of Paget's disease of bone. J Bone Miner Res. 2006 Dec;21 Suppl 2:P22-7.
13. Takada J, Imoto K, Iba K, Yamashita T: [Bone and bone related biochemical examinations. Bone and collagen related metabolites. DPD (total, free)]. Clin Calcium. 2006 Jun;16(6):994-1000.