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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:37:02 UTC
HMDB IDHMDB0000569
Secondary Accession Numbers
  • HMDB00569
Metabolite Identification
Common NameDeoxypyridinoline
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 ).
Structure
Thumb
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 Weight412.4375
Monoisotopic Molecular Weight412.19579927
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
CAS Registry Number83462-55-9
SMILES
N[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 Identifier
InChI=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
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Platelet
  • Skeletal Muscle
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0007 +/- 0.00018 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.005 (0.001 - 0.015) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.0086 (0.0004-0.016) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.0047 +/- 0.0004 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0006 +/- 0.0001 uMAdult (>18 years old)BothGrowth hormone deficiency details
UrineDetected and Quantified0.015 (0.001 - 0.03) umol/mmol creatinineAdult (>18 years old)Not SpecifiedMultiple myeloma details
UrineDetected and Quantified0.019 +/- 0.0026 umol/mmol creatinineAdult (>18 years old)BothCongestive heart failure details
UrineDetected and Quantified0.0066 +/- 0.0006 umol/mmol creatinineAdult (>18 years old)BothLiver fibrosis details
Associated Disorders and Diseases
Disease References
Growth hormone deficiency
  1. Rodriguez-Arnao J, James I, Jabbar A, Trainer PJ, Perrett D, Besser GM, Ross RJ: Serum collagen crosslinks as markers of bone turn-over during GH replacement therapy in growth hormone deficient adults. Clin Endocrinol (Oxf). 1998 Apr;48(4):455-62. [PubMed:9640412 ]
Multiple myeloma
  1. Dizdar O, Barista I, Kalyoncu U, Karadag O, Hascelik G, Cila A, Pinar A, Celik I, Kars A, Tekuzman G: Biochemical markers of bone turnover in diagnosis of myeloma bone disease. Am J Hematol. 2007 Mar;82(3):185-91. [PubMed:17022050 ]
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 ]
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 IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013750
KNApSAcK IDNot Available
Chemspider ID9479456
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDeoxypyridinoline
METLIN ID5552
PubChem Compound11304480
PDB IDNot Available
ChEBI ID89510
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000190
Good Scents IDNot Available
References
Synthesis ReferenceHatch, Robert P. Method for the synthesis of deoxypyridinoline. U.S. (1998), 7 pp.
Material Safety Data Sheet (MSDS)Not Available
General References