Pyridinoline (CED0005797)

Record Information
Version1.0
Creation Date2016-05-25 18:14:02 UTC
Update Date2026-04-06 12:10:34 UTC
SynCED IDCED0005797
Secondary Accession Numbers
  • CHEM021853
Identification
Common NamePyridinoline
ClassSmall Molecule
Description
Pyridinoline belongs to the amino acids, peptides, and analogues, a subclass of carboxylic acids and derivatives within the organic compounds. It has the formula C18H28N4O8 and an average molecular weight of 428.44 g/mol.
Contaminant TypeNot Available
Chemical Structure
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 Mass428.437 g/mol
Monoisotopic Mass428.191 g/mol
CAS Registry Number63800-01-1
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
SMILESN[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 IdentifierInChI=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
Biological Properties
StatusDetected and Not Quantified
OriginNot Available
Cellular LocationsNot Available
Biofluid LocationsNot Available
Tissue LocationsNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Organoleptic EffectsNot Available
Physical Properties
StateNot Available
AppearanceNot Available
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot 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
Spectra
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Predicted GC-MSPredicted GC-MS Spectrumsplash10-001i-1139100000-5d8fc20ccc7b98532363Not AvailableView Spectrum
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Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-004i-1100900000-c38c200cd8e6b732fd69Not AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-00di-7921000000-79aa7de87908b35ae0f5Not AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-01si-0049600000-efbf48db5b13ec3bbc8cNot AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-00m1-0079100000-8c7b3a51061cf35c058dNot AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-0bt9-5191000000-2ca942a932b82f93dd7aNot AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-0arr-1046900000-0dcaf90573f090897648Not AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-0feb-6795000000-c3f12a8a1fc8ebb5c46eNot AvailableView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrumsplash10-0006-7593000000-56e695190149fe7749c2Not AvailableView Spectrum
1D NMR13C NMR Spectrum (1D, D2O, predicted)Not AvailableNot AvailableView Spectrum
1D NMR1H NMR Spectrum (1D, D2O, predicted)Not AvailableNot AvailableView Spectrum
Toxicity Profile
Toxicity Values
Toxicity ValueOrganismDose DescriptorRoute of ExposurePredicted or ExperimentalToxicity RatingReference
3785.0 Log mg/kg [2100:6700]RatLD50oralpredictedNot AvailableNot Available
Toxicity / Toxin ClassNot Available
Mechanism of ToxicityNot Available
Carcinogenicity (IARC Classification)Not Available
Minimum Risk LevelNot Available
SymptomsNot Available
TreatmentNot Available
Health Effects
Health EffectRelationshipDirectionDescriptionReference
multiple myelomaNot AvailableNot AvailableA myeloid neoplasm that is located in the plasma cells in bone marrow. (DO)PMC6223128 , PMC11215383
neutropeniaAssociated With?Not AvailableA disorder characterized by an abnormally low level of neutrophils.PMC11215383
thrombocytopeniaAssociated With?Not AvailableNot AvailablePMC11215383
pneumoniaAssociated With?Not AvailableA lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing. (DO)PMC11215383
Exposure Sources
Source IDSourceSectorReference
CEDs000010Insecticides?Insecticides are synthetic chemicals designed to control or eliminate insect pests that threaten crops and other agricultural products.Agriculture & land managementPubChem
CEDs000013Soil?Soil serves as a critical medium for plant growth and sustains various ecological functions; however, it can become a reservoir for synthetic chemical contamination.Agriculture & land managementPMC8894337 , PMC8894337
CEDs000233Brushes?Brushes used in personal care and cosmetics can be a source of synthetic chemical contamination due to the materials and coatings used in their manufacturing.Personal care & cosmeticsPubChem
CEDs000468Industrial wastewater?Industrial wastewater is a byproduct generated during various manufacturing and processing activities, which often contains a complex mixture of organic and inorganic synthetic chemicals.Wastewater, sanitation & biosolidsPMC10902511
CEDs000519Electrodes?Electrodes, used in various electrical and electronic applications, can be a source of synthetic chemical contamination due to the materials from which they are constructed and the processes involved in their manufacturing.Electrical & Electronic EquipmentPubChem
CEDs000521Fixed Capacitors And Their Manufacture?Fixed capacitors are passive electronic components used to store and release electrical energy, playing a critical role in various circuits.Electrical & Electronic EquipmentPubChem
CEDs000545Food Preservation?Food preservation often involves the use of synthetic chemicals, such as preservatives, flavor enhancers, and color additives, to extend shelf life and enhance the sensory qualities of food products.Food, food processing & cookwarePubChem
CEDs000561Perfumes Within Detergents And Soaps?Perfumes within detergents and soaps are synthetic fragrance compounds added to enhance the sensory experience of cleaning products.Household cleaning & consumer productsPubChem
CEDs000596Acaricides?Acaricides are synthetic chemicals specifically designed to target and control mite populations that can damage crops and plants.Agriculture & land managementPubChem
CEDs000606Plant Growth Regulators?Plant Growth Regulators (PGRs) are synthetic chemicals designed to influence the growth and development of plants.Agriculture & land managementPubChem
CEDs000610Aftersun Products?Aftersun products are designed to soothe and hydrate the skin after sun exposure, often containing various synthetic chemicals such as emollients, preservatives, and fragrances.Personal care & cosmeticsPubChem
CEDs000614Essential Oils Or Perfumes?Essential oils and perfumes are complex mixtures of volatile compounds derived from natural or synthetic sources, commonly used for their aromatic properties.Personal care & cosmeticsPubChem
CEDs000632Apparel?Apparel production often involves the use of various synthetic chemicals, including dyes, finishing agents, and preservatives.Textiles, leather & furnishingsPubChem
CEDs000684Cements?Cements are a composite material primarily used as a binding agent in construction applications, formed by the calcination of limestone and clay minerals at high temperatures.Building & ConstructionPubChem
CEDs000696Nanotechnology?Nanotechnology involves the manipulation of materials at the molecular or atomic level, typically within the range of 1 to 100 nanometers.Industrial manufacturing & chemical processingPubChem
CEDs000735Explosives?Explosives are chemical compounds or mixtures designed to undergo rapid decomposition, releasing energy in the form of gas and heat.Defense & military infrastructurePubChem
CEDs000739Inks?Inks are complex mixtures composed of pigments or dyes, solvents, resins, and additives used primarily for printing and writing applications.Paper, pulp & fiber productsPubChem
CEDs000740Paper?Paper production involves the processing of wood fibers and the use of various chemicals, which can lead to synthetic chemical contamination.Paper, pulp & fiber productsPubChem
CEDs000744Water, Wastewater, & Sewage Treatment?Water, wastewater, and sewage treatment processes are critical for managing and mitigating pollutants in water systems.Wastewater, sanitation & biosolidsPubChem
CEDs01170EggsFood, food processing & cookwarePMC11393805
CEDs01195YogurtFood, food processing & cookwarePMC12197317
CEDs01375Skim MilkFood, food processing & cookwarePMC11393805
CEDs01502White BreadFood, food processing & cookwarePMC11393805
CEDs02255WaterAquatic systems & sedimentsPMC8038380 , PMC11393805
CEDs02264SedimentAquatic systems & sedimentsPMC13005872 , PMC11393805
CEDs02265River WaterAquatic systems & sedimentsPMC11393805
CEDs02289StreamAquatic systems & sedimentsPMC13005872
CEDs02330River SedimentsAquatic systems & sedimentsPMC11393805
CEDs02498Marine DebrisAquatic systems & sedimentsPMC11187594
CEDs02592PM2.5Air, dust & atmospheric transportPMC10022636
CEDs02629PM10Air, dust & atmospheric transportPMC10022636
CEDs03009Waste WaterWastewater, sanitation & biosolidsPMC12940842
CEDs03292Roadside DustAutomotive & urban infrastructurePMC11393805
Pathways
0 pathwaysPathway Source: PathBank

No pathways found

No metabolic pathways have been associated with this synthetic chemical

Targets
StructureProteinUniProt IDOrganismRelationshipDetails
Glutamate receptor 1 structureClick to view 3D structureGlutamate receptor 1P42261HumansPredicted (SEA)
Prediction Confidence Score
0.278
Applicability Domain
0.295 Low confidence
Statistical Significance
0.0011
Supporting Reference Compounds
37
E-value
8.40772
Click to view 3D structureGlutamate receptor 3P42263HumansPredicted (SEA)
Prediction Confidence Score
0.278
Applicability Domain
0.295 Low confidence
Statistical Significance
4.30e-04
Supporting Reference Compounds
16
E-value
3.34752
Glutamate receptor ionotropic, kainate 1 structureClick to view 3D structureGlutamate receptor ionotropic, kainate 1P39086HumansPredicted (SEA)
Prediction Confidence Score
0.277
Applicability Domain
0.295 Low confidence
Statistical Significance
7.50e-04
Supporting Reference Compounds
31
E-value
5.83869
Click to view 3D structureGlutamate receptor 4P48058HumansPredicted (SEA)
Prediction Confidence Score
0.277
Applicability Domain
0.295 Low confidence
Statistical Significance
5.90e-04
Supporting Reference Compounds
25
E-value
4.5931
Click to view 3D structureGlutamate receptor ionotropic, kainate 5Q16478HumansPredicted (SEA)
Prediction Confidence Score
0.272
Applicability Domain
0.295 Low confidence
Statistical Significance
5.70e-04
Supporting Reference Compounds
17
E-value
4.43741
Glutamate receptor 2 structureClick to view 3D structureGlutamate receptor 2P42262HumansPredicted (SEA)
Prediction Confidence Score
0.272
Applicability Domain
0.288 Low confidence
Statistical Significance
8.80e-04
Supporting Reference Compounds
41
E-value
6.85073
Glutamate receptor ionotropic, kainate 3 structureClick to view 3D structureGlutamate receptor ionotropic, kainate 3P42264Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.268
Applicability Domain
0.295 Low confidence
Statistical Significance
0.0013
Supporting Reference Compounds
26
E-value
10.5096
Click to view 3D structureS-methylmethionine--homocysteine S-methyltransferase BHMT2Q9H2M3HumansPredicted (SEA)
Prediction Confidence Score
0.263
Applicability Domain
0.263 Low confidence
Statistical Significance
5.00e-04
Supporting Reference Compounds
1
E-value
3.89246
Click to view 3D structureGlutamate receptor ionotropic kainate 2B9V8S1Xenopus laevisPredicted (SEA)
Prediction Confidence Score
0.262
Applicability Domain
0.295 Low confidence
Statistical Significance
1.20e-04
Supporting Reference Compounds
2
E-value
0.934191
Glutamate receptor ionotropic, kainate 2 structureClick to view 3D structureGlutamate receptor ionotropic, kainate 2P42260Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.25
Applicability Domain
0.288 Low confidence
Statistical Significance
8.40e-04
Supporting Reference Compounds
18
E-value
6.53933
Click to view 3D structureMetabotropic glutamate receptor 8P47743Mus musculusPredicted (SEA)
Prediction Confidence Score
0.248
Applicability Domain
0.255 Low confidence
Statistical Significance
8.90e-04
Supporting Reference Compounds
2
E-value
6.92858
Metabotropic glutamate receptor 4 structureClick to view 3D structureMetabotropic glutamate receptor 4Q14833HumansPredicted (SEA)
Prediction Confidence Score
0.246
Applicability Domain
0.255 Low confidence
Statistical Significance
0.0337
Supporting Reference Compounds
69
E-value
262.585
Metabotropic glutamate receptor 8 structureClick to view 3D structureMetabotropic glutamate receptor 8O00222HumansPredicted (SEA)
Prediction Confidence Score
0.244
Applicability Domain
0.255 Low confidence
Statistical Significance
0.0063
Supporting Reference Compounds
48
E-value
48.7336
Click to view 3D structureMetabotropic glutamate receptor 6O15303HumansPredicted (SEA)
Prediction Confidence Score
0.243
Applicability Domain
0.255 Low confidence
Statistical Significance
0.0082
Supporting Reference Compounds
39
E-value
64.2256
Click to view 3D structureKynureninaseP70712Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.242
Applicability Domain
0.242 Low confidence
Statistical Significance
0.0028
Supporting Reference Compounds
1
E-value
22.0313
Click to view 3D structureMetabotropic glutamate receptor 6P35349Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.241
Applicability Domain
0.255 Low confidence
Statistical Significance
0.0042
Supporting Reference Compounds
24
E-value
32.9302
Click to view 3D structureMetabotropic glutamate receptor 4P31423Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.24
Applicability Domain
0.255 Low confidence
Statistical Significance
0.0262
Supporting Reference Compounds
38
E-value
204.199
Click to view 3D structureS-ribosylhomocysteine lyaseP45578Escherichia coli K-12Predicted (SEA)
Prediction Confidence Score
0.238
Applicability Domain
0.238 Low confidence
Statistical Significance
5.50e-04
Supporting Reference Compounds
1
E-value
4.28171
Click to view 3D structureS-ribosylhomocysteine lyaseQ9Z5X1Vibrio campbelliiPredicted (SEA)
Prediction Confidence Score
0.238
Applicability Domain
0.238 Low confidence
Statistical Significance
5.50e-04
Supporting Reference Compounds
1
E-value
4.28171
Tyrosine 3-monooxygenase structureClick to view 3D structureTyrosine 3-monooxygenaseP04177Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.288
Applicability Domain
0.288 Low confidence
Statistical Significance
5.80e-04
Supporting Reference Compounds
1
E-value
4.51525
Glutamate receptor 3 structureClick to view 3D structureGlutamate receptor 3P19492Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.28
Applicability Domain
0.295 Low confidence
Statistical Significance
5.10e-04
Supporting Reference Compounds
30
E-value
3.97031
Glutamate receptor 2 structureClick to view 3D structureGlutamate receptor 2P19491Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.28
Applicability Domain
0.295 Low confidence
Statistical Significance
5.10e-04
Supporting Reference Compounds
34
E-value
3.97031
Glutamate receptor 4 structureClick to view 3D structureGlutamate receptor 4P19493Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.28
Applicability Domain
0.295 Low confidence
Statistical Significance
4.20e-04
Supporting Reference Compounds
25
E-value
3.26967
Glutamate receptor 1 structureClick to view 3D structureGlutamate receptor 1P19490Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.28
Applicability Domain
0.295 Low confidence
Statistical Significance
0.0049
Supporting Reference Compounds
37
E-value
38.5354
Glutamate receptor ionotropic, kainate 1 structureClick to view 3D structureGlutamate receptor ionotropic, kainate 1P22756Rattus norvegicusPredicted (SEA)
Prediction Confidence Score
0.279
Applicability Domain
0.295 Low confidence
Statistical Significance
0.0013
Supporting Reference Compounds
45
E-value
9.809
Concentrations
Not Available
External Links
DrugBank IDNot Available
HMDB IDHMDB0000851
FooDB IDFDB010805
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG IDNot Available
BioCyc IDNot Available
METLIN ID5814
PDB IDNot Available
Wikipedia LinkPyridinoline
Chemspider ID94798
ChEBI ID88539
PubChem Compound ID105068
Kegg Compound IDNot Available
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General ReferencesNot Available