Bovine Metabolome Database: Showing metabocard for Pyridinoline (BMDB0000851)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:37:31 UTC

Update Date

2020-05-11 20:48:06 UTC

BMDB ID

BMDB0000851

Secondary Accession Numbers

BMDB00851

Metabolite Identification

Common Name

Pyridinoline

Description

Pyridinoline 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. Based on a literature review a significant number of articles have been published on Pyridinoline.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(+)-Pyridinoline	HMDB
1-(2S)-(+)-Pyridinoline	HMDB
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	HMDB
Hydroxylysylpyridinoline	HMDB
Hydroxylysyl pyridinoline	HMDB
Pyridinoline	MeSH

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 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

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

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
logP	-3.9	ALOGPS
logP	-13	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	0.73	ChemAxon
pKa (Strongest Basic)	9.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	237.13 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	114.84 m³·mol⁻¹	ChemAxon
Polarizability	43.12 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-1139100000-5d8fc20ccc7b98532363	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-001u-3200292000-91125c23cde5753b8015	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_47) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_4_47) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Pyridinoline,4TMS,#47" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0001900000-1071214d48bc921584a2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00ba-0009400000-b7f8b4454b46b9b588a6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-054t-1429200000-e0435f18dbbf7dca10c3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0000900000-843d31dfa041aff3e01e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-1100900000-c38c200cd8e6b732fd69	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-7921000000-79aa7de87908b35ae0f5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01si-0049600000-efbf48db5b13ec3bbc8c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00m1-0079100000-8c7b3a51061cf35c058d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0bt9-5191000000-2ca942a932b82f93dd7a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0arr-1046900000-0dcaf90573f090897648	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0feb-6795000000-c3f12a8a1fc8ebb5c46e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-7593000000-56e695190149fe7749c2	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Bladder
Cartilage
Epidermis
Fibroblasts
Prostate Tissue

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Bladder	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Cartilage	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000851

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB010805

KNApSAcK ID

Not Available

Chemspider ID

94798

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pyridinoline

METLIN ID

5814

PubChem Compound

105068

PDB ID

Not Available

ChEBI ID

88539

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

Not Available

Showing metabocard for Pyridinoline (BMDB0000851)

Structure for BMDB0000851 (Pyridinoline)