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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2018-03-28 17:02:59 UTC
HMDB IDHMDB0000450
Secondary Accession Numbers
  • HMDB0006827
  • HMDB00450
  • HMDB06827
Metabolite Identification
Common Name5-Hydroxylysine
Description5-Hydroxylysine is a hydroxylated derivative of the amino acid lysine that is present in certain collagens. Hydroxylysine is an amino acid and is most widely known as a component of collagen. A standard amino acid with the R' group consisting of an amino terminated butyl hydrocarbon chain, with a hydroxyl group on the carbon atom before the amino group.
Structure
Thumb
Synonyms
ValueSource
(2S,5R)-5-HydroxylysineChEBI
(5R)-5-Hydroxy-L-lysineChEBI
alpha,epsilon-diamino-delta-Hydroxycaproic acidChEBI
L-erythro-5-HydroxylysineChEBI
L-Normal-5-hydroxylysineChEBI
a,epsilon-diamino-delta-HydroxycaproateGenerator
a,epsilon-diamino-delta-Hydroxycaproic acidGenerator
alpha,epsilon-diamino-delta-HydroxycaproateGenerator
α,epsilon-diamino-δ-hydroxycaproateGenerator
α,epsilon-diamino-δ-hydroxycaproic acidGenerator
a,epsilon-diamino-δ-hydroxycaproateGenerator
a,epsilon-diamino-δ-hydroxycaproic acidGenerator
(2S,5R)-2,6-diamino-5-HydroxyhexanoateHMDB
(2S,5R)-2,6-diamino-5-Hydroxyhexanoic acidHMDB
5-Hydroxy-L-lysineHMDB
5-Hydroxy-lysineHMDB
D-Hydroxy-L-lysineHMDB
D-HydroxylysineHMDB
delta-DL-HydroxylysineHMDB
delta-Hydroxy-L-lysineHMDB
delta-HydroxylysineHMDB
erythro-5-Hydroxy-L-lysineHMDB
Hydroxy-lysineHMDB
HydroxylysineHMDB
L-D-HydroxylysineHMDB
L-delta-HydroxylysineHMDB
Procollagen 5-hydroxy-L-lysineHMDB
Procollagen L-erythro-5-hydroxy-L-lysineHMDB
2,6-diamino-5-Hydroxyhexanoic acidMeSH
Chemical FormulaC6H14N2O3
Average Molecular Weight162.187
Monoisotopic Molecular Weight162.100442324
IUPAC Name(2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
Traditional NameL-hydroxylysine
CAS Registry Number1190-94-9
SMILES
NC[C@H](O)CC[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H14N2O3/c7-3-4(9)1-2-5(8)6(10)11/h4-5,9H,1-3,7-8H2,(H,10,11)/t4-,5+/m1/s1
InChI KeyYSMODUONRAFBET-UHNVWZDZSA-N
Chemical Taxonomy
DescriptionThis compound 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
  • Medium-chain fatty acid
  • Amino fatty acid
  • Hydroxy fatty acid
  • Fatty acyl
  • Fatty acid
  • 1,2-aminoalcohol
  • Amino acid
  • Secondary alcohol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility23 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility124 g/LALOGPS
logP-3.8ALOGPS
logP-4.4ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)2.45ChemAxon
pKa (Strongest Basic)9.75ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area109.57 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity39.17 m³·mol⁻¹ChemAxon
Polarizability16.55 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9100000000-81a6012646b8f5a82841View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0ukc-9370000000-6e3c7f27f020c40d5deaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-1900000000-af0587f21cf098832243View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-e76f81591af86b08b817View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-cc12ca7d17e7da426b8eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-2900000000-35cede633d459f50ae78View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-6900000000-b73caf4bbd05704b8925View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9200000000-fb4fab4226b28fff337cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0900000000-87768bb99db94b42d449View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03ec-3900000000-a25ff2e4de71d6d51ba5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00fr-9300000000-7dbaec809eb754d6a850View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0-2.5 uMNewborn (0-30 days old)Both
Normal
    • BC Children's Hos...
details
BloodDetected and Quantified0-2.5 uMInfant (1 - 3 months old)Both
Normal
    • BC Children's Hos...
details
BloodDetected and Quantified0-2.5 uMChildren (3 months - 6 years old)Both
Normal
    • BC Children's Hos...
details
BloodDetected and Quantified0-2.5 uMChildren (6 - 18 years old)Both
Normal
    • BC Children's Hos...
details
BloodDetected and Quantified2.5 (1.8-3.2) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Cerebrospinal Fluid (CSF)Detected and Quantified0-0.8 uMChildren (0 - 10 years old)Both
Normal
    • BC Children's Hos...
details
Cerebrospinal Fluid (CSF)Detected and Quantified0-0.8 uMAdolescent (>11 years old)Both
Normal
    • BC Children's Hos...
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Not SpecifiedBoth
Normal
details
FecesDetected but not Quantified Adult (>18 years old)FemaleNormal details
UrineDetected and Quantified4.97 - 116.90 umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified2.04 - 71.91 umol/mmol creatinineInfant (1 - 6 months old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified2.04 - 71.91 umol/mmol creatinineInfant (6 months - <1 year old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified2.04 - 71.91 umol/mmol creatinineChildren (1 - 2 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified0 - 8.03 umol/mmol creatinineChildren (2 - 4 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified0 - 8.03 umol/mmol creatinineChildren (4 - 13 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified0 - 8.03 umol/mmol creatinineAdolescent (13 - 21 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified0 - 8.03 umol/mmol creatinineAdult (>21 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified0.11 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.78-1.2 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified1.0 (0.45-2.26) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.82-1.2 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified0.35 +/- 0.62 umol/mmol creatinineInfant (0-1 year old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.50 +/- 0.028 uMElderly (>65 years old)BothAlzheimer's disease details
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
UrineDetected and Quantified20.963 umol/mmol creatinineAdolescent (13-18 years old)MaleHydroxylysinuria details
UrineDetected and Quantified7.262 +/- 2.023 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified5.507-7.110 umol/mmol creatinineAdolescent (13-18 years old)MaleHydroxylysinuria details
Associated Disorders and Diseases
Disease References
Alzheimer's disease
  1. Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed:17031479 ]
Hydroxylysinuria
  1. Hoefnagel D, Pomeroy J: Hydroxylysinuria. Lancet. 1970 Jun 20;760(1):1342-3. [PubMed:4194840 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012682
KNApSAcK IDNot Available
Chemspider ID2297721
KEGG Compound IDC16741
BioCyc IDCPD-14226
BiGG ID53055
Wikipedia LinkNot Available
METLIN ID5439
PubChem Compound3032849
PDB IDLYZ
ChEBI ID18040
References
Synthesis ReferenceAllevi, P.; Anastasia, M. Synthesis of all four possible stereoisomers of 5-hydroxylysine. Tetrahedron: Asymmetry (2000), 11(15), 3151-3160.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  2. Ohdoi C, Nyhan WL, Kuhara T: Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 15;792(1):123-30. [PubMed:12829005 ]
  3. Schor DS, Verhoeven NM, Struys EA, ten Brink HJ, Jakobs C: Quantification of 3-hydroxyglutaric acid in urine, plasma, cerebrospinal fluid and amniotic fluid by stable-isotope dilution negative chemical ionization gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Nov 15;780(1):199-204. [PubMed:12383496 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.
Gene Name:
PLOD1
Uniprot ID:
Q02809
Molecular weight:
83549.55
General function:
Involved in oxidoreductase activity
Specific function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.
Gene Name:
PLOD2
Uniprot ID:
O00469
Molecular weight:
84685.07
General function:
Involved in oxidoreductase activity
Specific function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.
Gene Name:
PLOD3
Uniprot ID:
O60568
Molecular weight:
84784.505
General function:
Not Available
Specific function:
Catalyzes the GTP-dependent phosphorylation of 5-hydroxy-L-lysine.
Gene Name:
AGPHD1
Uniprot ID:
A2RU49
Molecular weight:
41932.82
Reactions
Guanosine triphosphate + 5-Hydroxylysine → Guanosine diphosphate + 5-phosphonooxy-L-lysinedetails