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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-06-10 21:22:21 UTC
HMDB IDHMDB00450
Secondary Accession Numbers
  • 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
5-HYDROXYLYSINEChEBI
alpha,epsilon-diamino-delta-Hydroxycaproic acidChEBI
L-erythro-5-HydroxylysineChEBI
L-Normal-5-hydroxylysineChEBI
(2S,5R)-2,6-diamino-5-HydroxyhexanoateGenerator
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
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
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 KeyInChIKey=YSMODUONRAFBET-UHNVWZDZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Hydroxy fatty acid
  • L-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Protein synthesis, amino acid biosynthesis
ApplicationNot Available
Cellular locations
  • Cytoplasm
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 Solubility124.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity39.17 m3·mol-1ChemAxon
Polarizability16.55 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
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
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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
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
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.50 +/- 0.028 uMElderly (>65 years old)BothAlzheimer's disease details
UrineDetected and Quantified7.262 +/- 2.023 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
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. [17031479 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB012682
KNApSAcK IDNot Available
Chemspider ID2297721
KEGG Compound IDC16741
BioCyc IDCPD-7689
BiGG ID53055
Wikipedia LinkHydroxylysine
NuGOwiki LinkHMDB00450
Metagene LinkHMDB00450
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. [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. [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. [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