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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-12 20:14:46 UTC
Update Date2021-10-13 04:41:35 UTC
HMDB IDHMDB0003405
Secondary Accession Numbers
  • HMDB03405
Metabolite Identification
Common NameD-Lysine
DescriptionD-Lysine, also known as D-lysin or DLY, belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Lysine exists in all living organisms, ranging from bacteria to humans. D-Lysine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make D-lysine a potential biomarker for the consumption of these foods. D-Lysine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on D-Lysine.
Structure
Data?1582752275
Synonyms
ValueSource
(R)-2,6-Diaminohexanoic acidChEBI
D-2,6-Diaminohexanoic acidChEBI
D-LysinChEBI
DLYChEBI
(R)-2,6-DiaminohexanoateGenerator
D-2,6-DiaminohexanoateGenerator
Chemical FormulaC6H14N2O2
Average Molecular Weight146.19
Monoisotopic Molecular Weight146.105527699
IUPAC Name(2R)-2,6-diaminohexanoic acid
Traditional NameD-lysine
CAS Registry Number923-27-3
SMILES
NCCCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1
InChI KeyKDXKERNSBIXSRK-RXMQYKEDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • D-alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point218.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point310.00 to 312.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility270000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.734 (est)The Good Scents Company Information System
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility105 g/LALOGPS
logP10(-3.8) g/LALOGPS
logP10(-3.2) g/LChemAxon
logS10(-0.14) g/LALOGPS
pKa (Strongest Acidic)2.74ChemAxon
pKa (Strongest Basic)10.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area89.34 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.81 m³·mol⁻¹ChemAxon
Polarizability15.91 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Lysine,1TMS,#1C[Si](C)(C)OC(=O)[C@H](N)CCCCN1465.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Lysine,1TMS,#2C[Si](C)(C)NCCCC[C@@H](N)C(=O)O1618.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Lysine,1TMS,#3C[Si](C)(C)N[C@H](CCCCN)C(=O)O1589.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Lysine,1TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)[C@H](N)CCCCN1694.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Lysine,1TBDMS,#2CC(C)(C)[Si](C)(C)NCCCC[C@@H](N)C(=O)O1876.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
D-Lysine,1TBDMS,#3CC(C)(C)[Si](C)(C)N[C@H](CCCCN)C(=O)O1836.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Lysine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 10V, Positive-QTOFsplash10-0f8a-2900000000-d5972dfce0860da55a0a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 20V, Positive-QTOFsplash10-0f89-9700000000-d8e3259076e214ba9a3f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 40V, Positive-QTOFsplash10-0a5c-9000000000-0b901a2eb0a82d41fc3d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 10V, Negative-QTOFsplash10-0002-0900000000-603377bb44b83d433b772016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 20V, Negative-QTOFsplash10-0002-3900000000-e5d6ccb8cd7879780faf2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 40V, Negative-QTOFsplash10-00di-9100000000-e7f9a18ab48141069fee2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 10V, Negative-QTOFsplash10-0002-0900000000-94cae94fd691bdbb4d742021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 20V, Negative-QTOFsplash10-0002-0900000000-600019f71b72fb289dee2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 40V, Negative-QTOFsplash10-0006-9000000000-bad9cb982e2df334ab552021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 10V, Positive-QTOFsplash10-001i-9600000000-dcc75a035223a66e72662021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 20V, Positive-QTOFsplash10-001i-9000000000-b8581377af4d2519e68c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Lysine 40V, Positive-QTOFsplash10-0a4i-9000000000-9e3d1f9dd58cb0efce552021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Feces
Tissue Locations
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03252
Phenol Explorer Compound IDNot Available
FooDB IDFDB023163
KNApSAcK IDNot Available
Chemspider ID51793
KEGG Compound IDC00739
BioCyc IDCPD-219
BiGG IDNot Available
Wikipedia LinkLysine
METLIN IDNot Available
PubChem Compound57449
PDB IDNot Available
ChEBI ID16855
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1107831
References
Synthesis ReferenceFurui, Masakatsu; Takahashi, Eiji; Seko, Hiroyasu. Process for preparing D-lysine. Eur. Pat. Appl. (1996), 7 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Wakisaka K, Arano Y, Uezono T, Akizawa H, Ono M, Kawai K, Ohomomo Y, Nakayama M, Saji H: A novel radioiodination reagent for protein radiopharmaceuticals with L-lysine as a plasma-stable metabolizable linkage to liberate m-iodohippuric acid after lysosomal proteolysis. J Med Chem. 1997 Aug 1;40(16):2643-52. [PubMed:9258371 ]
  2. Darling PB, Bross R, Wykes LJ, Ball RO, Pencharz PB: Isotopic enrichment of amino acids in urine following oral infusions of L-[1-(13)C]phenylalanine and L-[1-(13)C]lysine in humans: confounding effect of D-[13C]amino acids. Metabolism. 1999 Jun;48(6):732-7. [PubMed:10381147 ]
  3. Bross R, Ball RO, Pencharz PB: Development of a minimally invasive protocol for the determination of phenylalanine and lysine kinetics in humans during the fed state. J Nutr. 1998 Nov;128(11):1913-9. [PubMed:9808642 ]
  4. Hayman MW, Smith KH, Cameron NR, Przyborski SA: Growth of human stem cell-derived neurons on solid three-dimensional polymers. J Biochem Biophys Methods. 2005 Mar 31;62(3):231-40. Epub 2004 Dec 30. [PubMed:15733583 ]