You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:22:00 UTC
Secondary Accession Numbers
  • HMDB00279
  • HMDB0062698
  • HMDB62698
Metabolite Identification
Common NameSaccharopine
DescriptionSaccharopine is an intermediate in the degradation of lysine, formed by the condensation of lysine and alpha-ketoglutarate. The saccharopine pathway is the main route for lysine degradation in mammals, and its first two reactions are catalyzed by enzymatic activities known as lysine-oxoglutarate reductase (LOR) and saccharopine dehydrogenase (SDH), which reside on a single bifunctional polypeptide (LOR/SDH) (EC The reactions involved with saccharopine dehydrogenases have very strict substrate specificity for L-lysine, 2-oxoglutarate, and NADPH. LOR/SDH has been detected in a number of mammalian tissues, mainly in the liver and kidney, contributing not only to the general nitrogen balance in the organism but also to the controlled conversion of lysine into ketone bodies. A tetrameric form has also been observed in human liver and placenta. LOR activity has also been detected in brain mitochondria during embryonic development, and this opens up the question of whether or not lysine degradation has any functional significance during brain development. As a result, there is now a new focus on the nutritional requirements for lysine in gestation and infancy. Finally, LOR and/or SDH deficiencies seem to be involved in a human autosomal genetic disorder known as familial hyperlysinemia, which is characterized by serious defects in the functioning of the nervous system and characterized by a deficiency in lysine-ketoglutarate reductase, saccharopine dehydrogenase, and saccharopine oxidoreductase activities. Saccharopinuria (high amounts of saccharopine in the urine) and saccharopinemia (an excess of saccharopine in the blood) are conditions present in some inherited disorders of lysine degradation (PMID: 463877 , 10567240 , 10772957 , 4809305 ). If present in sufficiently high levels, saccharopine can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Saccharopine is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). Many affected children with organic acidemias experience intellectual disability or delayed development.
N-[(S)-5-Amino-5-carboxypentyl]-L-glutamic acidChEBI
(S)-N-(5-Amino-5-carboxypentyl)-L-glutamic acidHMDB
L-N-(5-Amino-5-carboxypentyl)-glutamic acidHMDB
N-(5-Amino-5-carboxypentyl)-glutamic acidHMDB
N-(5-Amino-5-carboxypentyl)-L-glutamic acidHMDB
N-[(5S)-5-Amino-5-carboxypentyl]-L-glutamic acidHMDB
Chemical FormulaC11H20N2O6
Average Molecular Weight276.2863
Monoisotopic Molecular Weight276.132136382
IUPAC Name(2S)-2-{[(5S)-5-amino-5-carboxypentyl]amino}pentanedioic acid
Traditional Namesaccharopine
CAS Registry Number997-68-2
InChI Identifier
Chemical Taxonomy
Description belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentGlutamic acid and derivatives
Alternative Parents
  • Glutamic acid or derivatives
  • Alpha-amino acid
  • L-alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Amino fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Secondary amine
  • Amine
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors

Route of exposure:


Biological location:


Naturally occurring process:


Indirect biological role:

Industrial application:

Physical Properties
Experimental Properties
Melting Point247 - 250 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility5.25 g/LALOGPS
pKa (Strongest Acidic)1.44ChemAxon
pKa (Strongest Basic)10.89ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area149.95 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity63.95 m³·mol⁻¹ChemAxon
Polarizability28.14 ųChemAxon
Number of Rings0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0a4i-0923000000-1964addb7be546c2a45aSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0a4j-0913000000-49fae417f545c42253ddSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4i-0923000000-1964addb7be546c2a45aSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-0913000000-49fae417f545c42253ddSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001u-6950000000-fed481b3c49c1ab6ccd2Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-006x-9220800000-77f63e444994f915feaaSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-001i-9240000000-d841eea4ebc5da1106f7Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0a4i-0290000000-c0b375ed0505ad2eab6cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0a4i-0290000000-c0b375ed0505ad2eab6cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-9240000000-d841eea4ebc5da1106f7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06ur-0190000000-34536967c85ac70477b5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01qi-2790000000-ef0279e3d556894509f0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0019-6900000000-76748510f1b49f459cafSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0190000000-417ff61b4b14d1bfe5fcSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01u9-1490000000-b4e2c5921f08ff4ee977Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0kms-7920000000-32382165ff3ba15b14d6Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Mitochondria
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Placenta
Normal Concentrations
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
      Not Available
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedBoth
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
UrineDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)FemaleNormal details
Abnormal Concentrations
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDDB04207
Phenol Explorer Compound IDNot Available
FooDB IDFDB000461
KNApSAcK IDC00007227
Chemspider ID141086
KEGG Compound IDC00449
BiGG ID1484994
Wikipedia LinkSaccharopine
PubChem Compound160556
PDB IDNot Available
ChEBI ID16927
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
Synthesis ReferenceBurkard, Ulrike; Walther, Ingrid; Effenberger, Franz. Amino acids. 6. Investigations on the synthesis of L-saccharopin. Liebigs Annalen der Chemie (1986), (6), 1030-43.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Krieger I, Bachmann C, Gronemeyer WH, Cejka J: Propionic acidemia and hyperlysinemia in a case with ornithine transcarbamylase (OTC) deficiency. J Clin Endocrinol Metab. 1976 Oct;43(4):796-802. [PubMed:977722 ]
  2. Cederbaum SD, Shaw KN, Dancis J, Hutzler J, Blaskovics JC: Hyperlysinemia with saccharopinuria due to combined lysine-ketoglutarate reductase and saccharopine dehydrogenase deficiencies presenting as cystinuria. J Pediatr. 1979 Aug;95(2):234-8. [PubMed:571908 ]
  3. Casey RE, Zaleski WA, Philp M, Mendelson IS, MacKenzie SL: Biochemical and clinical studies of a new case of alpha-aminoadipic aciduria. J Inherit Metab Dis. 1978;1(4):129-35. [PubMed:117247 ]
  4. Dancis J, Hutzler J, Cox RP: Familial hyperlysinemia: enzyme studies, diagnostic methods, comments on terminology. Am J Hum Genet. 1979 May;31(3):290-9. [PubMed:463877 ]
  5. Papes F, Kemper EL, Cord-Neto G, Langone F, Arruda P: Lysine degradation through the saccharopine pathway in mammals: involvement of both bifunctional and monofunctional lysine-degrading enzymes in mouse. Biochem J. 1999 Dec 1;344 Pt 2:555-63. [PubMed:10567240 ]
  6. IJlst L, de Kromme I, Oostheim W, Wanders RJ: Molecular cloning and expression of human L-pipecolate oxidase. Biochem Biophys Res Commun. 2000 Apr 21;270(3):1101-5. [PubMed:10772957 ]
  7. Fellows FC, Carson NA: Enzyme studies in a patient with saccharopinuria: a defect of lysine metabolism. Pediatr Res. 1974 Jan;8(1):42-9. [PubMed:4809305 ]
  8. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]


General function:
Involved in oxidoreductase activity
Specific function:
Bifunctional enzyme that catalyzes the first two steps in lysine degradation. The N-terminal and the C-terminal contain lysine-ketoglutarate reductase and saccharopine dehydrogenase activity, respectively.
Gene Name:
Uniprot ID:
Molecular weight:
Saccharopine + NADP + Water → L-Lysine + Oxoglutaric acid + NADPH + Hydrogen Iondetails
Saccharopine + NAD + Water → L-Glutamic acid + Allysine + NADH + Hydrogen Iondetails
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
General function:
Involved in catalytic activity
Specific function:
N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD(+) + H(2)O = L-glutamate + 2-aminoadipate 6-semialdehyde + NADH
Gene Name:
Uniprot ID:
Molecular weight:
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
Uniprot ID:
Molecular weight: