Human Metabolome Database Version 3.5

Showing metabocard for Saccharopine (HMDB00279)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:25:20 -0600
HMDB ID HMDB00279
Secondary Accession Numbers None
Metabolite Identification
Common Name Saccharopine
Description Saccharopine is an intermediate in the degradation of lysine, formed by condensation of lysine and alpha-ketoglutarate. The saccharopine pathway is the main route for lysine degradation in mammal 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 (EC EC 1.5.1.8, LOR/SDH). The reactions involved by saccharopine dehydrogenases have a 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 the question of whether the degradation of lysine has any functional significance during brain development and puts 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 autosomic genetic disorder known as familial hyperlysinemia, which is characterized by serious defects in the functioning of the nervous system, and characterized by 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 Link_out, 10567240 Link_out, 10772957 Link_out, 4809305 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (S)-N-(5-amino-5-carboxypentyl)-L-Glutamic acid
  2. epsilon-N-(L-Glutar-2-yl)-L-lysine
  3. L-N-(5-Amino-5-carboxypentyl)-Glutamic acid
  4. L-Saccharopin
  5. L-Saccharopine
  6. N(6)-(L-1,3-Dicarboxypropyl)-L-lysine
  7. N-(5-Amino-5-carboxypentyl)-glutamic acid
  8. N-(5-Amino-5-carboxypentyl)-L-glutamic acid
  9. N-[(5S)-5-Amino-5-carboxypentyl]-L-Glutamic acid
  10. N6-(L-1,3-Dicarboxypropyl)-L-lysine
  11. Saccharopin
Chemical Formula C11H20N2O6
Average Molecular Weight 276.2863
Monoisotopic Molecular Weight 276.132136382
IUPAC Name (2S)-2-{[(5S)-5-amino-5-carboxypentyl]amino}pentanedioic acid
Traditional IUPAC Name saccharopine
CAS Registry Number 997-68-2
SMILES N[C@@H](CCCCN[C@@H](CCC(O)=O)C(O)=O)C(O)=O
InChI Identifier InChI=1S/C11H20N2O6/c12-7(10(16)17)3-1-2-6-13-8(11(18)19)4-5-9(14)15/h7-8,13H,1-6,12H2,(H,14,15)(H,16,17)(H,18,19)/t7-,8-/m0/s1
InChI Key ZDGJAHTZVHVLOT-YUMQZZPRSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Amino Acids, Peptides, and Analogues
Class Amino Acids and Derivatives
Sub Class Alpha Amino Acids and Derivatives
Other Descriptors
  • Aliphatic Acyclic Compounds
  • Amino Fatty Acids
  • Organic Compounds
Substituents
  • Carboxylic Acid
  • Polyamine
  • Primary Aliphatic Amine (Alkylamine)
  • Secondary Aliphatic Amine (Dialkylamine)
  • Tricarboxylic Acid Derivative
Direct Parent Alpha Amino Acids and Derivatives
Ontology
Status Detected and Not Quantified
Origin
  • Endogenous
Biofunction
  • Protein synthesis, amino acid biosynthesis
Application Not Available
Cellular locations
  • Mitochondria
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 247 - 250 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 5.25 g/L ALOGPS
LogP -2.77 ALOGPS
LogP -5.4 ChemAxon
LogS -1.72 ALOGPS
pKa (strongest acidic) 1.44 ChemAxon
pKa (strongest basic) 10.89 ChemAxon
Hydrogen Acceptor Count 8 ChemAxon
Hydrogen Donor Count 5 ChemAxon
Polar Surface Area 149.95 A2 ChemAxon
Rotatable Bond Count 11 ChemAxon
Refractivity 63.95 ChemAxon
Polarizability 27.98 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -1 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Mitochondria
Biofluid Locations
  • Blood
  • Urine
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Lysine Degradation SMP00037 map00310 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Expected but not Quantified
Not Applicable Not Available Not Available Comment Normal
  • Not Applicable
Urine Detected but not Quantified
Not Applicable Children (1-13 year old) Female Normal
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID DB04207 Link_out
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB000461
KNApSAcK ID C00007227 Link_out
Chemspider ID 141086 Link_out
KEGG Compound ID C00449 Link_out
BioCyc ID SACCHAROPINE Link_out
BiGG ID 1484994 Link_out
Wikipedia Link Saccharopine Link_out
NuGOwiki Link HMDB00279 Link_out
Metagene Link HMDB00279 Link_out
METLIN ID 383 Link_out
PubChem Compound 160556 Link_out
PDB ID SHR Link_out
ChEBI ID 16927 Link_out
References
Synthesis Reference Burkard, 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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out

Enzymes
Name: Alpha-aminoadipic semialdehyde synthase, mitochondrial
Reactions:
Saccharopine + NADP + Water unknown L-Lysine + Oxoglutaric acid + NADPH + Hydrogen Ion details
Saccharopine + NAD + Water unknown L-Glutamic acid + (S)-2-amino-6-oxohexanoate + NADH + Hydrogen Ion details
Gene Name: AASS
Uniprot ID: Q9UDR5 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Probable saccharopine dehydrogenase
Reactions: Not Available
Gene Name: SCCPDH
Uniprot ID: Q8NBX0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Aminoadipate-semialdehyde synthase
Reactions: Not Available
Gene Name: AASS
Uniprot ID: A4D0W4 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA