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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-09-22 18:34:13 UTC
HMDB IDHMDB0000425
Secondary Accession Numbers
  • HMDB00425
Metabolite Identification
Common Name3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid
Description3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid (KDN) is a sialic acid (Sia) that is ubiquitously expressed in vertebrates during normal development and tumorigenesis. Its expression is thought to be regulated by multiple biosynthetic steps catalyzed by several enzymes, including CMP-Sia synthetase. (PMID 11479279 ) Sialic acids are frequently the terminal sugars on secreted and cell surface glycoproteins and glycolipids, and their presence can have considerable influence on the biological properties of a cell. For example, the temporal appearance and disappearance of polysialic polymers has been intimately linked with the proper development of neural tissues during embryogenesis. In pathogenic diseases, including meningitis and gastric inflammation, particular microbes recognize cell surface sialic acids when invading host cells. Sialic acid residues can also mask recognition sites such as galactose residues on glycoproteins to prevent their in vivo removal by asialoglycoprotein receptors. In certain cancers, changes in sialic acid amounts, types, and linkages have been associated with tumorogenesis and cancer metastasis. (PMID 10749855 ).
Structure
Thumb
Synonyms
Chemical FormulaC9H16O9
Average Molecular Weight268.2179
Monoisotopic Molecular Weight268.07943211
IUPAC Name(4S,5R,6R,7R,8S)-4,5,6,7,8,9-hexahydroxy-2-oxononanoic acid
Traditional NamesiaX
CAS Registry Number22594-61-2
SMILES
OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)CC(=O)C(O)=O
InChI Identifier
InChI=1S/C9H16O9/c10-2-5(13)7(15)8(16)6(14)3(11)1-4(12)9(17)18/h3,5-8,10-11,13-16H,1-2H2,(H,17,18)/t3-,5-,6+,7+,8+/m0/s1
InChI KeyFQHUAUMYHAJTDH-IMSDGWMTSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Nonose monosaccharide
  • Medium-chain keto acid
  • Sugar acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • Monosaccharide
  • Keto acid
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Carbonyl group
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022038
KNApSAcK IDNot Available
Chemspider ID17215951
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5414
PubChem Compound22833524
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDKDN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNakamura, Mitsunobu; Fujita, Shuji; Furuhata, Kimio; Ogura, Haruo. Synthesis of the nucleoside analogs of 3-deoxy-D-glycero-D-galacto-2-nonulosonic acid (KDN). Nucleic Acids Symposium Series (1991), 25(Symp. Nucleic Acids Chem., 18th, 1991), 137-9.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Lawrence SM, Huddleston KA, Pitts LR, Nguyen N, Lee YC, Vann WF, Coleman TA, Betenbaugh MJ: Cloning and expression of the human N-acetylneuraminic acid phosphate synthase gene with 2-keto-3-deoxy-D-glycero- D-galacto-nononic acid biosynthetic ability. J Biol Chem. 2000 Jun 9;275(23):17869-77. [PubMed:10749855 ]
  2. Nakata D, Munster AK, Gerardy-Schahn R, Aoki N, Matsuda T, Kitajima K: Molecular cloning of a unique CMP-sialic acid synthetase that effectively utilizes both deaminoneuraminic acid (KDN) and N-acetylneuraminic acid (Neu5Ac) as substrates. Glycobiology. 2001 Aug;11(8):685-92. [PubMed:11479279 ]

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
Gene Name:
DLD
Uniprot ID:
P09622
Molecular weight:
54176.91
General function:
Involved in oxidoreductase activity
Specific function:
Maintains thioredoxin in a reduced state. Implicated in the defenses against oxidative stress. May play a role in redox-regulated cell signaling.
Gene Name:
TXNRD2
Uniprot ID:
Q9NNW7
Molecular weight:
56506.275
General function:
Involved in oxidoreductase activity
Specific function:
Maintains high levels of reduced glutathione in the cytosol.
Gene Name:
GSR
Uniprot ID:
P00390
Molecular weight:
56256.565
General function:
Involved in lipopolysaccharide biosynthetic process
Specific function:
Catalyzes the activation of N-acetylneuraminic acid (NeuNAc) to cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-NeuNAc), a substrate required for the addition of sialic acid. Has some activity toward NeuNAc, N-glycolylneuraminic acid (Neu5Gc) or 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN).
Gene Name:
CMAS
Uniprot ID:
Q8NFW8
Molecular weight:
48378.835
General function:
Involved in catalytic activity
Specific function:
Broad specificity oxidoreductase that catalyzes the NADPH-dependent reduction of a variety of flavins, such as riboflavin, FAD or FMN, biliverdins, methemoglobin and PQQ (pyrroloquinoline quinone). Contributes to heme catabolism and metabolizes linear tetrapyrroles. Can also reduce the complexed Fe(3+) iron to Fe(2+) in the presence of FMN and NADPH. In the liver, converts biliverdin to bilirubin.
Gene Name:
BLVRB
Uniprot ID:
P30043
Molecular weight:
22119.215
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q59ET7
Molecular weight:
55217.7
General function:
Involved in oxidoreductase activity
Specific function:
NOH-1S is a voltage-gated proton channel that mediates the H(+) currents of resting phagocytes and other tissues. It participates in the regulation of cellular pH and is blocked by zinc. NOH-1L is a pyridine nucleotide-dependent oxidoreductase that generates superoxide and might conduct H(+) ions as part of its electron transport mechanism, whereas NOH-1S does not contain an electron transport chain
Gene Name:
NOX1
Uniprot ID:
Q9Y5S8
Molecular weight:
64870.5
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
PYROXD1
Uniprot ID:
Q8WU10
Molecular weight:
55792.4