ChemFOnt: Showing chemical card for 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid (CFc000000323)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:44:41 UTC

Chemfont ID

CFc000000323

Molecule Identification

Common Name

3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid

Definition

3-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

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3-Deoxy-D-glycero-D-galacto-2-nonulosonate	Generator
2-KDN	HMDB
2-Keto-3-deoxy-D-glycero-D-galacto-NONONate	HMDB
2-Keto-3-deoxy-D-glycero-D-galacto-NONONic acid	HMDB
2-oxo-3-Deoxy-D-glycero-galactononulosonate	HMDB
2-oxo-3-Deoxy-D-glycero-galactononulosonic acid	HMDB
3-Deoxy-D-glycero-D-galacto-nonulosonate	HMDB
3-Deoxy-D-glycero-D-galacto-nonulosonic acid	HMDB
3-Deoxyglycero-galacto-nonulosonate	HMDB
3-Deoxyglycero-galacto-nonulosonic acid	HMDB
3-Deoxyglycerogalacto-2-nonulopyranosonate	HMDB
3-Deoxyglycerogalacto-2-nonulopyranosonic acid	HMDB
Deoxy-KDN	HMDB
KDN	HMDB
Sialosonate	HMDB
Sialosonic acid	HMDB
SiaX	HMDB
(4S,5R,6R,7R,8S)-4,5,6,7,8,9-Hexahydroxy-2-oxononanoate	HMDB
3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid	MeSH

Chemical Formula

C₉H₁₆O₉

Average Molecular Weight

268.2179

Monoisotopic Molecular Weight

268.07943211

IUPAC Name

(4S,5R,6R,7R,8S)-4,5,6,7,8,9-hexahydroxy-2-oxononanoic acid

Traditional Name

siaX

CAS Registry Number

22594-61-2

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 Key

FQHUAUMYHAJTDH-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar 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 Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0000425)

Source

Endogenous

Endogenous (HMDB: HMDB0000425)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	55.2 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-3.7	ChemAxon
logS	-0.69	ALOGPS
pKa (Strongest Acidic)	2.84	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	175.75 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	54.2 m³·mol⁻¹	ChemAxon
Polarizability	23.7 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0000425

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022038

KNApSAcK ID

Not Available

Chemspider ID

17215951

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5414

PubChem Compound

22833524

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Nakamura, 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.

Showing chemical card for 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid (CFc000000323)

MOL for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

3D MOL for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

3D SDF for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

3D-SDF for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

PDB for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

3D PDB for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

SMILES for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

INCHI for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

Structure for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)

3D Structure for CFc000000323 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)