Bovine Metabolome Database: Showing metabocard for 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid (BMDB0000425)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:30:32 UTC

Update Date

2020-04-22 15:03:32 UTC

BMDB ID

BMDB0000425

Secondary Accession Numbers

BMDB00425

Metabolite Identification

Common Name

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

Description

3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid, also known as 2-KDN or 2-keto-3-deoxy-D-glycero-D-galacto-NONONate, 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. 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

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

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0r00-9740000000-c930432b896f25d4d1ae	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-03di-3234029000-d1022a9541c88b2f1a32	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_4_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_4_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_15) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_16) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_24) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_5_36) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid,4TBDMS,#7" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0v4i-2390000000-e93669a48299b1218c95	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ir0-9410000000-0a259af5426f14d78fe5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074l-9100000000-2b12c65b43609f80c27e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-052k-9740000000-c5b31710f8ea5790c599	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052r-9600000000-a7365904eac0c55dc059	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0btl-9300000000-4c90c187ac68bf1ec40a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-016s-2960000000-c973ce8f4b6eb9a09b83	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zj0-6900000000-ec6b6fdadbc150dbc165	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9000000000-9c3207c739457b16a779	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gb9-1970000000-a4f86ecfad5d0922bdf8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0w30-5900000000-0142aa21eb8b357d7d77	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03mi-9100000000-172be348fc5231e8e7f1	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Not Available

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

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

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.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid (BMDB0000425)

Structure for BMDB0000425 (3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid)