P. aeruginosa Metabolome Database: 3-Deoxy-D-manno-octulosonate (PAMDB000918)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000918

Identification

Name:

3-Deoxy-D-manno-octulosonate

Description:

3-deoxy-D-manno-octulosonate is a member of the chemical class known as Octoses. These are monosaccahride compounds in which the sugar moiety is an octose (8 carbon atoms). 3-Deoxy-D-manno-octulosonic acid (KDO) is an eight-carbon sugar ubiquitous in Gram-negative bacterial lipopolysaccharides (LPS). (PMID 20801884) The enzyme 3-deoxy-D-manno-octulosonic acid (KDO) transferase is encoded by the kdtA gene of Pseudomonas aeruginosa and plays a key role in lipopolysaccharide biosynthesis.(PMID 1577828) KDO is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. (PMID 19726684) KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria. (PMID 10734095)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

2-Dehydro-3-deoxy-D-octonate
2-Dehydro-3-deoxy-D-octonic acid
2-Keto-3-deoxy-D-manno-octonate
2-Keto-3-deoxy-D-manno-octonic acid
2-Keto-3-deoxyoctonate
2-Keto-3-deoxyoctonic acid
2-Keto-3-deoxyoctulosonate
2-Keto-3-deoxyoctulosonic acid
3-Deoxy-2-Octulosonate
3-Deoxy-2-Octulosonic acid
3-Deoxy-a-D-manno-2-octulosonate
3-Deoxy-a-D-manno-2-octulosonic acid
3-Deoxy-alpha-D-manno-2-octulosonate
3-Deoxy-alpha-D-manno-2-octulosonic acid
3-Deoxy-D-manno-2-octulosonate
3-Deoxy-D-manno-2-octulosonic acid
3-deoxy-D-manno-octulosonate
3-Deoxy-D-manno-octulosonic acid
3-Deoxy-D-mannoctulosonate
3-Deoxy-D-mannoctulosonic acid
3-Deoxy-D-mannooctulosonate
3-Deoxy-D-mannooctulosonic acid
3-Deoxy-α-D-manno-2-octulosonate
3-Deoxy-α-D-manno-2-octulosonic acid
3-Deoxyoctulosonate
3-Deoxyoctulosonic acid
3-KDO
Deoxy-manno-octulosonate
Deoxy-manno-octulosonic acid
DManOA
KDO
Ketodeoxyoctonate
Ketodeoxyoctonic acid

Chemical Formula:

C₈H₁₃O₈

Average Molecular Weight:

237.185

Monoisotopic Molecular Weight:

237.061590959

InChI Key:

KYQCXUMVJGMDNG-UHFFFAOYSA-M

InChI:

InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/p-1

CAS number:

1069-03-0

IUPAC Name:

(4R,5R,6R,7R)-4,5,6,7,8-pentahydroxy-2-oxooctanoic acid

Traditional IUPAC Name:

3-deoxy-D-manno-octulosonate

SMILES:

OCC(O)C(O)C(O)C(O)CC(=O)C([O-])=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Hydroxy fatty acid
Medium-chain keto acid
Keto acid
Beta-hydroxy ketone
Beta-ketoaldehyde
Alpha-keto acid
Alpha-hydroxy ketone
Secondary alcohol
Polyol
Ketone
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-deoxy-D-manno-octulosonic acid (CHEBI:32817 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	64.9 mg/mL	ALOGPS
logP	-2.5	ALOGPS
logP	-3	ChemAxon
logS	-0.57	ALOGPS
pKa (Strongest Acidic)	2.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	155.52 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	48.24 m³·mol^-1	ChemAxon
Polarizability	20.91 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Pathways:

Lipopolysaccharide biosynthesis pae00540
Metabolic pathways pae01100

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dr-2590000000-c8365537f240bd17c092	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03k9-9420000000-7c62b05f704b94da4ed3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074m-9200000000-1f9f181dd8666e848b35	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002s-7920000000-37d0c8b357cc7b9ec55b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-35aeded87e6a52f7d9d0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06rf-9300000000-6953cb4ddc486610ea71	View in MoNA

References

References:

Belunis, C. J., Raetz, C. R. (1992). "Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli." J Biol Chem 267:9988-9997. Pubmed: 1577828
Biswas, T., Yi, L., Aggarwal, P., Wu, J., Rubin, J. R., Stuckey, J. A., Woodard, R. W., Tsodikov, O. V. (2009). "The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase." J Biol Chem 284:30594-30603. Pubmed: 19726684
Chalabaev, S., Kim, T. H., Ross, R., Derian, A., Kasper, D. L. (2010). "3-Deoxy-D-manno-octulosonic acid (Kdo) hydrolase identified in Francisella tularensis, Helicobacter pylori, and Legionella pneumophila." J Biol Chem 285:34330-34336. Pubmed: 20801884
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Radaev, S., Dastidar, P., Patel, M., Woodard, R. W., Gatti, D. L. (2000). "Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase." J Biol Chem 275:9476-9484. Pubmed: 10734095
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	32817
HMDB ID	Not Available
Pubchem Compound ID	817
Kegg ID	C01187
ChemSpider ID	794
Wikipedia ID	Not Available
BioCyc ID	KDO
EcoCyc ID	KDO

3-Deoxy-D-manno-octulosonate (PAMDB000918)

Structure for 3-Deoxy-D-manno-octulosonate (PAMDB000918)