P. aeruginosa Metabolome Database: CMP-3-Deoxy-D-manno-octulosonate (PAMDB000981)

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

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000981

Identification

Name:

CMP-3-Deoxy-D-manno-octulosonate

Description:

CMP-3-deoxy-D-manno-octulosonate is a member of the chemical class known as Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. CMP KDO is involved in the biosynthesis of lipopolysaccharides. CKS is a pharmaceutical target because CMP-KDO is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. (PMID 11545592) Pseudomonas aeruginosa KdtA (EcKdtA) is a bifunctional enzyme that transfers two KDO units from two CMP-KDO molecules to lipid IV(A). (PMID 20394418)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

CMK
CMP-α-Kdo
CMP-2-Dehydro-3-deoxy-D-octonate
CMP-2-Dehydro-3-deoxy-D-octonic acid
CMP-2-keto-3-DEOXY-octulosonate
CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID
CMP-3-Deoxy-D-manno-octulosonic acid
CMP-a-KDO
CMP-alpha-KDO
CMP-DManOA
CMP-Kdo
CMP-α-KDO

Chemical Formula:

C₁₇H₂₆N₃O₁₅P

Average Molecular Weight:

543.3732

Monoisotopic Molecular Weight:

543.110153689

InChI Key:

YWWJKULNWGRYAS-XKKDATLGSA-N

InChI:

InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17+/m1/s1

CAS number:

Not Available

IUPAC Name:

(2S,4R,5R,6R)-2-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

Traditional IUPAC Name:

(2S,4R,5R,6R)-2-({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy)-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

SMILES:

[H][C@@](O)(CO)[C@@]1([H])O[C@@](C[C@@]([H])(O)[C@@]1([H])O)(OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)C(O)=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
C-glucuronide
N-glycosyl compound
Glycosyl compound
C-glycosyl compound
Monosaccharide phosphate
Pyran carboxylic acid
Pyran carboxylic acid or derivatives
Hydroxypyrimidine
Dialkyl phosphate
Aminopyrimidine
Alkyl phosphate
Pyrimidine
Pyran
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Organic phosphate
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Oxolane
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

CMP-sugar (CHEBI:18014 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	15.5 mg/mL	ALOGPS
logP	-2.5	ALOGPS
logP	-5.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.44	ChemAxon
pKa (Strongest Basic)	2.41	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	292.58 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	119.77 m³·mol^-1	ChemAxon
Polarizability	47.02 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	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	splash10-03di-0912010000-c95ca105a90c9bee40f6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2901000000-f1f2e070390b27d5be4c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-6910000000-1ee99630fbd08166a369	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-022c-3623890000-d177a6c58bcdec474c6e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0i6r-8903000000-995189481426d066ebff	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0201-9300000000-312ab44de18da7b89d88	View in MoNA

References

References:

Chung, H. S., Raetz, C. R. (2010). "Interchangeable domains in the Kdo transferases of Escherichia coli and Haemophilus influenzae." Biochemistry 49:4126-4137. Pubmed: 20394418
Jelakovic, S., Schulz, G. E. (2001). "The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogs." J Mol Biol 312:143-155. Pubmed: 11545592
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
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	18014
HMDB ID	Not Available
Pubchem Compound ID	445888
Kegg ID	C04121
ChemSpider ID	393385
Wikipedia ID	Not Available
BioCyc ID	CMP-KDO
EcoCyc ID	CMP-KDO

Enzymes

Protein Details

• 3-deoxy-manno-octulosonate cytidylyltransferase

General function:: Involved in lipopolysaccharide biosynthetic process
Specific function:: Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria
Gene Name:: kdsB
Locus Tag:: PA2979
Molecular weight:: 27.6 kDa

Reactions

CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.

Protein Details

• 3-deoxy-D-manno-octulosonic-acid transferase

General function:: Involved in biosynthetic process
Specific function:: Essential step in lipopolysaccharides biosynthesis. Acts at transfer of 3-deoxy-D-mono octulonic acid (KDO) from CMP-KDO to a tetraacyldisaccharide 1,4'-bisphosphate precursor of lipid A (lipid IVA). Transfers two molecules of KDO to lipid IVA. Degraded by FtsH; therefore FtsH regulates the addition of the sugar moiety of the LPS and thus the maturation of the LPS precursor
Gene Name:: waaA
Locus Tag:: PA4988
Molecular weight:: 46.5 kDa

CMP-3-Deoxy-D-manno-octulosonate (PAMDB000981)

Structure for CMP-3-Deoxy-D-manno-octulosonate (PAMDB000981)

Enzymes

Reactions