Record Information
Version2.0
Creation Date2012-05-31 14:29:14 -0600
Update Date2015-06-03 17:19:22 -0600
Secondary Accession Numbers
  • ECMDB20133
Identification
Name:CMP-3-Deoxy-D-manno-octulosonate
DescriptionCMP-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) E. coli KdtA (EcKdtA) is a bifunctional enzyme that transfers two KDO units from two CMP-KDO molecules to lipid IV(A). (PMID 20394418)
Structure
Thumb
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
Weight:Average: 543.3732
Monoisotopic: 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)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-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)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-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
Description belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct Parent1,2-diols
Alternative Parents
Substituents
  • Secondary alcohol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
  • 3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]acrylic acid (CHEBI:61462 )
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility49.6 g/LALOGPS
logP-2.8ALOGPS
logP-4.8ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-0.22ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area291.59 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity108.36 m³·mol⁻¹ChemAxon
Polarizability47.02 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Cytidine triphosphate + 3-Deoxy-D-manno-octulosonate <> CMP-3-Deoxy-D-manno-octulosonate + Pyrophosphate
CMP-3-Deoxy-D-manno-octulosonate + Phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA > Cytidine monophosphate + Hydrogen ion + Kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA
CMP-3-Deoxy-D-manno-octulosonate + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate > Cytidine monophosphate + Hydrogen ion + KDO-lipid IV(A)
CMP-3-Deoxy-D-manno-octulosonate + KDO-lipid IV(A) > Cytidine monophosphate + Hydrogen ion + KDO(2)-lipid IV(A)
2,3,2'3'-Tetrakis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate + CMP-3-Deoxy-D-manno-octulosonate + 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate <> KDO-lipid IV(A) + Cytidine monophosphate
KDO-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate <> Di[3-deoxy-D-manno-octulosonyl]-lipid IV(A) + Cytidine monophosphate
Di[3-deoxy-D-manno-octulosonyl]-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate <> alpha-Kdo-(2->8)-alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA + Cytidine monophosphate
a lipopolysaccharide + CMP-3-Deoxy-D-manno-octulosonate KDOIII-lipopolysaccharide + Cytidine monophosphate
3-Deoxy-D-manno-octulosonate + Cytidine triphosphate > CMP-3-Deoxy-D-manno-octulosonate + Pyrophosphate
CMP-3-Deoxy-D-manno-octulosonate + lipid IV<sub>A</sub> <> Hydrogen ion + KDO-lipid IV(A) + Cytidine monophosphate
KDO-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate <> Hydrogen ion + &alpha;-Kdo-(2->4)-&alpha;-Kdo-(2->6)-lipid IV<SUB>A</SUB> + Cytidine monophosphate
2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate + CMP-3-Deoxy-D-manno-octulosonate > alpha-Kdo-(2->6)-lipid IV(A) + Cytidine monophosphate
Alpha-Kdo-(2->6)-lipid IV(A) + CMP-3-Deoxy-D-manno-octulosonate > alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IV(A) + Cytidine monophosphate
3-deoxy-D-manno-octulosonate + Cytidine triphosphate + 3-Deoxy-D-manno-octulosonate > Pyrophosphate + CMP-3-Deoxy-D-manno-octulosonate
CMP-3-Deoxy-D-manno-octulosonate + (2-N,3-O-bis(3-Hydroxytetradecanoyl)-4-O-phosphono-beta-D-glucosaminyl)-(1->6)-(2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl phosphate) > Cytidine monophosphate + Hydrogen ion + alpha-Kdo-(2→6)-lipid IVA + Cytidine monophosphate
alpha-Kdo-(2→6)-lipid IVA + CMP-3-Deoxy-D-manno-octulosonate > Cytidine monophosphate + Hydrogen ion + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + Cytidine monophosphate + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA
Cytidine triphosphate + 3 3-Deoxy-D-manno-octulosonate <> CMP-3-Deoxy-D-manno-octulosonate + Pyrophosphate
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIPW001905 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIIPW002059 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0912010000-c95ca105a90c9bee40f6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2901000000-f1f2e070390b27d5be4cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6910000000-1ee99630fbd08166a369View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-022c-3623890000-d177a6c58bcdec474c6eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0i6r-8903000000-995189481426d066ebffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0201-9300000000-312ab44de18da7b89d88View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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
External Links:
ResourceLink
CHEBI ID18014
HMDB IDNot Available
Pubchem Compound ID445888
Kegg IDC04121
ChemSpider ID393385
Wikipedia IDNot Available
BioCyc IDCMP-KDO
EcoCyc IDCMP-KDO

Enzymes

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
Uniprot ID:
P04951
Molecular weight:
27614
Reactions
CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.
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
Uniprot ID:
P0AC75
Molecular weight:
47291
General function:
Involved in lipopolysaccharide biosynthetic process
Specific function:
Specific function unknown
Gene Name:
rfaZ
Uniprot ID:
P27241
Molecular weight:
32920