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
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) 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)-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
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct ParentPyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • C-glucuronide
  • C-glycosyl compound
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Aminopyrimidine
  • Pyrimidone
  • Dialkyl phosphate
  • Alkyl phosphate
  • Imidolactam
  • Pyrimidine
  • Hydropyrimidine
  • Pyran
  • Primary aromatic amine
  • Monosaccharide
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Oxane
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Amino acid or derivatives
  • Amino acid
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Amine
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary amine
  • Primary alcohol
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility15.5 g/LALOGPS
logP-2.5ALOGPS
logP-5.3ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.44ChemAxon
pKa (Strongest Basic)2.41ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area292.58 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity119.77 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)
Cytidine triphosphate + 3-Deoxy-D-manno-octulosonate <> Pyrophosphate + CMP-3-Deoxy-D-manno-octulosonate
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
Cytidine triphosphate + 3-Deoxy-D-manno-octulosonate > Pyrophosphate + CMP-3-Deoxy-D-manno-octulosonate
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
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 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
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