Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000981
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)
  • 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-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
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
Chemical Taxonomy
Taxonomy DescriptionThis 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 ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine ribonucleoside monophosphates
Alternative Parents
  • 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
Physical Properties
State: Not Available
Melting point: Not Available
Experimental Properties:
Predicted Properties
Water Solubility15.5 mg/mLALOGPS
pKa (Strongest Acidic)1.44ChemAxon
pKa (Strongest Basic)2.41ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area292.58 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity119.77 m3·mol-1ChemAxon
Polarizability47.02 Å3ChemAxon
Number of Rings3ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
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
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??)-lipid IVA + Cytidine monophosphate
alpha-Kdo-(2??)-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
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
  • 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:
HMDB IDNot Available
Pubchem Compound ID445888
Kegg IDC04121
ChemSpider ID393385
Wikipedia IDNot Available


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:
Locus Tag:
Molecular weight:
27.6 kDa
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:
Locus Tag:
Molecular weight:
46.5 kDa