Shikimic acid (PAMDB000477)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000477
Identification
Name: Shikimic acid
Description:Shikimic acid, more commonly known as its anionic form shikimate, is an important biochemical intermediate in plants and microorganisms. Its name comes from the Japanese flower shikimi (
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (-)-Shikimate
  • (-)-Shikimic acid
  • L-Shikimate
  • L-Shikimic acid
  • Shikimate
  • Shikimic acid
  • Skikimate
  • Skikimic acid
Chemical Formula: C7H10O5
Average Molecular Weight: 174.1513
Monoisotopic Molecular Weight: 174.05282343
InChI Key: JXOHGGNKMLTUBP-HSUXUTPPSA-N
InChI:InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
CAS number: 138-59-0
IUPAC Name:(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
Traditional IUPAC Name: (-)-shikimate
SMILES:O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as cyclitols and derivatives. These are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Alcohols and polyols
Sub ClassCyclic alcohols and derivatives
Direct Parent Cyclitols and derivatives
Alternative Parents
Substituents
  • Cyclitol derivative
  • Secondary alcohol
  • Polyol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular Framework Aliphatic homomonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-1
Melting point: 186 °C
Experimental Properties:
PropertyValueSource
Water Solubility:150 mg/mL at 21 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility206.0 mg/mLALOGPS
logP-1.7ALOGPS
logP-1.6ChemAxon
logS0.07ALOGPS
pKa (Strongest Acidic)4.1ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity38.96 m3·mol-1ChemAxon
Polarizability15.75 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
3-Dehydro-shikimate + Hydrogen ion + NADPH <> NADP + Shikimic acid
Adenosine triphosphate + Shikimic acid <> ADP + Hydrogen ion + Shikimate 3-phosphate
Adenosine triphosphate + Shikimic acid <> ADP + Shikimate 3-phosphate
Shikimic acid + NAD <> 3-Dehydro-shikimate + NADH + Hydrogen ion
NAD(P)<sup>+</sup> + Shikimic acid < NAD(P)H + 3-Dehydro-shikimate + Hydrogen ion
Quinate + NAD + NADP + Shikimic acid <> 3-Dehydroquinate + NADH + NADPH + Hydrogen ion + 3-Dehydro-shikimate
3-dehydroshikimate + Hydrogen ion + NADPH + 3-Dehydro-shikimate + NADPH > NADP + Shikimic acid
Shikimic acid + Adenosine triphosphate > Adenosine diphosphate + Hydrogen ion + shikimate 3-phosphate + ADP + Shikimate 3-phosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udj-0970000000-42465cd3f3e138b0bc12View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0udi-0790000000-1100443abb8605953f58View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-00di-9450000000-e6ca954dc1a9c1cc4285View in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0udi-0491000000-49993b9b18e12b9461fcView in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-e6ca4ce5acb44dc23a74View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004r-9700000000-18afe769b0ef5ba3fbdbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-000i-9100000000-7d0218e803b828de53b2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-01b9-1900000000-fd80f5e7f51d927e8e15View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0a4i-9300000000-cf8a3148fd132540bf97View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0a4i-9000000000-ed28bc20ae43473043c9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0a4i-9000000000-65249fc24f2de4acf2c7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0a4i-9000000000-26dfc876ae35c2cdb845View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-006x-9600000000-3a5ab91754d9d837d8b4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • 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
  • Liu Y, Xie MX, Jiang M, Wang YD: Spectroscopic investigation of the interaction between human serum albumin and three organic acids. Spectrochim Acta A Mol Biomol Spectrosc. 2005 Jul;61(9):2245-51. Pubmed: 15911418
  • Rose GA: Studies on the chemical nature of urinary chemiluminescence. Br J Urol. 1976 Feb;48(1):61-71. Pubmed: 5168
  • 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
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • 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) Download (PDF)
External Links:
ResourceLink
CHEBI ID16119
HMDB IDHMDB03070
Pubchem Compound ID8742
Kegg IDC00493
ChemSpider ID8412
WikipediaShikimic acid
BioCyc IDSHIKIMATE
EcoCyc IDSHIKIMATE
Ligand ExpoSKM

Enzymes

Protein Details
• Shikimate kinase 1
General function:
Involved in shikimate kinase activity
Specific function:
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
Gene Name:
aroK
Locus Tag:
PA5039
Molecular weight:
19.2 kDa
Reactions
ATP + shikimate = ADP + shikimate 3-phosphate.
Protein Details
• Shikimate dehydrogenase
General function:
Involved in nucleotide binding
Specific function:
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
Gene Name:
aroE
Locus Tag:
PA0025
Molecular weight:
29.5 kDa
Reactions
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH.

Transporters