You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2006-05-22 15:12:30 UTC
Update Date2016-02-11 01:05:59 UTC
HMDB IDHMDB03070
Secondary Accession NumbersNone
Metabolite Identification
Common NameShikimic acid
DescriptionShikimic 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 (シキミ, Illicium anisatum), from which it was first isolated. Shikimic acid is a precursor for: the aromatic amino acids phenylalanine and tyrosine; indole, indole derivatives and tryptophan; many alkaloids and other aromatic metabolites; tannins; and lignin. In pharmaceutical industry, shikimic acid from chinese star anise is used as a base material for production of Tamiflu (oseltamivir). Although shikimic acid is present in most autotrophic organisms, it is a biosynthetic intermediate and generally found in very low concentrations (Wikipedia).
Structure
Thumb
Synonyms
ValueSource
3,4,5-Trihydroxy-1-cyclohexenecarboxylic acidChEBI
3alpha,4alpha,5beta-Trihydroxy-1-cyclohexene-1-carboxylic acidChEBI
[3R-(3alpha,4alpha,5beta)]-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylic acidChEBI
ShikimateChEBI
3,4,5-Trihydroxy-1-cyclohexenecarboxylateGenerator
(3R,4S,5R)-3,4,5-Trihydroxycyclohexene-1-carboxylateGenerator
3a,4a,5b-Trihydroxy-1-cyclohexene-1-carboxylateGenerator
3a,4a,5b-Trihydroxy-1-cyclohexene-1-carboxylic acidGenerator
3alpha,4alpha,5beta-Trihydroxy-1-cyclohexene-1-carboxylateGenerator
3α,4α,5β-trihydroxy-1-cyclohexene-1-carboxylateGenerator
3α,4α,5β-trihydroxy-1-cyclohexene-1-carboxylic acidGenerator
(-)-ShikimateHMDB
(-)-Shikimic acidHMDB
L-ShikimateHMDB
L-Shikimic acidHMDB
SkikimateHMDB
Skikimic acidHMDB
Chemical FormulaC7H10O5
Average Molecular Weight174.1513
Monoisotopic Molecular Weight174.05282343
IUPAC Name(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
Traditional Name(-)-shikimate
CAS Registry Number138-59-0
SMILES
O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
InChI Identifier
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
InChI KeyInChIKey=JXOHGGNKMLTUBP-HSUXUTPPSA-N
Chemical 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.
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassAlcohols and polyols
Sub ClassCyclic alcohols and derivatives
Direct ParentCyclitols 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 FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
  • Microbial
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point186 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility150 mg/mL at 21 °CNot Available
LogPNot AvailableNot Available
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
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
Predicted GC-MSPredicted GC-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
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.027 +/- 0.006 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.056 +/- 0.015 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.039 +/- 0.015 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.051 +/- 0.014 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.042 +/- 0.01 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.057 +/- 0.027 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.03 +/- 0.006 uMAdult (>18 years old)Male
Normal
details
BloodDetected and Quantified0.13 +/- 0.098 uMAdult (>18 years old)Male
Normal
details
UrineDetected and Quantified0.004 +/- 0.001 umol/mmol creatinineAdult (>18 years old)Male
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)BothProstate Cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB003991
KNApSAcK IDC00001203
Chemspider ID8412
KEGG Compound IDC00493
BioCyc ID3-DEHYDRO-SHIKIMATE
BiGG IDNot Available
Wikipedia LinkShikimic acid
NuGOwiki LinkHMDB03070
Metagene LinkHMDB03070
METLIN ID338
PubChem Compound8742
PDB IDSKM
ChEBI ID16119
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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. [15911418 ]
  2. Rose GA: Studies on the chemical nature of urinary chemiluminescence. Br J Urol. 1976 Feb;48(1):61-71. [5168 ]