MiMeDB: Showing metabocard for Shikimate (MMDBc0049947)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:46:50 UTC

Update Date

2022-12-15 22:52:19 UTC

Metabolite ID

MMDBc0049947

Metabolite Identification

Common Name

Shikimate

Description

Shikimic acid, more commonly known as its anionic form shikimate, is a cyclohexene, a cyclitol and a cyclohexanecarboxylic acid. It is an important biochemical intermediate in plants and microorganisms. Its name comes from the Japanese flower shikimi (the Japanese star anise, 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.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.4928667.030   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8668.8268666.259   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.4928668.571   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8664.8218662.406   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8662.1528667.030   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8662.1528663.947   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8664.8218667.029   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8663.4888666.259   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8663.4888664.719   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8664.8218663.949   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8666.1558664.719   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8666.1558666.259   0.000  0.00  0.00           C+0
CONECT    1    2    3   12                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4   10                                                            
CONECT    5    8                                                            
CONECT    6    9                                                            
CONECT    7    8   12                                                       
CONECT    8    7    9    5                                                  
CONECT    9    8   10    6                                                  
CONECT   10    9   11    4                                                  
CONECT   11   10   12                                                       
CONECT   12    7   11    1                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
3,4,5-Trihydroxy-1-cyclohexenecarboxylic acid	ChEBI
3alpha,4alpha,5beta-Trihydroxy-1-cyclohexene-1-carboxylic acid	ChEBI
[3R-(3alpha,4alpha,5beta)]-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylic acid	ChEBI
L-Shikimic acid	ChEBI
Shikimate	ChEBI
3,4,5-Trihydroxy-1-cyclohexenecarboxylate	Generator
3a,4a,5b-Trihydroxy-1-cyclohexene-1-carboxylate	Generator
3a,4a,5b-Trihydroxy-1-cyclohexene-1-carboxylic acid	Generator
3alpha,4alpha,5beta-Trihydroxy-1-cyclohexene-1-carboxylate	Generator
3Α,4α,5β-trihydroxy-1-cyclohexene-1-carboxylate	Generator
3Α,4α,5β-trihydroxy-1-cyclohexene-1-carboxylic acid	Generator
[3R-(3a,4a,5b)]-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylate	Generator
[3R-(3a,4a,5b)]-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylic acid	Generator
[3R-(3alpha,4alpha,5beta)]-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylate	Generator
[3R-(3Α,4α,5β)]-3,4,5-trihydroxy-1-cyclohexene-1-carboxylate	Generator
[3R-(3Α,4α,5β)]-3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid	Generator
L-Shikimate	Generator
Acid, shikimic	MeSH
(-)-Shikimate	HMDB
(-)-Shikimic acid	HMDB
Skikimate	HMDB
Skikimic acid	HMDB
(3R,4S,5R)-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylic acid	PhytoBank
(-)-3,4,5-Trihydroxy-1-cyclohexene-1-carboxylic acid	PhytoBank
Shikimic acid	PhytoBank

Molecular Formula

C₇H₁₀O₅

Average Mass

174.1513

Monoisotopic Mass

174.05282343

IUPAC Name

(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid

Traditional Name

(-)-shikimate

CAS Registry Number

Not Available

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 Key

JXOHGGNKMLTUBP-HSUXUTPPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as shikimic acids and derivatves. These are cyclitols containing a cyclohexanecarboxylic acid substituted with three hydroxyl groups at positions 3, 4, and 5.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Shikimic acids and derivatves

Alternative Parents

Substituents

Shikimic acid or derivatives
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

alpha,beta-unsaturated monocarboxylic acid (CHEBI:16119 )
cyclohexenecarboxylic acid (CHEBI:16119 )
hydroxy monocarboxylic acid (CHEBI:16119 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	206 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.6	ChemAxon
logS	0.07	ALOGPS
pKa (Strongest Acidic)	4.1	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	38.96 m³·mol⁻¹	ChemAxon
Polarizability	15.75 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-0udj-0970000000-42465cd3f3e138b0bc12	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0udi-0790000000-1100443abb8605953f58	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)	splash10-00di-9450000000-e6ca954dc1a9c1cc4285	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0udi-0491000000-49993b9b18e12b9461fc	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0udi-0391000000-ddb2c574233062a911fa	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udj-0970000000-42465cd3f3e138b0bc12	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0790000000-1100443abb8605953f58	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9450000000-e6ca954dc1a9c1cc4285	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-0491000000-49993b9b18e12b9461fc	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-4900000000-817f1ed3feb4c763285f	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-0092-7119400000-67b0989b5019a72e1016	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-01b9-1900000000-fd80f5e7f51d927e8e15	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0a4i-9300000000-cf8a3148fd132540bf97	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-9000000000-ed28bc20ae43473043c9	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0a4i-9000000000-65249fc24f2de4acf2c7	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0a4i-9000000000-26dfc876ae35c2cdb845	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-006x-9600000000-3a5ab91754d9d837d8b4	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-01b9-1900000000-6cba5b9b7c4891522045	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9300000000-12d15a049b141a37f34e	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-ed28bc20ae43473043c9	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-9864f7359ffed65d6ef0	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-26dfc876ae35c2cdb845	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-006x-9600000000-3a5ab91754d9d837d8b4	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-00di-7900000000-d77a830354efe8731a42	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-01vx-9700000000-d2060c544171987e3dcd	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-01vx-9500000000-baa64c3938f3d039c6e4	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9000000000-d5821372fd8a830dc962	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-00dl-9000000000-cb13aba83ba37150b931	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-01vo-9600000000-3433190ea61f16d92efd	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-022l-9600000000-60e85b9b59edb135e4c4	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9000000000-58e1775d1e013c416201	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-1f370d2806fd8245ebfb	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-01vx-9600000000-d502f575cada8c0b5aea	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-00dl-9400000000-d0ff38d5a290b8e8248d	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-e6ca4ce5acb44dc23a74	2012-07-25	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004r-9700000000-18afe769b0ef5ba3fbdb	2012-07-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-05	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)		2016-10-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)		2016-10-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)		2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites
Eukaryota/Fungi	Ascomycota	54	Human feces
Eukaryota/Fungi	Basidiomycota	15	Human feces
Bacteria	Proteobacteria	328	Human ; Pig ; Human feces; Cattle ; River trout ; Turkey ; Lion ; Chicken ; Rat ; Sheep ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human sputum; Human saliva; Human feces; pleural fluid plaque; bal; Human stool
Bacteria	Actinobacteria	30	Human ; Cattle ; Human feces
Archaea/Archaea	Crenarchaeota	14
Bacteria	Firmicutes	119	Human feces; Human ; Cattle
Bacteria	Aquificae	3
Archaea/Archaea	Euryarchaeota	28
Bacteria	Bacteroidetes	9	Human ; Human feces
Bacteria	Chlorobi	11
Bacteria	Chlamydiae	3	Human
Bacteria	Chloroflexi	3
Bacteria	Deinococcus-thermus	3
Bacteria	Dictyoglomi	2
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Cyanobacteria	28	Human
Bacteria	Spirochaetes	6	Human
Bacteria	Verrucomicrobia	1
Archaea	Euryarchaeota	2
Bacteria	Planctomycetes	1
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria	Thermotogae	4
Archaea/Archaea	Thaumarchaeota	1
Archaea	Crenarchaeota	1

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified							HMDB
Human Urine	Detected and Quantified	0.004	0.001	umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.027	0.006	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.03	0.006	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.039	0.015	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.042	0.01	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.051	0.014	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.056	0.015	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.057	0.027	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218
Human Blood	Detected and Quantified	0.13	0.098	uM	Adult (>18 years old)	Male	Normal	HMDB	19812218

External Links

HMDB ID

HMDB0003070

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Shikimic_acid

METLIN ID

338

PubChem Compound

8742

PDB ID

Not Available

ChEBI ID

16119

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Rose GA: Studies on the chemical nature of urinary chemiluminescence. Br J Urol. 1976 Feb;48(1):61-71. doi: 10.1111/j.1464-410x.1976.tb02744.x. [PubMed:5168 ]
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. doi: 10.1016/j.saa.2004.09.004. [PubMed:15911418 ]

Showing metabocard for Shikimate (MMDBc0049947)

MOL for #<Metabolite:0x00007fdb13d3b670>

3D MOL for #<Metabolite:0x00007fdb13d3b670>

3D SDF for #<Metabolite:0x00007fdb13d3b670>

3D-SDF for #<Metabolite:0x00007fdb13d3b670>

PDB for #<Metabolite:0x00007fdb13d3b670>

3D PDB for #<Metabolite:0x00007fdb13d3b670>

SMILES for #<Metabolite:0x00007fdb13d3b670>

INCHI for #<Metabolite:0x00007fdb13d3b670>

Structure for #<Metabolite:0x00007fdb13d3b670>

3D Structure for #<Metabolite:0x00007fdb13d3b670>