Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-24 07:21:44 UTC

Update Date

2022-09-22 18:34:37 UTC

HMDB ID

HMDB0304122

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-dehydroshikimate

Description

3-dehydro-shikimate is a member of the class of compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. 3-dehydro-shikimate is soluble (in water) and a weakly acidic compound (based on its pKa). 3-dehydro-shikimate can be found in a number of food items such as pot marjoram, salmonberry, purple laver, and lichee, which makes 3-dehydro-shikimate a potential biomarker for the consumption of these food products. 3-dehydro-shikimate may be a unique E.coli metabolite.

Structure

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

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    4                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Dehydroshikimic acid	Generator

Chemical Formula

C₇H₇O₅

Average Molecular Weight

171.129

Monoisotopic Molecular Weight

171.029896905

IUPAC Name

4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate

Traditional Name

4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate

CAS Registry Number

Not Available

SMILES

OC1CC(=CC(=O)C1O)C([O-])=O

InChI Identifier

InChI=1S/C7H8O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,5-6,9-10H,2H2,(H,11,12)/p-1

InChI Key

SLWWJZMPHJJOPH-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclohexenones

Alternative Parents

Substituents

Cyclohexenone
Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Alcohol
Organic anion
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

a small molecule (3-DEHYDRO-SHIKIMATE )

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.2	ALOGPS
logP	-1	ChemAxon
logS	0.27	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.66 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	49.03 m³·mol⁻¹	ChemAxon
Polarizability	14.58 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	137.404	32859911
AllCCS	[M+H-H2O]+	133.086	32859911
AllCCS	[M+Na]+	142.587	32859911
AllCCS	[M+NH4]+	141.427	32859911
AllCCS	[M-H]-	128.172	32859911
AllCCS	[M+Na-2H]-	129.052	32859911
AllCCS	[M+HCOO]-	130.083	32859911
DeepCCS	[M+H]+	132.103	30932474
DeepCCS	[M-H]-	128.273	30932474
DeepCCS	[M-2H]-	165.33	30932474
DeepCCS	[M+Na]+	140.758	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-dehydroshikimate,3TMS,isomer #1	C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)CC(C(=O)[O-])=C1	1778.4	Semi standard non polar	33892256
3-dehydroshikimate,3TMS,isomer #1	C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)CC(C(=O)[O-])=C1	1755.8	Standard non polar	33892256
3-dehydroshikimate,3TMS,isomer #1	C[Si](C)(C)OC1=C(O[Si](C)(C)C)C(O[Si](C)(C)C)CC(C(=O)[O-])=C1	2022.0	Standard polar	33892256
3-dehydroshikimate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CC(C(=O)[O-])=C1	2497.0	Semi standard non polar	33892256
3-dehydroshikimate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CC(C(=O)[O-])=C1	2379.4	Standard non polar	33892256
3-dehydroshikimate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CC(C(=O)[O-])=C1	2317.5	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydroshikimate 10V, Negative-QTOF	splash10-0uk9-0900000000-db9503ae5c1cea01876a	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydroshikimate 20V, Negative-QTOF	splash10-0kdi-0900000000-9ff3c52952521fe5bbaa	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydroshikimate 40V, Negative-QTOF	splash10-056s-9700000000-c8c4a4ce8fc92084e3f5	2019-02-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030416

KNApSAcK ID

Not Available

Chemspider ID

21231994

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 3-dehydroshikimate (HMDB0304122)

MOL for HMDB0304122 (3-dehydroshikimate)

3D MOL for HMDB0304122 (3-dehydroshikimate)

3D SDF for HMDB0304122 (3-dehydroshikimate)

3D-SDF for HMDB0304122 (3-dehydroshikimate)

PDB for HMDB0304122 (3-dehydroshikimate)

3D PDB for HMDB0304122 (3-dehydroshikimate)

SMILES for HMDB0304122 (3-dehydroshikimate)

INCHI for HMDB0304122 (3-dehydroshikimate)

Structure for HMDB0304122 (3-dehydroshikimate)

3D Structure for HMDB0304122 (3-dehydroshikimate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra

NMR Spectra