MiMeDB: Showing metabocard for 3-Dehydroshikimic acid (MMDBc0032974)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:29:32 UTC

Update Date

2022-08-31 21:54:43 UTC

Metabolite ID

MMDBc0032974

Metabolite Identification

Common Name

3-Dehydroshikimic acid

Description

3-Dehydroshikimic acid is an intermediate in the chorismate biosynthesis pathway also called shikimate pathway. This pathway occurs in plants and microorganisms. Chorismate is an important intermediate that leads to the biosynthesis of several essential metabolites, including the aromatic amino acids L-phenylalanine, L-tyrosine and L-tryptophan, vitamins E and K, ubiquinone and certain siderophore. [Biocyc ARO-PWY]

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      20.198 -15.045   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.534 -15.811   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.870 -15.811   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.192 -13.519   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.534 -17.358   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.870 -17.358   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      21.513 -12.753   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      18.863 -12.760   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      20.198 -18.138   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      22.863 -18.117   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.541 -18.117   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      20.192 -19.671   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7    8                                                  
CONECT    5    2    9   10                                                  
CONECT    6    3   11    9                                                  
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5   12    6                                                  
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    9                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
(-)-3-Dehydroshikimic acid	ChEBI
5-Dehydroshikimate	ChEBI
5-Dehydroshikimic acid	ChEBI
(-)-3-Dehydroshikimate	Generator
3-Dehydroshikimic acid	Generator
3-Dehydroshikimate	ChEBI

Molecular Formula

C₇H₈O₅

Average Mass

172.1354

Monoisotopic Mass

172.037173366

IUPAC Name

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

Traditional Name

3-dehydroshikimic acid

CAS Registry Number

27655-56-7

SMILES

O[C@@H]1CC(=CC(=O)[C@H]1O)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)/t5-,6-/m1/s1

InChI Key

SLWWJZMPHJJOPH-PHDIDXHHSA-N

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
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

alpha,beta-unsaturated monocarboxylic acid (CHEBI:30918 )
4-oxo monocarboxylic acid (CHEBI:30918 )
5-hydroxy monocarboxylic acid (CHEBI:30918 )
4-hydroxy monocarboxylic acid (CHEBI:30918 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	137 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1	ChemAxon
logS	-0.1	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	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	38.19 m³·mol⁻¹	ChemAxon
Polarizability	14.91 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-MS (1 MEOX; 3 TMS)	splash10-001r-4951000000-73e5d4c38702a9a74934	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-05as-2981000000-48228f5a995cc5391fde	2014-06-16	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03dl-9800000000-4262d1ae298a71a287f4	2016-09-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-056r-1900000000-78f25cc3fd642b56e1ec	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-022i-2900000000-0cfcedb79843656d9142	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-0900000000-45bd7f9b77de178fcfb1	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-0900000000-6f5c6b968d61d620eac8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-02bg-9400000000-247e23f7d40eb8dc3bed	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0900000000-337af02382c0ad0609aa	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00b9-2900000000-cf94e3e6a57bbc9e99d5	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00bc-9300000000-1745a70ff77286c29676	2016-09-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013681	NADP(+)	3-Dehydroshikimic acid	Pentafunctional AROM polypeptide	Dehydrogenation	RHEA	34755880
MMDBr0013682	NAD	3-Dehydroshikimic acid	Quinate/shikimate dehydrogenase (NAD(+))	Dehydrogenation	RHEA	34755880
MMDBr0014068	3-Dehydroquinate	3-Dehydroshikimic acid	Catabolic 3-dehydroquinase	Hydration/dehydration of C-O bond; Synthesis	RHEA	34755880
MMDBr0014493	3-Dehydroshikimic acid	3,4-dihydroxybenzoic acid	3-dehydroshikimate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014494	3-Dehydroshikimic acid	3,4-dihydroxybenzoic acid	3-dehydroshikimate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0025260	Shikimate	3-Dehydroshikimic acid	Quinate/shikimate dehydrogenase (quinone)	Dehydrogenation	RHEA	34755880

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	Microbial Links
Eukaryota/Fungi	Ascomycota	58	Human feces; Human saliva	Unknown
Eukaryota/Fungi	Basidiomycota	7
Bacteria	Chlamydiae	3	Human
Bacteria	Proteobacteria	335	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human sputum; Human saliva; Chicken
Archaea/Archaea	Crenarchaeota	15
Bacteria	Firmicutes	137	Human feces; Human ; Cattle ; Catfish
Bacteria	Aquificae	2
Archaea/Archaea	Euryarchaeota	32
Bacteria	Actinobacteria	26	Human ; Cattle
Bacteria	Chlorobi	8
Bacteria	Cyanobacteria	27	Human
Bacteria	Chloroflexi	6
Bacteria	Dictyoglomi	2
Bacteria	Spirochaetes	4	Human
Archaea	Euryarchaeota	2
Bacteria/NULL	Proteobacteria	2	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human sputum; Human saliva; Chicken
Archaea/Archaea	Thaumarchaeota	1
Archaea	Crenarchaeota	1
Bacteria	Bacteroidetes	1
Bacteria	nah	1
Bacteria	Thermotogae	4
Bacteria	Deinococcus-thermus	3
Bacteria	Nitrospirae	1
Bacteria	Elusimicrobia	1
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Gemmatimonadetes	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

DB04347

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00019663

Chemspider ID

Not Available

KEGG Compound ID

C02637

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

3-Dehydroshikimic_acid

METLIN ID

Not Available

PubChem Compound

439774

PDB ID

Not Available

ChEBI ID

30918

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 3-Dehydroshikimic acid (MMDBc0032974)

MOL for #<Metabolite:0x000055d249345000>

3D MOL for #<Metabolite:0x000055d249345000>

3D SDF for #<Metabolite:0x000055d249345000>

3D-SDF for #<Metabolite:0x000055d249345000>

PDB for #<Metabolite:0x000055d249345000>

3D PDB for #<Metabolite:0x000055d249345000>

SMILES for #<Metabolite:0x000055d249345000>

INCHI for #<Metabolite:0x000055d249345000>

Structure for #<Metabolite:0x000055d249345000>

3D Structure for #<Metabolite:0x000055d249345000>