ECMDB: 3-Dehydroquinate (ECMDB04049) (M2MDB000582)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (3)XML

Proteins (923)

Record Information

Version

2.0

Creation Date

2012-05-31 14:03:28 -0600

Update Date

2015-06-03 15:54:40 -0600

Secondary Accession Numbers

ECMDB04049

Identification

Name:

3-Dehydroquinate

Description

3-dehydroquinate is a member of the chemical class known as Cyclitols and Derivatives. These are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms. 3-dehydroquinate is invovled in phenylalanine, tyrosine and tryptophan biosynthesis, and the biosynthesis of secondary metabolites. Dehydroquinate is involved in the shikimate pathway. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. (PMID 17586643) The aroB gene encoding dehydroquinate synthase (DHQS), which is a potential antibiotic target, was identified from the plant-pathogenic bacterium Xanthomonas oryzae pv. (PMID 19052366)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

3-Dehydroquinic acid
3DQA
5-De-H-quinate
5-De-H-quinic acid
5-Dehydroquinate
5-Dehydroquinic acid
Cyclohexan-1,4,5-triol-3-one-1-carboxylate
Cyclohexan-1,4,5-triol-3-one-1-carboxylic acid

Chemical Formula:

C₇H₁₀O₆

Weight:

Average: 190.1507
Monoisotopic: 190.047738052

InChI Key:

WVMWZWGZRAXUBK-SYTVJDICSA-N

InChI:

InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1

CAS number:

Not Available

IUPAC Name:

(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexane-1-carboxylic acid

Traditional IUPAC Name:

3-dehydroquinic acid

SMILES:

O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as alpha hydroxy acids and derivatives. These are organic compounds containing a carboxylic acid substituted with a hydroxyl group on the adjacent carbon.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Alpha hydroxy acids and derivatives

Direct Parent

Alpha hydroxy acids and derivatives

Alternative Parents

Substituents

Alpha-hydroxy acid
Cyclitol or derivatives
Cyclic alcohol
Tertiary alcohol
Cyclic ketone
Secondary alcohol
Ketone
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

4-oxo monocarboxylic acid (CHEBI:17947 )
5-hydroxy monocarboxylic acid (CHEBI:17947 )
4-hydroxy monocarboxylic acid (CHEBI:17947 )
2-hydroxy monocarboxylic acid (CHEBI:17947 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	702 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.1	ChemAxon
logS	0.57	ALOGPS
pKa (Strongest Acidic)	3.3	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	38.7 m³·mol⁻¹	ChemAxon
Polarizability	16.46 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

NAD + Quinate <> 3-Dehydroquinate +2 Hydrogen ion + NADH
3-Dehydroquinate <> 3-Dehydro-shikimate + Water
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate <> 3-Dehydroquinate + Phosphate
Quinate + NAD <> 3-Dehydroquinate + NADH + Hydrogen ion
Quinate + NADP <> 3-Dehydroquinate + NADPH + Hydrogen ion
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate > Phosphate + 3-Dehydroquinate
NAD(P)<sup>+</sup> + Quinate NAD(P)H + 3-Dehydroquinate + Hydrogen ion
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate > 3-Dehydroquinate + Inorganic phosphate
3-Dehydroquinate > 3-dehydroshikimate + Water
Quinate + NAD(P)(+) > 3-Dehydroquinate + NAD(P)H
Quinate + NAD + NADP + Shikimic acid <> 3-Dehydroquinate + NADH + NADPH + Hydrogen ion + 3-Dehydro-shikimate
3-deoxy-D-arabino-heptulosonate-7-phosphate > Phosphate + 3-Dehydroquinate
3-Dehydroquinate > Water + 3-dehydroshikimate + 3-Dehydro-shikimate
2 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate <>3 3-Dehydroquinate + Phosphate
2 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate <>3 3-Dehydroquinate + Phosphate

SMPDB Pathways:

Chorismate biosynthesis	PW000816
Secondary Metabolites: Shikimate Pathway	PW000985

KEGG Pathways:

Metabolic pathways eco01100
Phenylalanine, tyrosine and tryptophan biosynthesis ec00400

EcoCyc Pathways:

3-dehydroquinate biosynthesis I PWY-6164
chorismate biosynthesis from 3-dehydroquinate PWY-6163

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-006t-0964100000-43f6105696288554732d	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-1931000000-57530b3291dd2e565178	View in MoNA
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-006t-0964100000-43f6105696288554732d	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-1931000000-57530b3291dd2e565178	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0596-9300000000-7ead36d659dabf409016	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-03di-3518900000-ee462a48968d50db188e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006y-0900000000-ac10acaee4770b187145	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00fv-0900000000-f009559eda021348f79a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-5900000000-28407ccc61bbac4e43a2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000j-0900000000-ac45e4ef633567de02be	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002k-2900000000-994d9ab39014948cbfa2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0adm-9600000000-2c76a62b61b2ac646326	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-f9faec316fab8e1b6197	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-2900000000-c25f297abc3454757445	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9200000000-4dbdf526aa7f456fc8b6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006x-0900000000-2ad6782757e1bce65eb8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0096-1900000000-de9c185519f913d3a447	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4m-9000000000-a65ba173f2844b86bd8f	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

de Mendonca, J. D., Ely, F., Palma, M. S., Frazzon, J., Basso, L. A., Santos, D. S. (2007). "Functional characterization by genetic complementation of aroB-encoded dehydroquinate synthase from Mycobacterium tuberculosis H37Rv and its heterologous expression and purification." J Bacteriol 189:6246-6252. Pubmed: 17586643
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
Ngo, P. T., Natarajan, S., Kim, H., Hung, H. K., Kim, J. G., Lee, B. M., Ahn, Y. J., Kang, L. W. (2008). "Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of 3-dehydroquinate synthase, Xoo1243, from Xanthomonas oryzae pv. oryzae." Acta Crystallogr Sect F Struct Biol Cryst Commun 64:1128-1131. Pubmed: 19052366
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	32364
HMDB ID	HMDB12710
Pubchem Compound ID	439351
Kegg ID	C00944
ChemSpider ID	388474
Wikipedia ID	3-Dehydroquinic_acid
BioCyc ID	DEHYDROQUINATE
EcoCyc ID	DEHYDROQUINATE
Ligand Expo	DQA

Enzymes

Protein Details

1. 3-dehydroquinate dehydratase

General function:: Involved in 3-dehydroquinate dehydratase activity
Specific function:: 3-dehydroquinate = 3-dehydroshikimate + H(2)O
Gene Name:: aroD
Uniprot ID:: P05194
Molecular weight:: 27466

Reactions

3-dehydroquinate = 3-dehydroshikimate + H(2)O.

Protein Details

2. 3-dehydroquinate synthase

General function:: Involved in 3-dehydroquinate synthase activity
Specific function:: 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate
Gene Name:: aroB
Uniprot ID:: P07639
Molecular weight:: 38881

Reactions

3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate.

Protein Details

3. Quinate/shikimate dehydrogenase

General function:: Involved in nucleotide binding
Specific function:: The physiological substrate is not known
Gene Name:: ydiB
Uniprot ID:: P0A6D5
Molecular weight:: 31228

Reactions

L-quinate + NAD(P)(+) = 3-dehydroquinate + NAD(P)H.
Shikimate + NAD(P)(+) = 3-dehydroshikimate + NAD(P)H.

3-Dehydroquinate (ECMDB04049) (M2MDB000582)

Structure for #<Compound:0xaffacaa8>

Enzymes

Reactions

Reactions

Reactions