MiMeDB: Showing metabocard for 5-Dehydro-4-deoxy-D-glucuronate (MMDBc0030027)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:51:10 UTC

Update Date

2022-08-31 17:38:50 UTC

Metabolite ID

MMDBc0030027

Metabolite Identification

Common Name

5-Dehydro-4-deoxy-D-glucuronate

Description

5-dehydro-4-deoxy-D-glucuronate is a member of the chemical class known as Medium-chain Keto Acids and Derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10231213002D          

 14 13  0  0  0  0            999 V2000
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  2  0  0  0  0
  3  8  1  6  0  0  0
  9  4  2  0  0  0  0
  5 10  1  6  0  0  0
 11  6  1  0  0  0  0
 12  6  2  0  0  0  0
  3 13  1  6  0  0  0
  5 14  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030027

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(CC(=O)C(O)=O)[C@@]([H])(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O6/c7-2-5(10)3(8)1-4(9)6(11)12/h2-3,5,8,10H,1H2,(H,11,12)/t3-,5-/m0/s1

> <INCHI_KEY>
IMUGYKFHMJLTOU-UCORVYFPSA-N

> <FORMULA>
C6H8O6

> <MOLECULAR_WEIGHT>
176.1241

> <EXACT_MASS>
176.032087988

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
14.62067271638125

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,5R)-4,5-dihydroxy-2,6-dioxohexanoic acid

> <ALOGPS_LOGP>
-0.83

> <JCHEM_LOGP>
-1.6133729546666669

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.469673254148052

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.74051007389193

> <JCHEM_PKA_STRONGEST_BASIC>
-3.307254984541694

> <JCHEM_POLAR_SURFACE_AREA>
111.9

> <JCHEM_REFRACTIVITY>
35.258300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.95e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,5R)-4,5-dihydroxy-2,6-dioxohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5    7                                                       
CONECT    3    1    5    8   13                                             
CONECT    4    1    6    9                                                  
CONECT    5    2    3   10   14                                             
CONECT    6    4   11   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    5                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
4-Deoxy-L-threo-5-hexulosuronic acid	ChEBI
4-Deoxy-L-threo-5-hexosulose uronate	Kegg
4-Deoxy-L-threo-5-hexulosuronate	Generator
4-Deoxy-L-threo-5-hexosulose uronic acid	Generator
5-Dehydro-4-deoxy-D-glucuronic acid	Generator

Molecular Formula

C₆H₈O₆

Average Mass

176.1241

Monoisotopic Mass

176.032087988

IUPAC Name

(4S,5R)-4,5-dihydroxy-2,6-dioxohexanoic acid

Traditional Name

(4S,5R)-4,5-dihydroxy-2,6-dioxohexanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H8O6/c7-2-5(10)3(8)1-4(9)6(11)12/h2-3,5,8,10H,1H2,(H,11,12)/t3-,5-/m0/s1

InChI Key

IMUGYKFHMJLTOU-UCORVYFPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-chain keto acids and derivatives

Alternative Parents

Substituents

Medium-chain keto acid
Alpha-keto acid
Beta-hydroxy aldehyde
Monosaccharide
Beta-hydroxy ketone
Alpha-hydroxy ketone
Alpha-hydroxyaldehyde
1,2-diol
Secondary alcohol
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Aldehyde
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

aldehyde (CHEBI:17782 )
hexuronic acid (CHEBI:17782 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	59.5 g/L	ALOGPS
logP	-0.83	ALOGPS
logP	-1.6	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	2.74	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	111.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	35.26 m³·mol⁻¹	ChemAxon
Polarizability	14.62 Å³	ChemAxon
Number of Rings	0	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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a6r-1900000000-a9f87e1e1b45b21a9c50	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052o-6900000000-29c988b39df0688cac74	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05g3-9200000000-1928f891d89be4d0a031	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-4900000000-d0ab666bff7db4170c90	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-298be5aa2cd24e61771e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pic-9200000000-1ba33abdcb4a9282b198	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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
MMDBr0013973	4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonic acid	5-Dehydro-4-deoxy-D-glucuronate	Oligogalacturonate lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0014393	5-Dehydro-4-deoxy-D-glucuronate	(4S)-4,6-Dihydroxy-2,5-dioxohexanoate	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase	Isomerization	RHEA	34755880
MMDBr0015022	2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnose	5-Dehydro-4-deoxy-D-glucuronate	Unsaturated rhamnogalacturonyl hydrolase YesR	Hydrolysis of bond	RHEA	34755880
MMDBr0015064	beta-D-Delta(4)-GlcA-(1->4)-beta-D-Glc-(1->4)-alpha-L-Rha-(1->3)-D-Glc	5-Dehydro-4-deoxy-D-glucuronate	Unsaturated glucuronyl hydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0015067	beta-D-4-deoxy-Delta(4)-GlcpA-(1->3)-beta-D-GalpNAc6S	5-Dehydro-4-deoxy-D-glucuronate	Unsaturated chondroitin disaccharide hydrolase	Hydrolysis of bond	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
Bacteria	Proteobacteria	72	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Firmicutes	17	Human feces; Human
Bacteria	Bacteroidetes	3	Human ; Human feces
Bacteria	Actinobacteria	1
Bacteria	Verrucomicrobia	1
Bacteria/NULL	Bacteroidetes	1	Human ; Human feces

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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04053

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460049

PDB ID

Not Available

ChEBI ID

17782

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 5-Dehydro-4-deoxy-D-glucuronate (MMDBc0030027)

MOL for #<Metabolite:0x000055d24b310470>

3D MOL for #<Metabolite:0x000055d24b310470>

3D SDF for #<Metabolite:0x000055d24b310470>

3D-SDF for #<Metabolite:0x000055d24b310470>

PDB for #<Metabolite:0x000055d24b310470>

3D PDB for #<Metabolite:0x000055d24b310470>

SMILES for #<Metabolite:0x000055d24b310470>

INCHI for #<Metabolite:0x000055d24b310470>

Structure for #<Metabolite:0x000055d24b310470>

3D Structure for #<Metabolite:0x000055d24b310470>