MiMeDB: Showing metabocard for 5-dehydro-4-deoxy-D-glucarate(2‚àí) (MMDBc0032119)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:03:11 UTC

Update Date

2024-10-13 09:07:02 UTC

Metabolite ID

MMDBc0032119

Metabolite Identification

Common Name

5-dehydro-4-deoxy-D-glucarate(2‚àí)

Description

NULL

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231216482D          

 13 12  0  0  1  0            999 V2000
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    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  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
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  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
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  CHG  2   7  -1  12  -1
M  END
> <DATABASE_ID>
MMDBc0032119

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2,4,7,9H,1H2,(H,10,11)(H,12,13)/p-2/t2-,4+/m0/s1

> <INCHI_KEY>
QUURPCHWPQNNGL-ZAFYKAAXSA-L

> <FORMULA>
C6H6O7

> <MOLECULAR_WEIGHT>
190.1076

> <EXACT_MASS>
190.011352546

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
14.694627719914205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-2,3-dihydroxy-5-oxohexanedioate

> <ALOGPS_LOGP>
-1.36

> <JCHEM_LOGP>
-1.4547567023333332

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.3383843993566726

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4970879331320455

> <JCHEM_PKA_STRONGEST_BASIC>
-3.348200381892739

> <JCHEM_POLAR_SURFACE_AREA>
137.79000000000002

> <JCHEM_REFRACTIVITY>
57.85790000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.62e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-dehydro-4-deoxy-D-glucarate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0       3.286   4.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    2   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2,3-DIHYDROXY-5-oxo-hexanedioATE	ChEBI
3-Deoxy-(L)-threo-2-hexulosarate	ChEBI
5-Dehydro-4-deoxy-D-glucarate	ChEBI
5-KDG	ChEBI
2,3-DIHYDROXY-5-oxo-hexanedioic acid	Generator
3-Deoxy-(L)-threo-2-hexulosaric acid	Generator
5-Dehydro-4-deoxy-D-glucaric acid	Generator
5-Dehydro-4-deoxy-D-glucaric acid(2−)	Generator
(2R,3S)-2,3-Dihydroxy-5-oxohexanedioate	ChEBI
(2R,3S)-2,3-Dihydroxy-5-oxohexanedioic acid	Generator

Molecular Formula

C₆H₆O₇

Average Mass

190.1076

Monoisotopic Mass

190.011352546

IUPAC Name

(2R,3S)-2,3-dihydroxy-5-oxohexanedioate

Traditional Name

5-dehydro-4-deoxy-D-glucarate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H8O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2,4,7,9H,1H2,(H,10,11)(H,12,13)/p-2/t2-,4+/m0/s1

InChI Key

QUURPCHWPQNNGL-ZAFYKAAXSA-L

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
Beta-hydroxy acid
Alpha-keto acid
Beta-hydroxy ketone
Dicarboxylic acid or derivatives
Hydroxy acid
Monosaccharide
Ketone
1,2-diol
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Carbonyl group
Alcohol
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:42819 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	262 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.5	ChemAxon
logS	0.06	ALOGPS
pKa (Strongest Acidic)	2.5	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	137.79 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	57.86 m³·mol⁻¹	ChemAxon
Polarizability	14.69 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

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018161	Galactaric acid	5-dehydro-4-deoxy-D-glucarate(2‚àí)	Galactarate dehydratase (L-threo-forming)	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018162	D-glucarate	5-dehydro-4-deoxy-D-glucarate(2‚àí)	Glucarate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018163	5-dehydro-4-deoxy-D-glucarate(2‚àí)	Tartronate semialdehyde	5-keto-4-deoxy-D-glucarate aldolase	Aldol addition (or reverse)	PathBank	31602464

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

DB03237

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

5-KETO-4-DEOXY-D-GLUCARATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5288442

PDB ID

Not Available

ChEBI ID

42819

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for 5-dehydro-4-deoxy-D-glucarate(2‚àí) (MMDBc0032119)

MOL for #<Metabolite:0x00007f9238b2b430>

3D MOL for #<Metabolite:0x00007f9238b2b430>

3D SDF for #<Metabolite:0x00007f9238b2b430>

3D-SDF for #<Metabolite:0x00007f9238b2b430>

PDB for #<Metabolite:0x00007f9238b2b430>

3D PDB for #<Metabolite:0x00007f9238b2b430>

SMILES for #<Metabolite:0x00007f9238b2b430>

INCHI for #<Metabolite:0x00007f9238b2b430>

Structure for #<Metabolite:0x00007f9238b2b430>

3D Structure for #<Metabolite:0x00007f9238b2b430>