MiMeDB: Showing metabocard for 5-Dehydro-4-deoxy-D-glucarate (MMDBc0030026)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:51:08 UTC

Update Date

2022-08-31 17:38:50 UTC

Metabolite ID

MMDBc0030026

Metabolite Identification

Common Name

5-Dehydro-4-deoxy-D-glucarate

Description

5-dehydro-4-deoxy-D-glucarate is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose. KDG is invovled in D-glucarate metabolism. Crystals of GlucD have been obtained into which the substrate D-glucarate and two competitive inhibitors, 4-deoxy-D-glucarate and xylarohydroxamate, could be diffused; D-glucarate is converted to the dehydration product, 5-keto-4-deoxy-D-glucarate (KDG). (PMID 10769114 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131209262D          

 15 14  0  0  0  0            999 V2000
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6829   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  2  7  1  6  0  0  0
  8  3  2  0  0  0  0
  4  9  1  6  0  0  0
 10  5  1  0  0  0  0
 11  5  2  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
  2 14  1  6  0  0  0
  4 15  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030026

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(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)/t2-,4+/m0/s1

> <INCHI_KEY>
QUURPCHWPQNNGL-ZAFYKAAXSA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
15.513442193856363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.23

> <JCHEM_LOGP>
-1.4547567023333332

> <ALOGPS_LOGS>
-0.56

> <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>
132.13

> <JCHEM_REFRACTIVITY>
36.183699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.27e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4    7   14                                             
CONECT    3    1    5    8                                                  
CONECT    4    2    6    9   15                                             
CONECT    5    3   10   11                                                  
CONECT    6    4   12   13                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    2                                                            
CONECT   15    4                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
(2R,3S)-2,3-Dihydroxy-5-oxohexanedioate	Kegg
(2R,3S)-2,3-Dihydroxy-5-oxohexanedioic acid	Generator
5-Dehydro-4-deoxy-D-glucaric acid	Generator

Molecular Formula

C₆H₈O₇

Average Mass

192.1235

Monoisotopic Mass

192.02700261

IUPAC Name

(2R,3S)-2,3-dihydroxy-5-oxohexanedioic acid

Traditional Name

5-dehydro-4-deoxy-D-glucarate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(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)/t2-,4+/m0/s1

InChI Key

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-hydroxy carboxylic acid (CHEBI:16369 )
oxo dicarboxylic acid (CHEBI:16369 )
2-hydroxydicarboxylic acid (CHEBI:16369 )
2-hydroxy carboxylic acid (CHEBI:16369 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	52.7 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1.5	ChemAxon
logS	-0.56	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	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	36.18 m³·mol⁻¹	ChemAxon
Polarizability	15.51 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_3_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-1900000000-dc22098bdfbe7bf4390d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-3900000000-d866ef19e96da0564480	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9400000000-a4c21560ef2a755924c8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-006w-2900000000-670ae8cd92a88762c2af	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fg2-7900000000-1e841b13a298bc87f638	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-9800000000-3d471b650b26cf2a0f96	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

Feces

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
MMDBr0007827	5-Dehydro-4-deoxy-D-glucarate	2-Hydroxy-3-oxopropanoate	Not Available	5-dehydro-4-deoxyglucarate aldolase	VMH	30371894
MMDBr0007828	Glucaric acid	5-Dehydro-4-deoxy-D-glucarate	Not Available	Glucarate dehydratase	VMH	30371894
MMDBr0008324	5-Dehydro-4-deoxy-D-glucarate	2,5-Dioxopentanoate	Not Available	5-Dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating)	VMH	30371894
MMDBr0012621	5-Dehydro-4-deoxy-D-glucarate	2,5-Dioxopentanoate	Not Available	5-Dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating), irreversible	VMH	30371894
MMDBr0013327	D-glucarate	5-Dehydro-4-deoxy-D-glucarate	Glucarate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0013484	Galactaric acid	5-Dehydro-4-deoxy-D-glucarate	Probable galactarate dehydratase (L-threo-forming)	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0013485	Galactaric acid	5-Dehydro-4-deoxy-D-glucarate	Galactarate dehydratase (L-threo-forming)	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014466	5-Dehydro-4-deoxy-D-glucarate	2,5-Dioxopentanoate	Probable 5-dehydro-4-deoxyglucarate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014726	5-Dehydro-4-deoxy-D-glucarate	2-Hydroxy-3-oxopropanoate	5-keto-4-deoxy-D-glucarate aldolase	Aldol addition (or reverse)	RHEA	34755880
MMDBr0015966	L-altrarate	5-Dehydro-4-deoxy-D-glucarate	L-talarate/galactarate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0015967	L-altrarate	5-Dehydro-4-deoxy-D-glucarate	L-talarate/galactarate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0016141	D-galactaro-1,4-lactone	5-Dehydro-4-deoxy-D-glucarate	D-galactarolactone cycloisomerase	Isomerization	RHEA	34755880
MMDBr0016142	D-glucaro-1,4-lactone	5-Dehydro-4-deoxy-D-glucarate	D-galactarolactone cycloisomerase	Isomerization	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	143	Human feces; Human sputum; Human ; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	30	Human feces; Pig ; Human	Metabolic reconstruction
Bacteria	Fusobacteria	2	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	20	Human feces; Human ; Human supragingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	4	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

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

C00679

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439290

PDB ID

Not Available

ChEBI ID

16369

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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-glucarate (MMDBc0030026)

MOL for #<Metabolite:0x000055d24aef20c8>

3D MOL for #<Metabolite:0x000055d24aef20c8>

3D SDF for #<Metabolite:0x000055d24aef20c8>

3D-SDF for #<Metabolite:0x000055d24aef20c8>

PDB for #<Metabolite:0x000055d24aef20c8>

3D PDB for #<Metabolite:0x000055d24aef20c8>

SMILES for #<Metabolite:0x000055d24aef20c8>

INCHI for #<Metabolite:0x000055d24aef20c8>

Structure for #<Metabolite:0x000055d24aef20c8>

3D Structure for #<Metabolite:0x000055d24aef20c8>