MiMeDB: Showing metabocard for 2-Dehydro-3-deoxy-D-gluconate (MMDBc0049977)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:28 UTC

Update Date

2022-09-01 02:17:40 UTC

Metabolite ID

MMDBc0049977

Metabolite Identification

Common Name

2-Dehydro-3-deoxy-D-gluconate

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131208502D          

 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  2  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  1  0  0  0  0
  3  8  1  6  0  0  0
  9  4  2  0  0  0  0
  5 10  1  1  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  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049977

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1

> <INCHI_KEY>
WPAMZTWLKIDIOP-WVZVXSGGSA-N

> <FORMULA>
C6H10O6

> <MOLECULAR_WEIGHT>
178.14

> <EXACT_MASS>
178.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.516391744095914

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

> <ALOGPS_LOGP>
-1.87

> <JCHEM_LOGP>
-1.7750312403333335

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.243645462336318

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9051234753891952

> <JCHEM_PKA_STRONGEST_BASIC>
-2.972361954381558

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
36.3163

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.34e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-dehydro-3-deoxy-D-gluconate

> <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  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
2-Dehydro-3-deoxy-D-gluconate	ChEBI
2-Keto-3-deoxy-D-gluconate	ChEBI
3-Deoxy-2-oxo-D-gluconate	ChEBI
3-Deoxy-D-erythro-2-hexulosonic acid	ChEBI
2-Dehydro-3-deoxy-D-gluconic acid	Generator
3-Deoxy-2-oxo-D-gluconic acid	Generator
3-Deoxy-D-erythro-2-hexulosonate	Generator
2-keto-3-Deoxygluconate	MeSH

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738052

IUPAC Name

(4S,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

Traditional Name

2-dehydro-3-deoxy-D-gluconate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1

InChI Key

WPAMZTWLKIDIOP-WVZVXSGGSA-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 ketone
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Primary alcohol
Organooxygen compound
Organic oxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:17032 )
hexonic acid (CHEBI:17032 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	134 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-1.8	ChemAxon
logS	-0.12	ALOGPS
pKa (Strongest Acidic)	2.91	ChemAxon
pKa (Strongest Basic)	-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	5	ChemAxon
Refractivity	36.32 m³·mol⁻¹	ChemAxon
Polarizability	15.52 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_2_10) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03fu-1900000000-b83e7928054ed87e61ea	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p6-7900000000-0ec05107fe4cacbafdc2	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dv-9200000000-1155f7c7fe0875a6e135	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-ac6a432df8fcf15017f9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-ad5a44111e40a3f47da6	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-059f-9200000000-b4281968f243d4a223b5	2015-09-15	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
MMDBr0007713	D-Altronate	2-Dehydro-3-deoxy-D-gluconate	Not Available	Altronate hydrolase	VMH	30371894
MMDBr0007746	2-Dehydro-3-deoxy-D-gluconate	2-Dehydro-3-deoxy-D-gluconate	Not Available	2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible	VMH	30371894
MMDBr0007912	D-Mannonate	2-Dehydro-3-deoxy-D-gluconate	Not Available	D-mannonate hydrolyase	VMH	30371894
MMDBr0008286	Gluconic acid	2-Dehydro-3-deoxy-D-gluconate	Not Available	Gluconate dehydratase	VMH	30371894
MMDBr0013124	2-amino-2-deoxy-D-gluconic acid	2-Dehydro-3-deoxy-D-gluconate	Glucosaminate ammonia-lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0013355	2-Dehydro-3-deoxy-D-gluconate	2-Keto-3-deoxy-6-phosphogluconic acid	2-dehydro-3-deoxygluconokinase	Phosphorylation	RHEA	34755880
MMDBr0013356	2-Dehydro-3-deoxy-D-gluconate	2-Keto-3-deoxy-6-phosphogluconic acid	2-dehydro-3-deoxygluconokinase	Phosphorylation	RHEA	34755880
MMDBr0013477	D-Altronate	2-Dehydro-3-deoxy-D-gluconate	Altronate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0013956	D-Mannonate	2-Dehydro-3-deoxy-D-gluconate	D-galactonate dehydratase family member ManD	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014121	D-gluconic acid	2-Dehydro-3-deoxy-D-gluconate	D-galactonate dehydratase family member RspA	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014427	2-Dehydro-3-deoxy-D-gluconate	(4S)-4,6-Dihydroxy-2,5-dioxohexanoate	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0015416	2-Dehydro-3-deoxy-D-gluconate	D-Glyceraldehyde	2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase	Aldol addition (or reverse)	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	190	Human feces; Human sputum; Human stool; Human ; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Pig	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	184	Human feces; Human ; Cattle	Metabolic reconstruction
Bacteria	Bacteroidetes	84	Human feces; Human ; Human urine; Human stool; Human gastric fluid; Human appendix biopsy; Human saliva	Metabolic reconstruction
Bacteria	Fusobacteria	5	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	26	Human feces; Human ; Human nasopharyngeal swab; Human supragingival plaque	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Spirochaetes	2	Human feces; Pig	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria	Deinococcus-thermus	1
Archaea/Archaea	nah	1
Bacteria/NULL	Proteobacteria	2	Human feces; Human sputum; Human stool; Human ; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Pig	Metabolic reconstruction
Bacteria	Elusimicrobia	1
Bacteria	Thermotogae	5
Bacteria/NULL	Bacteroidetes	1	Human feces; Human ; Human urine; Human stool; Human gastric fluid; Human appendix biopsy; 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

C00204

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161227

PDB ID

Not Available

ChEBI ID

17032

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 2-Dehydro-3-deoxy-D-gluconate (MMDBc0049977)

MOL for #<Metabolite:0x00007f5ab00b2ab8>

3D MOL for #<Metabolite:0x00007f5ab00b2ab8>

3D SDF for #<Metabolite:0x00007f5ab00b2ab8>

3D-SDF for #<Metabolite:0x00007f5ab00b2ab8>

PDB for #<Metabolite:0x00007f5ab00b2ab8>

3D PDB for #<Metabolite:0x00007f5ab00b2ab8>

SMILES for #<Metabolite:0x00007f5ab00b2ab8>

INCHI for #<Metabolite:0x00007f5ab00b2ab8>

Structure for #<Metabolite:0x00007f5ab00b2ab8>

3D Structure for #<Metabolite:0x00007f5ab00b2ab8>