MiMeDB: Showing metabocard for 5-dehydro-2-deoxy-D-gluconic acid (MMDBc0055554)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:45 UTC

Update Date

2022-08-12 20:09:24 UTC

Metabolite ID

MMDBc0055554

Metabolite Identification

Common Name

5-dehydro-2-deoxy-D-gluconic acid

Description

5-dehydro-2-deoxy-D-gluconate belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. Based on a literature review very few articles have been published on 5-dehydro-2-deoxy-D-gluconate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 14 13  0  0  1  0            999 V2000
    2.9684    0.4125    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
    2.2539    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  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
    1.5395    0.4125    0.0000 C   0  0  1  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
    2.2539   -0.8250    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  5  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
    2.2539    0.8250    0.0000 H   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
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  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
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
  6 12  1  6  0  0  0
  3 13  1  6  0  0  0
  6 14  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0055554

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/p-1/t3-,6+/m1/s1

> <INCHI_KEY>
UCYNJPYWOSFBAT-CVYQJGLWSA-M

> <FORMULA>
C6H9O6

> <MOLECULAR_WEIGHT>
177.133

> <EXACT_MASS>
177.04046159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.983760625866406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S)-3,4,6-trihydroxy-5-oxohexanoate

> <JCHEM_LOGP>
-2.2315988933333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.124380169821285

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.821926222658468

> <JCHEM_PKA_STRONGEST_BASIC>
-3.327588544284506

> <JCHEM_POLAR_SURFACE_AREA>
117.89000000000001

> <JCHEM_REFRACTIVITY>
46.9281

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.127  -0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.208   0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.875  -1.540   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       4.207   1.540   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.874  -0.770   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8   13                                             
CONECT    4    2    6    9                                                  
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12   14                                             
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    6                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
5-Dehydro-2-deoxy-D-gluconic acid	Generator

Molecular Formula

C₆H₉O₆

Average Mass

177.133

Monoisotopic Mass

177.04046159

IUPAC Name

(3R,4S)-3,4,6-trihydroxy-5-oxohexanoate

Traditional Name

5-dehydro-2-deoxy-D-gluconate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/p-1/t3-,6+/m1/s1

InChI Key

UCYNJPYWOSFBAT-CVYQJGLWSA-M

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Acyloin
Fatty acyl
Fatty acid
Beta-hydroxy ketone
Monosaccharide
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Alcohol
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organic oxide
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonate (CHEBI:16669 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.2	ChemAxon
pKa (Strongest Acidic)	3.82	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	117.89 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	46.93 m³·mol⁻¹	ChemAxon
Polarizability	14.98 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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013223	5-dehydro-2-deoxy-D-gluconic acid	6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)	5-dehydro-2-deoxygluconokinase	Phosphorylation	RHEA	34755880
MMDBr0014588	5-deoxy-D-glucuronic acid	5-dehydro-2-deoxy-D-gluconic acid	5-deoxy-glucuronate isomerase	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
Bacteria	Firmicutes	27	Human feces; Human ; Human supragingival plaque; Catfish
Bacteria	Tenericutes	3	Pig
Bacteria	Proteobacteria	1

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

5256729

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6857389

PDB ID

Not Available

ChEBI ID

16669

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-2-deoxy-D-gluconic acid (MMDBc0055554)

MOL for #<Metabolite:0x00007fe2a550b2b8>

3D MOL for #<Metabolite:0x00007fe2a550b2b8>

3D SDF for #<Metabolite:0x00007fe2a550b2b8>

3D-SDF for #<Metabolite:0x00007fe2a550b2b8>

PDB for #<Metabolite:0x00007fe2a550b2b8>

3D PDB for #<Metabolite:0x00007fe2a550b2b8>

SMILES for #<Metabolite:0x00007fe2a550b2b8>

INCHI for #<Metabolite:0x00007fe2a550b2b8>

Structure for #<Metabolite:0x00007fe2a550b2b8>

3D Structure for #<Metabolite:0x00007fe2a550b2b8>