MiMeDB: Showing metabocard for 2-Dehydro-3-deoxy-D-galactonate 6-phosphate (MMDBc0031748)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:39 UTC

Update Date

2022-08-31 18:24:15 UTC

Metabolite ID

MMDBc0031748

Metabolite Identification

Common Name

2-Dehydro-3-deoxy-D-galactonate 6-phosphate

Description

2-Dehydro-3-deoxy-D-galactonate-6-phosphate is a member of the chemical class known as Organophosphate Esters. These are organic compounds containing phosphoric acid ester functional group. It is a substrate for 2-dehydro-3-deoxy-6-phosphogalactonate aldolase which breaks it down to pyruvate and D-glyceraldehyde 3-phosphate. It is a product of carbohydrate acid metabolism, specifically D-galactonate degradation.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533005141515392D          

 16 15  0  0  0  0            999 V2000
   -2.0651    1.3841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8902    1.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3026    0.6696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8902   -0.0448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0651   -0.0448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3028    2.0985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1278    2.0985    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.8903    2.8130    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3028   -0.7593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1278   -0.7592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8903   -1.4737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0653   -1.4738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4073   -1.4740    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3745   -2.3002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3964   -0.6257    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.5823   -1.4743    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  6  1  0  0  0  0
  1  2  2  0  0  0  0
  6  8  2  0  0  0  0
  6  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  9 11  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 10  1  0  0  0  0
M  CHG  3   7  -1  15  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0031748

> <DATABASE_NAME>
MIME

> <SMILES>
OC(COP([O-])([O-])=O)C(O)CC(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O9P/c7-3(1-4(8)6(10)11)5(9)2-15-16(12,13)14/h3,5,7,9H,1-2H2,(H,10,11)(H2,12,13,14)/p-3

> <INCHI_KEY>
OVPRPPOVAXRCED-UHFFFAOYSA-K

> <FORMULA>
C6H8O9P

> <MOLECULAR_WEIGHT>
255.096

> <EXACT_MASS>
254.992239575

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.08492126816899

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dihydroxy-2-oxo-6-(phosphonatooxy)hexanoate

> <ALOGPS_LOGP>
-1.35

> <JCHEM_LOGP>
-1.8985972716666666

> <ALOGPS_LOGS>
-0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.98091974057207

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.479791419702818

> <JCHEM_PKA_STRONGEST_BASIC>
-3.266803065880614

> <JCHEM_POLAR_SURFACE_AREA>
170.07999999999998

> <JCHEM_REFRACTIVITY>
55.782900000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.85e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydroxy-2-oxo-6-(phosphonatooxy)hexanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  O   UNK     0      -3.855   2.584   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.395   2.584   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.165   1.250   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.395  -0.084   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.855  -0.084   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -6.165   3.917   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -7.705   3.917   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0      -5.395   5.251   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -6.165  -1.417   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -7.705  -1.417   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -5.395  -2.751   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.855  -2.751   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -2.627  -2.751   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -2.566  -4.294   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.607  -1.168   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      -1.087  -2.752   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    3    6    1                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4                                                            
CONECT    6    2    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    4   11   10                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   15   16   12   14                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
2-Dehydro-3-deoxy-D-galactonic acid 6-phosphoric acid	Generator

Molecular Formula

C₆H₈O₉P

Average Mass

255.096

Monoisotopic Mass

254.992239575

IUPAC Name

4,5-dihydroxy-2-oxo-6-(phosphonatooxy)hexanoate

Traditional Name

4,5-dihydroxy-2-oxo-6-(phosphonatooxy)hexanoate

CAS Registry Number

Not Available

SMILES

OC(COP([O-])([O-])=O)C(O)CC(=O)C([O-])=O

InChI Identifier

InChI=1S/C6H11O9P/c7-3(1-4(8)6(10)11)5(9)2-15-16(12,13)14/h3,5,7,9H,1-2H2,(H,10,11)(H2,12,13,14)/p-3

InChI Key

OVPRPPOVAXRCED-UHFFFAOYSA-K

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
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Beta-hydroxy ketone
Alpha-keto acid
Secondary alcohol
Ketone
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (DEHYDRO-DEOXY-GALACTONATE-PHOSPHATE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	48.5 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.9	ChemAxon
logS	-0.8	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	170.08 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	55.78 m³·mol⁻¹	ChemAxon
Polarizability	19.08 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

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
MMDBr0008147	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	Glyceraldehyde 3-phosphate	Not Available	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	VMH	30371894
MMDBr0013539	2-Keto-3-deoxy-D-gluconic acid	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	2-dehydro-3-deoxygalactonokinase	Phosphorylation	RHEA	34755880
MMDBr0013540	2-Keto-3-deoxy-D-gluconic acid	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase	Phosphorylation	RHEA	34755880
MMDBr0014458	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	D-Glyceraldehyde 3-phosphate	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	Aldol addition (or reverse)	RHEA	34755880
MMDBr0018317	2-Keto-3-deoxy-D-gluconic acid	Hydrogen Ion	2-dehydro-3-deoxygalactonokinase	Phosphorylation	PathBank	31602464
MMDBr0018318	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	Pyruvic acid	2-dehydro-3-deoxy-6-phosphogalactonate 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	Proteobacteria	136	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	61	Human feces; Human ; Human nasopharyngeal swab; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Bacteroidetes	61	Human feces; Human appendix biopsy; Human ; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque; Human stool	Metabolic reconstruction
Bacteria	Firmicutes	133	Human feces; Human ; Human subgingival plaque; Cattle	Metabolic reconstruction
Bacteria	Fusobacteria	4	Human feces; Human	Metabolic reconstruction
Archaea	Crenarchaeota	2	Human feces
Archaea/Archaea	Euryarchaeota	2
Archaea/Archaea	Crenarchaeota	2	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
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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25203281

PDB ID

Not Available

ChEBI ID

Not Available

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 ]
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 ]
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-galactonate 6-phosphate (MMDBc0031748)

MOL for #<Metabolite:0x000055d24b1dc770>

3D MOL for #<Metabolite:0x000055d24b1dc770>

3D SDF for #<Metabolite:0x000055d24b1dc770>

3D-SDF for #<Metabolite:0x000055d24b1dc770>

PDB for #<Metabolite:0x000055d24b1dc770>

3D PDB for #<Metabolite:0x000055d24b1dc770>

SMILES for #<Metabolite:0x000055d24b1dc770>

INCHI for #<Metabolite:0x000055d24b1dc770>

Structure for #<Metabolite:0x000055d24b1dc770>

3D Structure for #<Metabolite:0x000055d24b1dc770>