MiMeDB: Showing metabocard for 2-Dehydro-3-deoxy-D-galactonate-6-phosphate (MMDBc0029767)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:40:45 UTC

Update Date

2022-08-31 17:16:48 UTC

Metabolite ID

MMDBc0029767

Metabolite Identification

Common Name

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

Description

2-Dehydro-3-deoxy-D-galactonate-6-phosphate is an intermediate in D-galactonate degradation. It is a substrate for the enzyme 2-dehydro-3-deoxygalactonokinase. This enzyme catalyzes the following reaction: ATP + 2-dehydro-3-deoxy-D-galactonate = ADP + 2-dehydro-3-deoxy-D-galactonate 6-phosphate.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131209032D          

 18 17  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  2  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
    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  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
   -0.3829   -2.2539    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.0809   -1.1270    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7441   -2.5559    0.0000 O   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
    0.3316   -1.8414    0.0000 P   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
  3  7  1  6  0  0  0
  8  4  2  0  0  0  0
  5  9  1  6  0  0  0
 10  6  1  0  0  0  0
 11  6  2  0  0  0  0
 15  2  1  0  0  0  0
 16 12  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  2  0  0  0  0
 16 15  1  0  0  0  0
  3 17  1  6  0  0  0
  5 18  1  6  0  0  0
M  CHG  3  10  -1  12  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0029767

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(COP([O-])([O-])=O)[C@]([H])(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/t3-,5-/m1/s1

> <INCHI_KEY>
OVPRPPOVAXRCED-NQXXGFSBSA-K

> <FORMULA>
C6H8O9P

> <MOLECULAR_WEIGHT>
255.0961

> <EXACT_MASS>
254.990593366

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
19.087513091415765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

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

> <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-1
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-1
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   17  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5   15                                                       
CONECT    3    1    5    7   17                                             
CONECT    4    1    6    8                                                  
CONECT    5    2    3    9   18                                             
CONECT    6    4   10   11                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12   16                                                            
CONECT   13   16                                                            
CONECT   14   16                                                            
CONECT   15    2   16                                                       
CONECT   16   12   13   14   15                                             
CONECT   17    3                                                            
CONECT   18    5                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

Synonyms

Value	Source
2-Dehydro-3-deoxy-6-phospho-D-galactonate	ChEBI
2-Dehydro-3-deoxy-D-galactonate 6-phosphate	ChEBI
6-Phosphonato-2-dehydro-3-deoxy-D-galactate	ChEBI
6-Phosphonato-2-dehydro-3-deoxy-D-galactate trianion	ChEBI
2-Dehydro-3-deoxy-6-phospho-D-galactonic acid	Generator
2-Dehydro-3-deoxy-D-galactonic acid 6-phosphoric acid	Generator
6-Phosphonato-2-dehydro-3-deoxy-D-galactic acid	Generator
6-Phosphonato-2-dehydro-3-deoxy-D-galactic acid trianion	Generator
2-Dehydro-3-deoxy-D-galactonic acid-6-phosphoric acid	Generator

Molecular Formula

C₆H₈O₉P

Average Mass

255.0961

Monoisotopic Mass

254.990593366

IUPAC Name

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

Traditional Name

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

CAS Registry Number

32120-43-7

SMILES

[H][C@@](O)(COP([O-])([O-])=O)[C@]([H])(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/t3-,5-/m1/s1

InChI Key

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carbohydrate acid derivative anion (CHEBI:58298 )
monocarboxylic acid anion (CHEBI:58298 )
organophosphate oxoanion (CHEBI:58298 )

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	19.09 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0090000000-ccd81029fc1edd59d640	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-1190000000-f90e3c37265203a7fa74	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-002b-9520000000-5882a8735868be858ff3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-1090000000-a6094f08a52ce8975fce	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-6290000000-74be9cee7ef2c6c79911	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001j-9000000000-52e121f3b1c1fb764bb4	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

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

Not Available

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

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

44229080

PDB ID

Not Available

ChEBI ID

58298

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]
Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]

Showing metabocard for 2-Dehydro-3-deoxy-D-galactonate-6-phosphate (MMDBc0029767)

MOL for #<Metabolite:0x00007feca7264d00>

3D MOL for #<Metabolite:0x00007feca7264d00>

3D SDF for #<Metabolite:0x00007feca7264d00>

3D-SDF for #<Metabolite:0x00007feca7264d00>

PDB for #<Metabolite:0x00007feca7264d00>

3D PDB for #<Metabolite:0x00007feca7264d00>

SMILES for #<Metabolite:0x00007feca7264d00>

INCHI for #<Metabolite:0x00007feca7264d00>

Structure for #<Metabolite:0x00007feca7264d00>

3D Structure for #<Metabolite:0x00007feca7264d00>