MiMeDB: Showing metabocard for 6-phospho-2-dehydro-D-gluconic acid (MMDBc0033159)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:37:06 UTC

Update Date

2022-08-31 22:26:50 UTC

Metabolite ID

MMDBc0033159

Metabolite Identification

Common Name

6-phospho-2-dehydro-D-gluconic acid

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222382D          

 17 16  0  0  1  0            999 V2000
    1.4290    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1435    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2869    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1435    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2869   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 13  1  0  0  0  0
  2  7  1  1  0  0  0
  2  3  1  0  0  0  0
  3  8  1  6  0  0  0
  3  4  1  0  0  0  0
  4  9  1  6  0  0  0
  4  5  1  0  0  0  0
  5 10  2  0  0  0  0
  5  6  1  0  0  0  0
  6 11  2  0  0  0  0
  6 12  1  0  0  0  0
 13 16  1  0  0  0  0
 16 14  1  0  0  0  0
 16 15  2  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033159

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O10P/c7-2(1-16-17(13,14)15)3(8)4(9)5(10)6(11)12/h2-4,7-9H,1H2,(H,11,12)(H2,13,14,15)/t2-,3-,4+/m1/s1

> <INCHI_KEY>
ZKUSPPOKDDRMIU-JJYYJPOSSA-N

> <FORMULA>
C6H11O10P

> <MOLECULAR_WEIGHT>
274.1193

> <EXACT_MASS>
274.008983084

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
20.837690653131133

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R,5R)-3,4,5-trihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-2.6137557323333334

> <ALOGPS_LOGS>
-1.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.7908724855368914

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4634723290194778

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5451291846761714

> <JCHEM_POLAR_SURFACE_AREA>
181.81999999999996

> <JCHEM_REFRACTIVITY>
48.52739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.81e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4R,5R)-3,4,5-trihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.336   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.335  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.002  -1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      10.669   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.334   0.770   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.334   0.770   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000  -1.540   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  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    7    3                                                  
CONECT    3    2    8    4                                                  
CONECT    4    3    9    5                                                  
CONECT    5    4   10    6                                                  
CONECT    6    5   11   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    1   16                                                       
CONECT   14   16                                                            
CONECT   15   16                                                            
CONECT   16   13   14   15   17                                             
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

Synonyms

Value	Source
2-Dehydro-D-gluconate 6-phosphate	ChEBI
6-O-Phosphono-D-fructosonic acid	ChEBI
6-Phospho-2-dehydro-D-gluconate	ChEBI
2-Dehydro-D-gluconic acid 6-phosphoric acid	Generator
6-O-Phosphono-D-fructosonate	Generator
6-Phospho-2-dehydro-D-gluconic acid	Generator
Gluconic acid 6-phosphoric acid	Generator

Molecular Formula

C₆H₁₁O₁₀P

Average Mass

274.1193

Monoisotopic Mass

274.008983084

IUPAC Name

(3S,4R,5R)-3,4,5-trihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

Traditional Name

(3S,4R,5R)-3,4,5-trihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

CAS Registry Number

Not Available

SMILES

O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C(=O)C(O)=O

InChI Identifier

InChI=1S/C6H11O10P/c7-2(1-16-17(13,14)15)3(8)4(9)5(10)6(11)12/h2-4,7-9H,1H2,(H,11,12)(H2,13,14,15)/t2-,3-,4+/m1/s1

InChI Key

ZKUSPPOKDDRMIU-JJYYJPOSSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexose phosphates. These are carbohydrate derivatives containing a hexose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexose phosphates

Alternative Parents

Substituents

Hexose phosphate
Monosaccharide phosphate
Medium-chain keto acid
Beta-hydroxy acid
Monoalkyl phosphate
Acyloin
Alpha-keto acid
Beta-hydroxy ketone
Hydroxy acid
Keto acid
Alkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid phosphate (CHEBI:2229 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	18.1 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.46	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	181.82 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	48.53 m³·mol⁻¹	ChemAxon
Polarizability	20.84 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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 (Non-derivatized) - 70eV, Positive	splash10-052b-9410000000-15e516a6eb4528df2e55	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1590000000-473049a8ab212babee28	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4m-5920000000-5d8d2e96d08d415c01f0	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9500000000-cccaa65ce975842470c7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-7920000000-1a6630c6f0dd4acc0f57	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9300000000-95e1be9194d2eebf89ad	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-9351d83d2e99c383ba18	2016-09-12	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019101	Gluconic acid	Hydrogen Ion	Thermosensitive gluconokinase	Phosphorylation	PathBank	31602464
MMDBr0019102	6-phospho-2-dehydro-D-gluconic acid	Water	Phosphogluconate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0019103	NADP	Carbon dioxide	6-phosphogluconate dehydrogenase, decarboxylating	Dehydrogenation	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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	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

C01218

BioCyc ID

CPD-339

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

2229

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 ]

Showing metabocard for 6-phospho-2-dehydro-D-gluconic acid (MMDBc0033159)

MOL for #<Metabolite:0x00007fa4b1bcdda8>

3D MOL for #<Metabolite:0x00007fa4b1bcdda8>

3D SDF for #<Metabolite:0x00007fa4b1bcdda8>

3D-SDF for #<Metabolite:0x00007fa4b1bcdda8>

PDB for #<Metabolite:0x00007fa4b1bcdda8>

3D PDB for #<Metabolite:0x00007fa4b1bcdda8>

SMILES for #<Metabolite:0x00007fa4b1bcdda8>

INCHI for #<Metabolite:0x00007fa4b1bcdda8>

Structure for #<Metabolite:0x00007fa4b1bcdda8>

3D Structure for #<Metabolite:0x00007fa4b1bcdda8>