MiMeDB: Showing metabocard for 3-dehydro-4-O-phospho-D-erythronate (MMDBc0055355)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:49:56 UTC

Update Date

2025-10-07 16:09:04 UTC

Metabolite ID

MMDBc0055355

Metabolite Identification

Common Name

3-dehydro-4-O-phospho-D-erythronate

Description

3-dehydro-4-O-phospho-D-erythronate is a phospho-derivative of erythronate and belongs to the class of phosphorylated carbohydrates. There is limited literature available on this metabolite, indicating that it has not been extensively studied in the context of biochemical pathways or physiological roles.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221492D          

 14 13  0  0  1  0            999 V2000
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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
    3.3000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  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
    0.8250    0.0000    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
    2.8875   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  3  6  1  1  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
 12  1  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
  3 14  1  1  0  0  0
M  CHG  3   8  -1   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0055355

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H7O8P/c5-2(3(6)4(7)8)1-12-13(9,10)11/h3,6H,1H2,(H,7,8)(H2,9,10,11)/p-3/t3-/m1/s1

> <INCHI_KEY>
SMTGVDDLBJESIT-GSVOUGTGSA-K

> <FORMULA>
C4H4O8P

> <MOLECULAR_WEIGHT>
211.043

> <EXACT_MASS>
210.966024827

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.44972932871796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-3-oxo-4-(phosphonooxy)butanoate

> <JCHEM_LOGP>
-1.6574642836666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.243244474598842

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1590837642836043

> <JCHEM_PKA_STRONGEST_BASIC>
-4.59352106558621

> <JCHEM_POLAR_SURFACE_AREA>
149.85000000000002

> <JCHEM_REFRACTIVITY>
45.0459

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-hydroxy-3-oxo-4-(phosphonooxy)butanoate

> <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       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.160  -2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.620  -0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.850  -4.001   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       6.930  -4.001   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       6.930  -1.334   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   14  H   UNK     0       5.390  -1.334   0.000  0.00  0.00           H+0
CONECT    1    2   12                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2    4    6   14                                             
CONECT    4    3    7    8                                                  
CONECT    5    2                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11   13                                                            
CONECT   12    1   13                                                       
CONECT   13    9   10   11   12                                             
CONECT   14    3                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
3-Dehydro-4-O-phospho-D-erythronate	ChEBI
3-Dehydro-4-O-phospho-D-erythronic acid	Generator
3-Dehydro-4-phospho-D-erythronic acid	Generator

Molecular Formula

C₄H₄O₈P

Average Mass

211.043

Monoisotopic Mass

210.966024827

IUPAC Name

(2R)-2-hydroxy-3-oxo-4-(phosphonooxy)butanoate

Traditional Name

(2R)-2-hydroxy-3-oxo-4-(phosphonooxy)butanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H7O8P/c5-2(3(6)4(7)8)1-12-13(9,10)11/h3,6H,1H2,(H,7,8)(H2,9,10,11)/p-3/t3-/m1/s1

InChI Key

SMTGVDDLBJESIT-GSVOUGTGSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Glycerone phosphates

Alternative Parents

Substituents

Glycerone phosphate
Short-chain keto acid
Beta-keto acid
Alkyl phosphate
1,3-dicarbonyl compound
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Keto acid
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.7	ChemAxon
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	149.85 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	45.05 m³·mol⁻¹	ChemAxon
Polarizability	14.45 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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	296.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	104.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	158.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	432.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	315.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	357.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	1124.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	291.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	947.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	224.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	219.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	216.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	67.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	408.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	746.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	76.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	269.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	999.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	688.7

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(=O)COP(=O)([O-])[O-]	standard non polar	2025-10-24	1847.52
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_2	C[Si](C)(C)OC(COP(=O)([O-])[O-])=C(O)C(=O)[O-]	standard non polar	2025-10-24	1883.28
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_3	C[Si](C)(C)OC(=COP(=O)([O-])[O-])[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2077.55
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_4	C[Si](C)(C)OC(COP(=O)([O-])[O-])=C(O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1970.71
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_5	C[Si](C)(C)OC(=COP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1639.16
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(=O)COP(=O)([O-])[O-]	standard polar	2025-10-24	1610.43
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_2	C[Si](C)(C)OC(COP(=O)([O-])[O-])=C(O)C(=O)[O-]	standard polar	2025-10-24	2269.28
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_3	C[Si](C)(C)OC(=COP(=O)([O-])[O-])[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2437.17
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_4	C[Si](C)(C)OC(COP(=O)([O-])[O-])=C(O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1751.03
Gas Chromatography	3-dehydro-4-O-phospho-D-erythronate_TMS_5	C[Si](C)(C)OC(=COP(=O)([O-])[O-])[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1572.85

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	11	Human ; Human feces; Cattle
Bacteria	Proteobacteria	1	Human ; Human feces; Cattle

Exposure Sources

Other Exposures

Source Type	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

76962881

KEGG Compound ID

Not Available

BioCyc ID

CPD-19881

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

126456490

PDB ID

Not Available

ChEBI ID

136593

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 3-dehydro-4-O-phospho-D-erythronate (MMDBc0055355)

MOL for #<Metabolite:0x00007fc974d504e0>

3D MOL for #<Metabolite:0x00007fc974d504e0>

3D SDF for #<Metabolite:0x00007fc974d504e0>

3D-SDF for #<Metabolite:0x00007fc974d504e0>

PDB for #<Metabolite:0x00007fc974d504e0>

3D PDB for #<Metabolite:0x00007fc974d504e0>

SMILES for #<Metabolite:0x00007fc974d504e0>

INCHI for #<Metabolite:0x00007fc974d504e0>

Structure for #<Metabolite:0x00007fc974d504e0>

3D Structure for #<Metabolite:0x00007fc974d504e0>