MiMeDB: Showing metabocard for 4-Phospho-D-erythronate (MMDBc0030021)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:57 UTC

Update Date

2022-08-31 17:38:43 UTC

Metabolite ID

MMDBc0030021

Metabolite Identification

Common Name

4-Phospho-D-erythronate

Description

4-phospho-D-erythronate is a member of the chemical class known as Beta Hydroxy Acids and Derivatives. These are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. To establish a possible role of E4PDH in pyridoxal 5'-phosphate biosynthesis, we showed that 4-phosphoerythronate is a likely substrate for the 2-hydroxy-acid dehydrogenase encoded by the pdxB gene. (PMID 7751290 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10211208552D          

 15 14  0  0  0  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  2  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  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    0.8250    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
    0.8250    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
    1.6500   -1.4289    0.0000 H   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
  2  5  1  6  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
  2 14  1  6  0  0  0
  3 15  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030021

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9O8P/c5-2(3(6)4(7)8)1-12-13(9,10)11/h2-3,5-6H,1H2,(H,7,8)(H2,9,10,11)/t2-,3-/m1/s1

> <INCHI_KEY>
ZCZXOHUILRHRQJ-PWNYCUMCSA-N

> <FORMULA>
C4H9O8P

> <MOLECULAR_WEIGHT>
216.0832

> <EXACT_MASS>
216.003503776

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
15.983749664120523

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2,3-dihydroxy-4-(phosphonooxy)butanoic acid

> <ALOGPS_LOGP>
-2.33

> <JCHEM_LOGP>
-2.2726404579999997

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.469281509972466

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4662169826577083

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6151014494314717

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
37.2189

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.96e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-phospho-D-erythronic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-OCT-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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+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+0
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+0
HETATM   13  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2   12                                                       
CONECT    2    1    3    5   14                                             
CONECT    3    2    4    6   15                                             
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    2                                                            
CONECT   15    3                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
4-Phosphoerythronate	ChEBI
4-Phosphoerythronic acid	Generator
4-Phospho-D-erythronic acid	Generator

Molecular Formula

C₄H₉O₈P

Average Mass

216.0832

Monoisotopic Mass

216.003503776

IUPAC Name

(2R,3R)-2,3-dihydroxy-4-(phosphonooxy)butanoic acid

Traditional Name

4-phospho-D-erythronic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H9O8P/c5-2(3(6)4(7)8)1-12-13(9,10)11/h2-3,5-6H,1H2,(H,7,8)(H2,9,10,11)/t2-,3-/m1/s1

InChI Key

ZCZXOHUILRHRQJ-PWNYCUMCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Beta-hydroxy acid
Short-chain hydroxy acid
Sugar acid
Monoalkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Hydroxy acid
Alkyl phosphate
Alpha-hydroxy acid
Fatty acid
Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Organic oxide
Carbonyl group
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

4-phosphoerythronic acid (CHEBI:49003 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.6 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.3	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	1.47	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	37.22 m³·mol⁻¹	ChemAxon
Polarizability	15.98 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9300000000-6fa3e5b82781cb309499	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kb-2920000000-a5fad921f0528d94b501	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006w-5900000000-2a302dc69738f987eaa5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ukd-9400000000-6ca80e65d20c4cbc9b25	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0200-9620000000-6d48091baa2eae7a7fa1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9200000000-bde656d6bf6a34ee39b8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-3a70f8c5027b4eb6e241	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

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
MMDBr0007327	D-Erythrose 4-phosphate	4-Phospho-D-erythronate	Not Available	Erythrose 4-phosphate dehydrogenase	VMH	30371894
MMDBr0013075	D-Erythrose 4-phosphate	4-Phospho-D-erythronate	D-erythrose-4-phosphate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0013811	4-Phospho-D-erythronate	(R)-3-hydroxy-2-oxo-4-phosphooxybutanoic acid	Erythronate-4-phosphate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0016590	Adenosine triphosphate	4-Phospho-D-erythronate	D-erythronate kinase	Phosphorylation	RHEA	34755880
MMDBr0016593	4-Phospho-D-erythronate	Carbon dioxide	D-erythronate 4-phosphate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0018448	Water	Hydrogen Ion	D-erythrose-4-phosphate dehydrogenase	Dehydrogenation	PathBank	31602464
MMDBr0018449	NAD	Hydrogen Ion	Erythronate-4-phosphate dehydrogenase	Dehydrogenation	PathBank	31602464
MMDBr0019950	Water	Hydrogen Ion	Glyceraldehyde-3-phosphate dehydrogenase 1	Dehydrogenation	PathBank	31602464
MMDBr0019951	NAD	Hydrogen Ion	Formate dehydrogenase 2	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
Bacteria	Proteobacteria	313	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; River trout	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	369	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Human saliva	Metabolic reconstruction
Bacteria	Actinobacteria	118	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	117	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria/NULL	Proteobacteria	1	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; River trout	Unknown; Metabolic reconstruction
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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

DB03108

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C03393

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

49003

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 4-Phospho-D-erythronate (MMDBc0030021)

MOL for #<Metabolite:0x00007f5abc40c478>

3D MOL for #<Metabolite:0x00007f5abc40c478>

3D SDF for #<Metabolite:0x00007f5abc40c478>

3D-SDF for #<Metabolite:0x00007f5abc40c478>

PDB for #<Metabolite:0x00007f5abc40c478>

3D PDB for #<Metabolite:0x00007f5abc40c478>

SMILES for #<Metabolite:0x00007f5abc40c478>

INCHI for #<Metabolite:0x00007f5abc40c478>

Structure for #<Metabolite:0x00007f5abc40c478>

3D Structure for #<Metabolite:0x00007f5abc40c478>