MiMeDB: Showing metabocard for 3-hydroxy-2,4-pentanedione 5-phosphate (MMDBc0032154)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:04:39 UTC

Update Date

2022-08-31 18:30:56 UTC

Metabolite ID

MMDBc0032154

Metabolite Identification

Common Name

3-hydroxy-2,4-pentanedione 5-phosphate

Description

3-Hydroxy-2,4-pentanedione 5-phosphate is an intermediate in autoinducer AI-2 degradation pathway in E.coli. It is a substrate for the enzyme 3-hydroxy-2,4-pentadione 5-phosphate thiolase which catalyzes the reaction 3-hydroxy-5-phosphonooxypentane-2,4-dione + coenzyme A -> glycerone phosphate + acetyl-CoA. It is also a product for enzyme phospho-AI-2 isomerase which catalyzes reaction (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione -> 3-hydroxy-5-phosphonooxypentane-2,4-dione (BioCyc compound: CPD0-2467).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04051518372D          

 13 12  0  0  0  0            999 V2000
    1.2375    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.8578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -3.5723    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -4.2868    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5230   -3.9848    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9519   -3.1598    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  7 10  1  0  0  0  0
  4 11  2  0  0  0  0
  3 12  1  0  0  0  0
  2 13  2  0  0  0  0
M  CHG  2   8  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0032154

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h5,8H,2H2,1H3,(H2,9,10,11)/p-2

> <INCHI_KEY>
AKHNGSPNHAFBII-UHFFFAOYSA-L

> <FORMULA>
C5H7O7P

> <MOLECULAR_WEIGHT>
210.079

> <EXACT_MASS>
209.994036723

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.873474087151559

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-1-(phosphonatooxy)pentane-2,4-dione

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-1.3278387609999998

> <ALOGPS_LOGS>
-0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.198682453531147

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.168833338809005

> <JCHEM_PKA_STRONGEST_BASIC>
-4.293448279014773

> <JCHEM_POLAR_SURFACE_AREA>
126.79000000000002

> <JCHEM_REFRACTIVITY>
37.75990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-1-(phosphonatooxy)pentane-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-APR-15         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.310  -4.001   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.540  -5.335   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0       2.310  -6.668   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0       3.080  -8.002   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       0.976  -7.438   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.644  -5.898   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.850  -1.334   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11    4                                                            
CONECT   12    3                                                            
CONECT   13    2                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
3-Hydroxy-2,4-pentanedione 5-phosphoric acid	Generator

Molecular Formula

C₅H₇O₇P

Average Mass

210.079

Monoisotopic Mass

209.994036723

IUPAC Name

3-hydroxy-1-(phosphonatooxy)pentane-2,4-dione

Traditional Name

3-hydroxy-1-(phosphonatooxy)pentane-2,4-dione

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H9O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h5,8H,2H2,1H3,(H2,9,10,11)/p-2

InChI Key

AKHNGSPNHAFBII-UHFFFAOYSA-L

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
1,3-diketone
Alkyl phosphate
1,3-dicarbonyl compound
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Organic oxide
Hydrocarbon derivative
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:84359 )
a small molecule (CPD0-2467 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	43.9 g/L	ALOGPS
logP	-0.9	ALOGPS
logP	-1.3	ChemAxon
logS	-0.75	ALOGPS
pKa (Strongest Acidic)	1.17	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	126.79 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	37.76 m³·mol⁻¹	ChemAxon
Polarizability	15.87 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	splash10-03di-0090000000-5f92fd5a4a8b5d370138	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-2490000000-6dad826f50ba8c48b41d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zfr-9700000000-85740365bec48464bc55	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ab9-7190000000-86727735b590c0f298f9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05fr-9240000000-2bbf4b2cf9e3505bc90f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05ai-9000000000-f23f45094a35c4ce70ed	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	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
MMDBr0016079	(2S)-2-hydroxy-3,4-dioxopentyl phosphate	3-hydroxy-2,4-pentanedione 5-phosphate	(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase	Isomerization	RHEA	34755880
MMDBr0016097	Acetyl-CoA	3-hydroxy-2,4-pentanedione 5-phosphate	3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase	Carbon‚Äìcarbon-bond formation	RHEA	34755880
MMDBr0018413	(4S)-4-hydroxy-2,3-pentanedione 5-phosphate	3-hydroxy-2,4-pentanedione 5-phosphate	(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase	Isomerization	PathBank	31602464
MMDBr0018414	Coenzyme A	Acetyl-CoA	3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase	Carbon‚Äìcarbon-bond formation	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	27	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

CPD0-2467

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

54758622

PDB ID

Not Available

ChEBI ID

84359

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 ]
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-hydroxy-2,4-pentanedione 5-phosphate (MMDBc0032154)

MOL for #<Metabolite:0x00007f5a6c0156f8>

3D MOL for #<Metabolite:0x00007f5a6c0156f8>

3D SDF for #<Metabolite:0x00007f5a6c0156f8>

3D-SDF for #<Metabolite:0x00007f5a6c0156f8>

PDB for #<Metabolite:0x00007f5a6c0156f8>

3D PDB for #<Metabolite:0x00007f5a6c0156f8>

SMILES for #<Metabolite:0x00007f5a6c0156f8>

INCHI for #<Metabolite:0x00007f5a6c0156f8>

Structure for #<Metabolite:0x00007f5a6c0156f8>

3D Structure for #<Metabolite:0x00007f5a6c0156f8>