MiMeDB: Showing metabocard for (4S)-4-hydroxy-2,3-pentanedione 5-phosphate (MMDBc0032153)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:04:35 UTC

Update Date

2022-08-31 18:30:56 UTC

Metabolite ID

MMDBc0032153

Metabolite Identification

Common Name

(4S)-4-hydroxy-2,3-pentanedione 5-phosphate

Description

(4S)-4-Hydroxy-2,3-pentanedione 5-phosphate is an intermediate in autoinducer AI-2 degradation pathway in E.coli. It is a substrate for the enzyme phospho-AI-2 isomerase which catalyzes the reaction (4S)-4-hydroxy-2,3-pentanedione 5-phosphate -> 3-hydroxy-2,4-pentanedione 5-phosphate. It is also a product for enzyme autoinducer-2 kinase which catalyzes reaction autoinducer 2 + ATP -> (4S)-4-hydroxy-2,3-pentanedione 5-phosphate + ADP + H+ (BioCyc compound: CPD-10551).

Structure

MOL SDF PDB SMILES InChI

CC(C(C(COP([O-])(=O)[O-])O)=O)=O
  Mrv0541 04051518312D          

 13 12  0  0  0  0            999 V2000
   -2.8180   -0.1116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1036    0.3008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3891   -0.1116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6746    0.3008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0398   -0.1116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7542    0.3008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1036    1.1258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3891   -0.9366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6746    1.1258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5494    0.2888    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.5744   -0.5573    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5542    1.0388    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.3743    0.2763    0.0000 O   0  5  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 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 13  1  0  0  0  0
 10 12  1  0  0  0  0
  4  9  1  0  0  0  0
  2  7  2  0  0  0  0
  3  8  2  0  0  0  0
M  CHG  2  12  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0032153

> <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/h4,7H,2H2,1H3,(H2,9,10,11)/p-2

> <INCHI_KEY>
DTZHMTDUIGHESZ-UHFFFAOYSA-L

> <FORMULA>
C5H7O7P

> <MOLECULAR_WEIGHT>
210.079

> <EXACT_MASS>
209.994036723

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
16.017719721960763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-5-(phosphonatooxy)pentane-2,3-dione

> <ALOGPS_LOGP>
-0.93

> <JCHEM_LOGP>
-1.0234603256666666

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.392246767109783

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3660608302300572

> <JCHEM_PKA_STRONGEST_BASIC>
-3.921738393505694

> <JCHEM_POLAR_SURFACE_AREA>
126.79000000000002

> <JCHEM_REFRACTIVITY>
37.91010000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.51e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-5-(phosphonatooxy)pentane-2,3-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-APR-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CC(C(C(COP([O-])(=O)[O-])O)=O)=O                  
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-APR-15         0                                  
HETATM    1  C   UNK     0      -5.260  -0.208   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.927   0.561   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.593  -0.208   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.259   0.561   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.074  -0.208   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.408   0.561   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -3.927   2.101   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.593  -1.748   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.259   2.101   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0       2.892   0.539   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0       2.939  -1.040   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.901   1.939   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       4.432   0.516   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5   10                                                       
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    6   11   13   12                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

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

Molecular Formula

C₅H₇O₇P

Average Mass

210.079

Monoisotopic Mass

209.994036723

IUPAC Name

4-hydroxy-5-(phosphonatooxy)pentane-2,3-dione

Traditional Name

4-hydroxy-5-(phosphonatooxy)pentane-2,3-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/h4,7H,2H2,1H3,(H2,9,10,11)/p-2

InChI Key

DTZHMTDUIGHESZ-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Beta-hydroxy ketone
Alpha-diketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (CPD-10551 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	45.1 g/L	ALOGPS
logP	-0.93	ALOGPS
logP	-1	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Acidic)	1.37	ChemAxon
pKa (Strongest Basic)	-3.9	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	37.91 m³·mol⁻¹	ChemAxon
Polarizability	16.02 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

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018412	(2R,4S)-2-Methyl-2,3,3,4-tetrahydroxytetrahydrofuran	(4S)-4-hydroxy-2,3-pentanedione 5-phosphate	Autoinducer-2 kinase	Phosphorylation	PathBank	31602464
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

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

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

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

25202065

PDB ID

Not Available

ChEBI ID

Not Available

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 (4S)-4-hydroxy-2,3-pentanedione 5-phosphate (MMDBc0032153)

MOL for #<Metabolite:0x00007f92300174e8>

3D MOL for #<Metabolite:0x00007f92300174e8>

3D SDF for #<Metabolite:0x00007f92300174e8>

3D-SDF for #<Metabolite:0x00007f92300174e8>

PDB for #<Metabolite:0x00007f92300174e8>

3D PDB for #<Metabolite:0x00007f92300174e8>

SMILES for #<Metabolite:0x00007f92300174e8>

INCHI for #<Metabolite:0x00007f92300174e8>

Structure for #<Metabolite:0x00007f92300174e8>

3D Structure for #<Metabolite:0x00007f92300174e8>