MiMeDB: Showing metabocard for 5-(methylsulfanyl)-2,3-dioxopentyl phosphate (MMDBc0032906)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:26:43 UTC

Update Date

2024-04-30 19:54:50 UTC

Metabolite ID

MMDBc0032906

Metabolite Identification

Common Name

5-(methylsulfanyl)-2,3-dioxopentyl phosphate

Description

5-(Methylthio)-2,3-dioxopentyl phosphate, also known as 1-phospho-2,3-diketo-5-S-methylthiopentane or 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P), belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain. 5-(Methylthio)-2,3-dioxopentyl phosphate is slightly soluble (in water) and a moderately acidic compound (based on its pKa). 5-(Methylthio)-2,3-dioxopentyl phosphate exists in all eukaryotes, ranging from yeast to humans. 5-(Methylthio)-2,3-dioxopentyl phosphate is a metabolite involved in the cysteine and methionine metabolism pathway. It is a substrate for both E1 enolase-phosphatase and methylthioribulose-1-phosphate dehydratase. Outside of the human body, 5-(methylthio)-2,3-dioxopentyl phosphate can be found in a number of food items such as lime, pineapple, spearmint, and yautia. This makes 5-(methylthio)-2,3-dioxopentyl phosphate a potential biomarker for the consumption of these food products.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652305171807392D          

 14 13  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.8414    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8888    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0638    2.5559    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  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 13 11  1  0  0  0  0
 14 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032906

> <DATABASE_NAME>
MIME

> <SMILES>
CSCCC(=O)C(=O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O6PS/c1-14-3-2-5(7)6(8)4-12-13(9,10)11/h2-4H2,1H3,(H2,9,10,11)

> <INCHI_KEY>
HKEAOVFNWRDVAJ-UHFFFAOYSA-N

> <FORMULA>
C6H11O6PS

> <MOLECULAR_WEIGHT>
242.187

> <EXACT_MASS>
242.001395286

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
21.009206917920018

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
{[5-(methylsulfanyl)-2,3-dioxopentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
0.5128286950000003

> <ALOGPS_LOGS>
-1.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.143880429984992

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1140333449772122

> <JCHEM_PKA_STRONGEST_BASIC>
-9.360354692322906

> <JCHEM_POLAR_SURFACE_AREA>
100.9

> <JCHEM_REFRACTIVITY>
51.197100000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.99e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-pdmsp

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       4.620   2.667   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      12.622   2.667   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      13.956   3.437   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      15.289   4.207   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      14.726   2.104   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      13.186   4.771   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
1-Phospho-2,3-diketo-5-S-methylthiopentane	ChEBI
2,3-Diketo-5-methylthio-1-phosphopentane	ChEBI
2,3-Diketo-5-methylthiopentyl-1-phosphate	ChEBI
5-Methylthio-1-(phosphonooxy)pentane-2,3-dione	ChEBI
5-(Methylsulfanyl)-2,3-dioxopentyl phosphate	Kegg
2,3-Diketo-5-methylthiopentyl-1-phosphoric acid	Generator
5-(Methylsulfanyl)-2,3-dioxopentyl phosphoric acid	Generator
5-(Methylsulphanyl)-2,3-dioxopentyl phosphate	Generator
5-(Methylsulphanyl)-2,3-dioxopentyl phosphoric acid	Generator
5-(Methylthio)-2,3-dioxopentyl phosphoric acid	Generator
1-PDMSP	HMDB
5-(Methylthio)-1-(phosphonooxy)-2,3-pentanedione	HMDB
DK-MTP-1-p	HMDB
5-(Methylthio)-2,3-dioxopentyl phosphate	ChEBI

Molecular Formula

C₆H₁₁O₆PS

Average Mass

242.187

Monoisotopic Mass

242.001395286

IUPAC Name

{[5-(methylsulfanyl)-2,3-dioxopentyl]oxy}phosphonic acid

Traditional Name

1-pdmsp

CAS Registry Number

Not Available

SMILES

CSCCC(=O)C(=O)COP(O)(O)=O

InChI Identifier

InChI=1S/C6H11O6PS/c1-14-3-2-5(7)6(8)4-12-13(9,10)11/h2-4H2,1H3,(H2,9,10,11)

InChI Key

HKEAOVFNWRDVAJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Monosaccharide
Alpha-diketone
Ketone
Dialkylthioether
Sulfenyl compound
Thioether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

aliphatic sulfide (CHEBI:50604 )
alpha-diketone (CHEBI:50604 )
oxoalkyl phosphate (CHEBI:50604 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.99 g/L	ALOGPS
logP	-0.08	ALOGPS
logP	0.51	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.11	ChemAxon
pKa (Strongest Basic)	-9.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	100.9 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	51.2 m³·mol⁻¹	ChemAxon
Polarizability	21.01 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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
MMDBp0195483	Enolase-phosphatase E1	Unknown	Q9UHY7	Homo sapiens
MMDBp0196895	Methylthioribulose-1-phosphate dehydratase	Unknown	Q96GX9

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019451	5-(methylsulfanyl)-2,3-dioxopentyl phosphate	1,2-Dihydroxy-3-keto-5-methylthiopentene	Enolase-phosphatase E1	Dephosphorylation	PathBank	31602464
MMDBr0019452	5-Methylthioribulose 1-phosphate	5-(methylsulfanyl)-2,3-dioxopentyl phosphate	Methylthioribulose-1-phosphate dehydratase	Hydration/dehydration of C-O bond	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	59	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Firmicutes	63	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	101	Human feces; Human ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	4	Human feces; Human ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	4	Human
Bacteria/Eubacteria	Aquificae	4
Eukaryota/Fungi	Basidiomycota	4
Bacteria/Eubacteria	Spirochaetes	6	Human
Bacteria/Eubacteria	Cyanobacteria	11	Human
Bacteria	Cyanobacteria	1	Human

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0059620

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030557

KNApSAcK ID

Not Available

Chemspider ID

545

KEGG Compound ID

C15650

BioCyc ID

CPD-8999

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

561

PDB ID

Not Available

ChEBI ID

50604

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]

Showing metabocard for 5-(methylsulfanyl)-2,3-dioxopentyl phosphate (MMDBc0032906)

MOL for #<Metabolite:0x00007f9253f51b70>

3D MOL for #<Metabolite:0x00007f9253f51b70>

3D SDF for #<Metabolite:0x00007f9253f51b70>

3D-SDF for #<Metabolite:0x00007f9253f51b70>

PDB for #<Metabolite:0x00007f9253f51b70>

3D PDB for #<Metabolite:0x00007f9253f51b70>

SMILES for #<Metabolite:0x00007f9253f51b70>

INCHI for #<Metabolite:0x00007f9253f51b70>

Structure for #<Metabolite:0x00007f9253f51b70>

3D Structure for #<Metabolite:0x00007f9253f51b70>