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Showing NP-Card for 5-(methylthio)-2,3-dioxopentyl phosphate (NP0338672)

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Record Information
Version2.0
Created at2024-09-11 16:53:42 UTC
Updated at2024-09-11 16:53:42 UTC
NP-MRD IDNP0338672
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-(methylthio)-2,3-dioxopentyl phosphate
Description5-(Methylthio)-2,3-dioxopentyl phosphate, also known as 1-phospho-2,3-diketo-5-S-methylthiopentane or 2,3-diketo-5-methylthio-1-phosphopentane, 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 an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 5-(Methylthio)-2,3-dioxopentyl phosphate has been detected, but not quantified in, several different foods, such as atlantic herrings, narrowleaf cattails, tartary buckwheats, allium (onion), and nectarines. It was first documented in 2013 (PMID: 23455439). This could make 5-(methylthio)-2,3-dioxopentyl phosphate a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)


  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
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3D MOL for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)

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3D SDF for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)

  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>
NP0338672

> <DATABASE_NAME>
NP-MRD

> <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

$$$$

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3D-SDF for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)
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PDB for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)
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

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3D PDB for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)
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SMILES for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)
CSCCC(=O)C(=O)COP(O)(O)=O
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INCHI for NP0338672 (5-(methylthio)-2,3-dioxopentyl phosphate)
InChI=1S/C6H11O6PS/c1-14-3-2-5(7)6(8)4-12-13(9,10)11/h2-4H2,1H3,(H2,9,10,11)
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Synonyms
ValueSource
1-Phospho-2,3-diketo-5-S-methylthiopentaneChEBI
2,3-Diketo-5-methylthio-1-phosphopentaneChEBI
2,3-Diketo-5-methylthiopentyl-1-phosphateChEBI
5-Methylthio-1-(phosphonooxy)pentane-2,3-dioneChEBI
5-(Methylsulfanyl)-2,3-dioxopentyl phosphateKegg
2,3-Diketo-5-methylthiopentyl-1-phosphoric acidGenerator
5-(Methylsulfanyl)-2,3-dioxopentyl phosphoric acidGenerator
5-(Methylsulphanyl)-2,3-dioxopentyl phosphateGenerator
5-(Methylsulphanyl)-2,3-dioxopentyl phosphoric acidGenerator
5-(Methylthio)-2,3-dioxopentyl phosphoric acidGenerator
1-PDMSPHMDB
5-(Methylthio)-1-(phosphonooxy)-2,3-pentanedioneHMDB
DK-MTP-1-pHMDB
5-(Methylthio)-2,3-dioxopentyl phosphateChEBI
Chemical FormulaC6H11O6PS
Average Mass242.1870 Da
Monoisotopic Mass242.00140 Da
IUPAC Name{[5-(methylsulfanyl)-2,3-dioxopentyl]oxy}phosphonic acid
Traditional Name1-pdmsp
CAS Registry NumberNot 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 KeyHKEAOVFNWRDVAJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassOrganic phosphoric acids and derivatives  
Sub ClassPhosphate esters  
Direct ParentMonoalkyl 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 FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.08ALOGPS
logP0.51ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.11ChemAxon
pKa (Strongest Basic)-9.4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area100.9 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity51.2 m³·mol⁻¹ChemAxon
Polarizability21.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0059620  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030557  
KNApSAcK IDNot Available
Chemspider ID545  
KEGG Compound IDC15650  
BioCyc IDCPD-8999  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound561  
PDB IDNot Available
ChEBI ID50604  
Good Scents IDNot Available
References
General References
  1. 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  ]