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

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:26:43 UTC
Update Date2024-04-30 19:54:50 UTC
Metabolite IDMMDBc0032906
Metabolite Identification
Common Name5-(methylsulfanyl)-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-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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecf99a3c18>


  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
Download

3D MOL for #<Metabolite:0x00007fecf99a3c18>

HMDB0059620
     RDKit          3D
5-(Methylthio)-2,3-dioxopentyl phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
    4.0903    0.1056    1.6859 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8058   -0.7741    0.7615 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6990   -0.2071   -0.9414 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6754   -0.8873   -1.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2824   -0.7825   -1.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387   -1.4865   -2.0567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2882   -0.0118   -0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4335    0.6924    0.4445 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7413   -0.0342   -0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0991    0.7585    1.0563 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7929    0.6865    1.2821 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.0312    0.4016    2.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3855   -0.5697    0.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5213    2.1290    0.8269 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2788   -0.3658    2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7573    1.1442    1.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0493    0.1691    1.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6977   -0.4503   -1.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6561    0.9158   -1.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8019   -0.6199   -2.8377 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242   -1.9926   -1.7255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2342    0.3312   -0.9681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0230   -1.0805    0.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8594   -0.2100   -0.4551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6367    2.1382   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fecf99a3c18>


  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

$$$$
Download

3D-SDF for #<Metabolite:0x00007fecf99a3c18>

HMDB0059620
     RDKit          3D
5-(Methylthio)-2,3-dioxopentyl phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
    4.0903    0.1056    1.6859 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8058   -0.7741    0.7615 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6990   -0.2071   -0.9414 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6754   -0.8873   -1.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2824   -0.7825   -1.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387   -1.4865   -2.0567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2882   -0.0118   -0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4335    0.6924    0.4445 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7413   -0.0342   -0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0991    0.7585    1.0563 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7929    0.6865    1.2821 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.0312    0.4016    2.7542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3855   -0.5697    0.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5213    2.1290    0.8269 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2788   -0.3658    2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7573    1.1442    1.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0493    0.1691    1.1115 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6977   -0.4503   -1.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6561    0.9158   -1.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8019   -0.6199   -2.8377 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242   -1.9926   -1.7255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2342    0.3312   -0.9681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0230   -1.0805    0.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8594   -0.2100   -0.4551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6367    2.1382   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

PDB for #<Metabolite:0x00007fecf99a3c18>

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 #<Metabolite:0x00007fecf99a3c18>

COMPND    HMDB0059620
HETATM    1  C1  UNL     1       4.090   0.106   1.686  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.806  -0.774   0.762  1.00  0.00           S  
HETATM    3  C2  UNL     1       2.699  -0.207  -0.941  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.675  -0.887  -1.764  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.282  -0.782  -1.353  1.00  0.00           C  
HETATM    6  O1  UNL     1      -0.539  -1.487  -2.057  1.00  0.00           O  
HETATM    7  C5  UNL     1      -0.288  -0.012  -0.288  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.434   0.692   0.445  1.00  0.00           O  
HETATM    9  C6  UNL     1      -1.741  -0.034  -0.035  1.00  0.00           C  
HETATM   10  O3  UNL     1      -2.099   0.758   1.056  1.00  0.00           O  
HETATM   11  P1  UNL     1      -3.793   0.687   1.282  1.00  0.00           P  
HETATM   12  O4  UNL     1      -4.031   0.402   2.754  1.00  0.00           O  
HETATM   13  O5  UNL     1      -4.385  -0.570   0.363  1.00  0.00           O  
HETATM   14  O6  UNL     1      -4.521   2.129   0.827  1.00  0.00           O  
HETATM   15  H1  UNL     1       4.279  -0.366   2.667  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.757   1.144   1.849  1.00  0.00           H  
HETATM   17  H3  UNL     1       5.049   0.169   1.111  1.00  0.00           H  
HETATM   18  H4  UNL     1       3.698  -0.450  -1.418  1.00  0.00           H  
HETATM   19  H5  UNL     1       2.656   0.916  -1.009  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.802  -0.620  -2.838  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.924  -1.993  -1.725  1.00  0.00           H  
HETATM   22  H8  UNL     1      -2.234   0.331  -0.968  1.00  0.00           H  
HETATM   23  H9  UNL     1      -2.023  -1.081   0.207  1.00  0.00           H  
HETATM   24  H10 UNL     1      -4.859  -0.210  -0.455  1.00  0.00           H  
HETATM   25  H11 UNL     1      -4.637   2.138  -0.156  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6    6    7
CONECT    7    8    8    9
CONECT    9   10   22   23
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x00007fecf99a3c18>

CSCCC(=O)C(=O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007fecf99a3c18>

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
Molecular FormulaC6H11O6PS
Average Mass242.187
Monoisotopic Mass242.001395286
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