Showing metabocard for 5-Methylthioribulose 1-phosphate (MMDBc0032926)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:27:38 UTC
Update Date2024-04-30 19:55:05 UTC
Metabolite IDMMDBc0032926
Metabolite Identification
Common Name5-Methylthioribulose 1-phosphate
Description5-Methylthioribulose 1-phosphate is an intermediate in the methionine salvage pathway. It is a microbial metabolite produced by gut microbes during methionine generation from methylthioadenosine. The first step is the phosphorolysis of methylthioadenosine to 5-methylthioribose-1-phosphate and adenine by the enzyme 5-deoxy- 5-methylthioadenosine phosphorylase (methylthioadenosine phosphorylase); 5-methylthioribose-1-phosphate is then converted to 5-methylthioribulose-1-phosphate (PMID: 6725268 ). 5-Deoxy-5-methylthioadenosine (methylthioadenosine) is a metabolite of S-adenosyl-L-methionine formed during the synthesis of the polyamines, spermidine and spermine.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923df80c38>


  Mrv1652307172020202D          

 15 14  0  0  0  0            999 V2000
 9988.4110 9988.2438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9987.6973 9987.8320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.1261 9987.8320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9988.4110 9989.0682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.9829 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.6973 9987.0070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9989.8414 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.1261 9987.0070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.2684 9987.8320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.5544 9987.8320    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
 9985.5540 9988.2438    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9991.2697 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.9653 9988.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.8355 9987.8300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.1405 9988.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  2  0  0  0  0
 11 14  1  0  0  0  0
 11 15  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923df80c38>

HMDB0001299
     RDKit          3D
5-Methylthioribulose 1-phosphate
 28 27  0  0  0  0  0  0  0  0999 V2000
    4.4185    0.5522    1.5869 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7905   -0.0103    1.0500 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5900    0.1951   -0.7288 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564   -0.2616   -1.1942 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9743   -1.5850   -0.9129 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1596    0.6891   -0.8711 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9413    0.2995   -1.6818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3167    0.7027    0.5191 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3938    1.1974    1.4188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6388    0.1320    0.8701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2450   -0.3673   -0.2419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7455   -1.0406    0.0194 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6410   -2.5236    0.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6663   -0.8486   -1.4041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5296   -0.2616    1.2886 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9807    0.9958    0.7247 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3623    1.3584    2.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0152   -0.2955    1.9724 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4211   -0.3786   -1.2087 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7686    1.2875   -0.9644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2891   -0.2174   -2.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1832   -1.6796   -0.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4215    1.7205   -1.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7611   -0.6110   -2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2609    0.8682    1.4297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4623   -0.6863    1.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5191    0.0670   -1.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2971    0.7015    1.3187 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
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  6
  5 22  1  0
  6 23  1  6
  7 24  1  0
 10 25  1  0
 10 26  1  0
 14 27  1  0
 15 28  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f923df80c38>


  Mrv1652307172020202D          

 15 14  0  0  0  0            999 V2000
 9988.4110 9988.2438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9987.6973 9987.8320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.1261 9987.8320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9988.4110 9989.0682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.9829 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.6973 9987.0070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9989.8414 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.1261 9987.0070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.2684 9987.8320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.5544 9987.8320    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
 9985.5540 9988.2438    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9991.2697 9988.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9985.9653 9988.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9984.8355 9987.8300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.1405 9988.9589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  2  0  0  0  0
 11 14  1  0  0  0  0
 11 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032926

> <DATABASE_NAME>
MIME

> <SMILES>
CSC[C@@H](O)[C@@H](O)C(=O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13O7PS/c1-15-3-5(8)6(9)4(7)2-13-14(10,11)12/h5-6,8-9H,2-3H2,1H3,(H2,10,11,12)/t5-,6+/m1/s1

> <INCHI_KEY>
CNSJRYUMVMWNMC-RITPCOANSA-N

> <FORMULA>
C6H13O7PS

> <MOLECULAR_WEIGHT>
260.202

> <EXACT_MASS>
260.011959972

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
22.58689642828518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4S)-3,4-dihydroxy-5-(methylsulfanyl)-2-oxopentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-0.43

> <JCHEM_LOGP>
-1.2777918353333326

> <ALOGPS_LOGS>
-1.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208835718373348

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1787298662051935

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3648057294312927

> <JCHEM_POLAR_SURFACE_AREA>
124.29000000000002

> <JCHEM_REFRACTIVITY>
53.305800000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylthioribulose-1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f923df80c38>

HMDB0001299
     RDKit          3D
5-Methylthioribulose 1-phosphate
 28 27  0  0  0  0  0  0  0  0999 V2000
    4.4185    0.5522    1.5869 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7905   -0.0103    1.0500 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.5900    0.1951   -0.7288 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564   -0.2616   -1.1942 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9743   -1.5850   -0.9129 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1596    0.6891   -0.8711 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9413    0.2995   -1.6818 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3167    0.7027    0.5191 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3938    1.1974    1.4188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6388    0.1320    0.8701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2450   -0.3673   -0.2419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7455   -1.0406    0.0194 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6410   -2.5236    0.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6663   -0.8486   -1.4041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5296   -0.2616    1.2886 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9807    0.9958    0.7247 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3623    1.3584    2.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0152   -0.2955    1.9724 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4211   -0.3786   -1.2087 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7686    1.2875   -0.9644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2891   -0.2174   -2.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1832   -1.6796   -0.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4215    1.7205   -1.2240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7611   -0.6110   -2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2609    0.8682    1.4297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4623   -0.6863    1.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5191    0.0670   -1.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2971    0.7015    1.3187 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
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  6
  5 22  1  0
  6 23  1  6
  7 24  1  0
 10 25  1  0
 10 26  1  0
 14 27  1  0
 15 28  1  0
M  END
Download

PDB for #<Metabolite:0x00007f923df80c38>

HEADER    PROTEIN                                 17-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-20         0                                  
HETATM    1  C   UNK     0    8645.0348644.722   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8643.7028643.953   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8646.3698643.953   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8645.0348646.261   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8642.3688644.722   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8643.7028642.413   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8647.7048644.722   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8646.3698642.413   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8641.0348643.953   0.000  0.00  0.00           O+0
HETATM   10  S   UNK     0    8649.0358643.953   0.000  0.00  0.00           S+0
HETATM   11  P   UNK     0    8639.7018644.722   0.000  0.00  0.00           P+0
HETATM   12  C   UNK     0    8650.3708644.722   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0    8640.4698646.057   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8638.3608643.949   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    8638.9298646.057   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2    9                                                       
CONECT    6    2                                                            
CONECT    7    3   10                                                       
CONECT    8    3                                                            
CONECT    9    5   11                                                       
CONECT   10    7   12                                                       
CONECT   11    9   13   14   15                                             
CONECT   12   10                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   11                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END
Download

3D PDB for #<Metabolite:0x00007f923df80c38>

COMPND    HMDB0001299
HETATM    1  C1  UNL     1       4.419   0.552   1.587  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.790  -0.010   1.050  1.00  0.00           S  
HETATM    3  C2  UNL     1       2.590   0.195  -0.729  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.256  -0.262  -1.194  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.974  -1.585  -0.913  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.160   0.689  -0.871  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.941   0.300  -1.682  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.317   0.703   0.519  1.00  0.00           C  
HETATM    9  O3  UNL     1       0.394   1.197   1.419  1.00  0.00           O  
HETATM   10  C6  UNL     1      -1.639   0.132   0.870  1.00  0.00           C  
HETATM   11  O4  UNL     1      -2.245  -0.367  -0.242  1.00  0.00           O  
HETATM   12  P1  UNL     1      -3.746  -1.041   0.019  1.00  0.00           P  
HETATM   13  O5  UNL     1      -3.641  -2.524   0.282  1.00  0.00           O  
HETATM   14  O6  UNL     1      -4.666  -0.849  -1.404  1.00  0.00           O  
HETATM   15  O7  UNL     1      -4.530  -0.262   1.289  1.00  0.00           O  
HETATM   16  H1  UNL     1       4.981   0.996   0.725  1.00  0.00           H  
HETATM   17  H2  UNL     1       4.362   1.358   2.356  1.00  0.00           H  
HETATM   18  H3  UNL     1       5.015  -0.295   1.972  1.00  0.00           H  
HETATM   19  H4  UNL     1       3.421  -0.379  -1.209  1.00  0.00           H  
HETATM   20  H5  UNL     1       2.769   1.288  -0.964  1.00  0.00           H  
HETATM   21  H6  UNL     1       1.289  -0.217  -2.370  1.00  0.00           H  
HETATM   22  H7  UNL     1       0.183  -1.680  -0.337  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.421   1.721  -1.224  1.00  0.00           H  
HETATM   24  H9  UNL     1      -0.761  -0.611  -2.010  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.261   0.868   1.430  1.00  0.00           H  
HETATM   26  H11 UNL     1      -1.462  -0.686   1.635  1.00  0.00           H  
HETATM   27  H12 UNL     1      -4.519   0.067  -1.769  1.00  0.00           H  
HETATM   28  H13 UNL     1      -4.297   0.702   1.319  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3
CONECT    3    4   19   20
CONECT    4    5    6   21
CONECT    5   22
CONECT    6    7    8   23
CONECT    7   24
CONECT    8    9    9   10
CONECT   10   11   25   26
CONECT   11   12
CONECT   12   13   13   14   15
CONECT   14   27
CONECT   15   28
END
Download

SMILES for #<Metabolite:0x00007f923df80c38>

CSC[C@@H](O)[C@@H](O)C(=O)COP(O)(O)=O
Download

INCHI for #<Metabolite:0x00007f923df80c38>

InChI=1S/C6H13O7PS/c1-15-3-5(8)6(9)4(7)2-13-14(10,11)12/h5-6,8-9H,2-3H2,1H3,(H2,10,11,12)/t5-,6+/m1/s1
Download
Synonyms
ValueSource
5-S-Methyl-1-O-phosphono-5-thio-D-ribuloseChEBI
5-(Methylsulfanyl)-D-ribulose 1-phosphateKegg
5-(Methylsulfanyl)-D-ribulose 1-phosphoric acidGenerator
5-(Methylsulphanyl)-D-ribulose 1-phosphateGenerator
5-(Methylsulphanyl)-D-ribulose 1-phosphoric acidGenerator
5-Methylthioribulose 1-phosphoric acidGenerator
1-Phospho-5-S-methylthioribuloseHMDB
1-PhosphomethylthioribuloseHMDB
1PMT-RibuloseHMDB
5-Methylthio-2-ribulose-1-phosphateHMDB
5-Methylthio-5-deoxy-D-ribulose 1-phosphateHMDB
5-Methylthio-5-deoxy-D-ribulose-1-phosphateHMDB
5-Methylthioribulose-1-phosphateHMDB
5-S-Methyl-5-thio-D-erythro-pent-2-ulose 1-(dihydrogen phosphate)HMDB
5-S-Methyl-5-thio-D-ribulose 1-(dihydrogen phosphate)HMDB
Methylthioribulose-1-phosphateHMDB
MTRu-1-pHMDB
S-Methyl-5-thio-D-ribulose 1-phosphateHMDB
1-PMT-RibuloseHMDB
Methylthioribulose 1-phosphateHMDB
5-(Methylthio)ribulose 1-phosphateHMDB
Molecular FormulaC6H13O7PS
Average Mass260.202
Monoisotopic Mass260.011959972
IUPAC Name{[(3R,4S)-3,4-dihydroxy-5-(methylsulfanyl)-2-oxopentyl]oxy}phosphonic acid
Traditional Namemethylthioribulose-1-phosphate
CAS Registry Number86316-83-8
SMILES
CSC[C@@H](O)[C@@H](O)C(=O)COP(O)(O)=O
InChI Identifier
InChI=1S/C6H13O7PS/c1-15-3-5(8)6(9)4(7)2-13-14(10,11)12/h5-6,8-9H,2-3H2,1H3,(H2,10,11,12)/t5-,6+/m1/s1
InChI KeyCNSJRYUMVMWNMC-RITPCOANSA-N