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Showing NP-Card for 5-Methylthioribulose 1-phosphate (NP0086750)

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Record Information
Version2.0
Created at2022-05-11 16:29:57 UTC
Updated at2022-05-11 16:29:57 UTC
NP-MRD IDNP0086750
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-Methylthioribulose 1-phosphate
Description5-Methylthioribulose 1-phosphate, also known as 1PMT-ribulose or 1-phospho-5-S-methylthioribulose, belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position. 5-Methylthioribulose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Methylthioribulose 1-phosphate is an intermediate in the methionine salvage pathway. 5-Deoxy-5-methylthioadenosine (methylthioadenosine) is a metabolite of S-adenosyl-L-methionine formed during the synthesis of the polyamines, spermidine and spermine. 5-Methylthioribulose 1-phosphate exists in all living species, ranging from bacteria to humans. Outside of the human body, 5-Methylthioribulose 1-phosphate has been detected, but not quantified in, several different foods, such as gooseberries, lemon balms, saffrons, arctic blackberries, and alliums. This could make 5-methylthioribulose 1-phosphate a potential biomarker for the consumption of these foods. 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 ). It is a microbial metabolite produced by gut microbes during methionine generation from methylthioadenosine.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086750 (5-Methylthioribulose 1-phosphate)


  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 NP0086750 (5-Methylthioribulose 1-phosphate)

     RDKit          3D

 28 27  0  0  0  0  0  0  0  0999 V2000
    4.8006    1.4451    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1553    1.4005    0.8554 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.2765   -0.0232    0.1505 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8808   -0.1452    0.7248 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1593    0.9809    0.4502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2620   -1.4084    0.1337 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1105   -2.4774    0.4879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0446   -1.6879    0.7415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1748   -2.6091    1.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2434   -0.8937    0.4074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9936    0.0526   -0.5689 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4301    0.8972   -0.8685 P   0  0  2  0  0  5  0  0  0  0  0  0
   -3.6479    1.0422   -2.3428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3139    2.4102   -0.1097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7434    0.0496   -0.2218 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1078    0.3992   -0.0950 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5616    1.8881    0.7695 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7050    1.9995   -0.8669 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8929   -0.9198    0.3737 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2584    0.1159   -0.9543 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9776   -0.2582    1.8159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4348    1.3946   -0.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2606   -1.3450   -0.9643 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4975   -2.2471    1.3695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0012   -1.6299    0.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6840   -0.4297    1.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2279    2.8140   -0.1598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8364   -0.8148   -0.7054 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
 12 11  1  6
 12 14  1  0
 12 15  1  0
 12 13  2  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  1
  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 NP0086750 (5-Methylthioribulose 1-phosphate)


  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>
NP0086750

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0086750 (5-Methylthioribulose 1-phosphate)

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PDB for NP0086750 (5-Methylthioribulose 1-phosphate)
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

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3D PDB for NP0086750 (5-Methylthioribulose 1-phosphate)
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SMILES for NP0086750 (5-Methylthioribulose 1-phosphate)
CSC[C@@H](O)[C@@H](O)C(=O)COP(O)(O)=O
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INCHI for NP0086750 (5-Methylthioribulose 1-phosphate)
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
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View in JSmol
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
Chemical FormulaC6H13O7PS
Average Mass260.2020 Da
Monoisotopic Mass260.01196 Da
IUPAC Name{[(3R,4S)-3,4-dihydroxy-5-(methylsulfanyl)-2-oxopentyl]oxy}phosphonic acid
Traditional Namemethylthioribulose-1-phosphate
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentGlycerone phosphates  
Alternative Parents
Substituents
  • Glycerone phosphate
    • 

  • Monoalkyl phosphate
    • 

  • Acyloin
    • 

  • Beta-hydroxy ketone
    • 

  • Monosaccharide
    • 

  • Organic phosphoric acid derivative
    • 

  • Phosphoric acid ester
    • 

  • Alkyl phosphate
    • 

  • Alpha-hydroxy ketone
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Thioether
    • 

  • Sulfenyl compound
    • 

  • Dialkylthioether
    • 

  • Organosulfur compound
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • 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-0.43ALOGPS
logP-1.3ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.18ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area124.29 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity53.31 m³·mol⁻¹ChemAxon
Polarizability22.59 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001299  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022541  
KNApSAcK IDNot Available
Chemspider ID152225  
KEGG Compound IDC04582  
BioCyc IDCPD-1063  
BiGG ID44103  
Wikipedia LinkNot Available
METLIN ID6143  
PubChem Compound174549  
PDB IDNot Available
ChEBI ID28096  
Good Scents IDNot Available
References
General References