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Showing metabocard for 5-Deoxyribose-1-phosphate (HMDB0060393)

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enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:59:16 UTC
Update Date2022-03-07 03:17:44 UTC
HMDB IDHMDB0060393
Secondary Accession Numbers
  • HMDB60393
Metabolite Identification
Common Name5-Deoxyribose-1-phosphate
Description5-Deoxyribose-1-phosphate belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 5-Deoxyribose-1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Deoxyribose-1-phosphate exists in all living organisms, ranging from bacteria to humans. fluorouracil and 5-deoxyribose-1-phosphate can be biosynthesized from 5'-deoxy-5-fluorouridine; which is catalyzed by the enzyme thymidine phosphorylase. In humans, 5-deoxyribose-1-phosphate is involved in capecitabine action pathway. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
Structure
Data?1563866054
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060393 (5-Deoxyribose-1-phosphate)


  Mrv0541 05161317592D          

 13 13  0  0  0  0            999 V2000
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3415   -2.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7478   -1.9119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -1.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  7  1  6  0  0  0
 11  2  1  0  0  0  0
 11  5  1  0  0  0  0
  5 12  1  6  0  0  0
 13  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
M  END
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3D MOL for HMDB0060393 (5-Deoxyribose-1-phosphate)

HMDB0060393
     RDKit          3D
5-Deoxyribose-1-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
   -1.8950    1.9917   -0.3236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4874    0.6058   -0.7989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1729    0.5606   -1.1693 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313   -0.1806   -0.2420 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6139   -0.8491   -0.7875 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9978   -0.3930    0.0929 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9311   -1.5664    0.2794 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7444    0.8489   -0.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273    0.1415    1.6205 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4642   -1.2417    0.2155 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5299   -2.2185   -0.7715 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7305   -0.4093    0.2714 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8635   -1.1621    0.0651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2044    2.3506    0.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8998    2.7054   -1.1744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9416    1.8654    0.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0985    0.3928   -1.7236 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8171    0.4696    0.6092 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4769    1.2734   -0.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1111   -0.1433    2.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1631   -1.6509    1.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3074   -2.0741   -1.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7422    0.0688    1.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2505   -1.3854    0.9476 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  1  0
  6  7  2  0
  6  8  1  0
  6  9  1  0
  4 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  4 18  1  1
  8 19  1  0
  9 20  1  0
 10 21  1  1
 11 22  1  0
 12 23  1  1
 13 24  1  0
M  END
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3D SDF for HMDB0060393 (5-Deoxyribose-1-phosphate)


  Mrv0541 05161317592D          

 13 13  0  0  0  0            999 V2000
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3415   -2.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7478   -1.9119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -1.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  7  1  6  0  0  0
 11  2  1  0  0  0  0
 11  5  1  0  0  0  0
  5 12  1  6  0  0  0
 13  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060393

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
XXQFKXPJJNBLSU-TXICZTDVSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.1242051971225

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.51

> <JCHEM_LOGP>
-1.3788603406666664

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.219526154575139

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.155981210696972

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6437250332552598

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
39.290099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-deoxyribose-1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0060393 (5-Deoxyribose-1-phosphate)

HMDB0060393
     RDKit          3D
5-Deoxyribose-1-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
   -1.8950    1.9917   -0.3236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4874    0.6058   -0.7989 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1729    0.5606   -1.1693 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313   -0.1806   -0.2420 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6139   -0.8491   -0.7875 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9978   -0.3930    0.0929 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9311   -1.5664    0.2794 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7444    0.8489   -0.7904 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273    0.1415    1.6205 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4642   -1.2417    0.2155 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5299   -2.2185   -0.7715 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7305   -0.4093    0.2714 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8635   -1.1621    0.0651 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2044    2.3506    0.4626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8998    2.7054   -1.1744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9416    1.8654    0.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0985    0.3928   -1.7236 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8171    0.4696    0.6092 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4769    1.2734   -0.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1111   -0.1433    2.3426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1631   -1.6509    1.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3074   -2.0741   -1.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7422    0.0688    1.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2505   -1.3854    0.9476 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  1  0
  6  7  2  0
  6  8  1  0
  6  9  1  0
  4 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  6
  4 18  1  1
  8 19  1  0
  9 20  1  0
 10 21  1  1
 11 22  1  0
 12 23  1  1
 13 24  1  0
M  END
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PDB for HMDB0060393 (5-Deoxyribose-1-phosphate)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.637  -4.349   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.396  -3.569   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.418  -2.316   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.011  -2.943   0.000  0.00  0.00           P+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4   11   12                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8   13                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11    2    5                                                       
CONECT   12    5   13                                                       
CONECT   13    8    9   10   12                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0060393 (5-Deoxyribose-1-phosphate)

COMPND    HMDB0060393
HETATM    1  C1  UNL     1      -1.895   1.992  -0.324  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.487   0.606  -0.799  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.173   0.561  -1.169  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.531  -0.181  -0.242  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.614  -0.849  -0.788  1.00  0.00           O  
HETATM    6  P1  UNL     1       2.998  -0.393   0.093  1.00  0.00           P  
HETATM    7  O3  UNL     1       3.931  -1.566   0.279  1.00  0.00           O  
HETATM    8  O4  UNL     1       3.744   0.849  -0.790  1.00  0.00           O  
HETATM    9  O5  UNL     1       2.527   0.142   1.620  1.00  0.00           O  
HETATM   10  C4  UNL     1      -0.464  -1.242   0.215  1.00  0.00           C  
HETATM   11  O6  UNL     1      -0.530  -2.218  -0.772  1.00  0.00           O  
HETATM   12  C5  UNL     1      -1.731  -0.409   0.271  1.00  0.00           C  
HETATM   13  O7  UNL     1      -2.864  -1.162   0.065  1.00  0.00           O  
HETATM   14  H1  UNL     1      -1.204   2.351   0.463  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.900   2.705  -1.174  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.942   1.865   0.080  1.00  0.00           H  
HETATM   17  H4  UNL     1      -2.098   0.393  -1.724  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.817   0.470   0.609  1.00  0.00           H  
HETATM   19  H6  UNL     1       4.477   1.273  -0.282  1.00  0.00           H  
HETATM   20  H7  UNL     1       3.111  -0.143   2.343  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.163  -1.651   1.177  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.307  -2.074  -1.386  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.742   0.069   1.285  1.00  0.00           H  
HETATM   24  H11 UNL     1      -3.251  -1.385   0.948  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   12   17
CONECT    3    4
CONECT    4    5   10   18
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   19
CONECT    9   20
CONECT   10   11   12   21
CONECT   11   22
CONECT   12   13   23
CONECT   13   24
END
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SMILES for HMDB0060393 (5-Deoxyribose-1-phosphate)

C[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
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INCHI for HMDB0060393 (5-Deoxyribose-1-phosphate)

InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/t2-,3-,4-,5-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Deoxy-1-O-phosphono-alpha-D-ribofuranoseChEBI
5-Deoxy-alpha-D-ribose-1-phosphateChEBI
5-Deoxy-1-O-phosphono-a-D-ribofuranoseGenerator
5-Deoxy-1-O-phosphono-α-D-ribofuranoseGenerator
5-Deoxy-a-D-ribose-1-phosphateGenerator
5-Deoxy-a-D-ribose-1-phosphoric acidGenerator
5-Deoxy-alpha-D-ribose-1-phosphoric acidGenerator
5-Deoxy-α-D-ribose-1-phosphateGenerator
5-Deoxy-α-D-ribose-1-phosphoric acidGenerator
5-Deoxyribose-1-phosphoric acidGenerator
5-Deoxy-a-D-ribose 1-phosphateHMDB
5-Deoxy-a-D-ribose 1-phosphoric acidHMDB
5-Deoxy-alpha-D-ribose 1-phosphoric acidHMDB
5-Deoxy-α-D-ribose 1-phosphateHMDB
5-Deoxy-α-D-ribose 1-phosphoric acidHMDB
5-Deoxyribose-1-phosphateChEBI
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]oxy}phosphonic acid
Traditional Name5-deoxyribose-1-phosphate
CAS Registry NumberNot Available
SMILES
C[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/t2-,3-,4-,5-/m1/s1
InChI KeyXXQFKXPJJNBLSU-TXICZTDVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility37.6 g/LALOGPS
logP-1.5ALOGPS
logP-1.4ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.16ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity39.29 m³·mol⁻¹ChemAxon
Polarizability17.12 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+146.27931661259
DarkChem[M-H]-144.04531661259
DeepCCS[M+H]+138.53430932474
DeepCCS[M-H]-136.23330932474
DeepCCS[M-2H]-170.94130932474
DeepCCS[M+Na]+145.16230932474
AllCCS[M+H]+147.532859911
AllCCS[M+H-H2O]+143.532859911
AllCCS[M+NH4]+151.132859911
AllCCS[M+Na]+152.232859911
AllCCS[M-H]-137.732859911
AllCCS[M+Na-2H]-138.632859911
AllCCS[M+HCOO]-139.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.21 minutes32390414
Predicted by Siyang on May 30, 20229.2238 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20227.65 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid493.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid300.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid33.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid182.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid66.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid296.7 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid229.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)722.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid571.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid38.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid610.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid181.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid281.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate789.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA447.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water395.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Deoxyribose-1-phosphateC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O2930.4Standard polar33892256
5-Deoxyribose-1-phosphateC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O1629.8Standard non polar33892256
5-Deoxyribose-1-phosphateC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O1740.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Deoxyribose-1-phosphate,1TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O[Si](C)(C)C)[C@@H]1O1830.5Semi standard non polar33892256
5-Deoxyribose-1-phosphate,1TMS,isomer #2C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H]1O[Si](C)(C)C1851.0Semi standard non polar33892256
5-Deoxyribose-1-phosphate,1TMS,isomer #3C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O)[C@@H]1O1796.8Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1855.9Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TMS,isomer #2C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O1853.2Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TMS,isomer #3C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C1866.0Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TMS,isomer #4C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O)[C@@H]1O1820.7Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1853.5Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1871.6Standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C2147.1Standard polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O1843.2Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O1899.9Standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O2109.7Standard polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C1854.3Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C1904.8Standard non polar33892256
5-Deoxyribose-1-phosphate,3TMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C2022.5Standard polar33892256
5-Deoxyribose-1-phosphate,4TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1887.2Semi standard non polar33892256
5-Deoxyribose-1-phosphate,4TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1923.8Standard non polar33892256
5-Deoxyribose-1-phosphate,4TMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1968.4Standard polar33892256
5-Deoxyribose-1-phosphate,1TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2053.1Semi standard non polar33892256
5-Deoxyribose-1-phosphate,1TBDMS,isomer #2C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2075.6Semi standard non polar33892256
5-Deoxyribose-1-phosphate,1TBDMS,isomer #3C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O2034.9Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2302.4Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TBDMS,isomer #2C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2275.0Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TBDMS,isomer #3C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2288.8Semi standard non polar33892256
5-Deoxyribose-1-phosphate,2TBDMS,isomer #4C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O2247.9Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2517.4Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2488.8Standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2490.6Standard polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2478.3Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2484.1Standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #2C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2470.6Standard polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2487.3Semi standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2479.8Standard non polar33892256
5-Deoxyribose-1-phosphate,3TBDMS,isomer #3C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2388.0Standard polar33892256
5-Deoxyribose-1-phosphate,4TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2696.7Semi standard non polar33892256
5-Deoxyribose-1-phosphate,4TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2628.3Standard non polar33892256
5-Deoxyribose-1-phosphate,4TBDMS,isomer #1C[C@H]1O[C@H](OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2426.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxyribose-1-phosphate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-c8a69fbbc409678cae692017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxyribose-1-phosphate GC-MS (2 TMS) - 70eV, Positivesplash10-0002-9120000000-879348d5449e2ca213cc2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxyribose-1-phosphate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 10V, Positive-QTOFsplash10-0002-9220000000-5f09dbaee2c5978505dc2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 20V, Positive-QTOFsplash10-0002-9310000000-114397a9155dbe99d55b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 40V, Positive-QTOFsplash10-0002-9100000000-c4d81d3c665e3a91af962017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 10V, Negative-QTOFsplash10-03fs-9180000000-dc874a1db4b973ead3842017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 20V, Negative-QTOFsplash10-004i-9000000000-801ecd7338d22d460f122017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 40V, Negative-QTOFsplash10-004i-9000000000-28a7bebfe7a8aa82e6892017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 10V, Positive-QTOFsplash10-014j-9640000000-3ca621ebf36b971978492021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 20V, Positive-QTOFsplash10-0002-9100000000-8103e0107ce5acf6a5bc2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 40V, Positive-QTOFsplash10-0006-9000000000-a20a01baf8e1dc7b7d142021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 10V, Negative-QTOFsplash10-002b-9000000000-bb9788533e65968dd6ef2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 20V, Negative-QTOFsplash10-004i-9000000000-a5e502a2627af2048a1f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxyribose-1-phosphate 40V, Negative-QTOFsplash10-004i-9000000000-a5e502a2627af2048a1f2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC16637
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound24906327
PDB IDNot Available
ChEBI ID48462
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Thymidine phosphorylase
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
5'-Deoxy-5-fluorouridine + Phosphate → Fluorouracil + 5-Deoxyribose-1-phosphatedetails