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Showing metabocard for Deoxyribose 5-phosphate (HMDB0001031)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:19:06 UTC
HMDB IDHMDB0001031
Secondary Accession Numbers
  • HMDB01031
Metabolite Identification
Common NameDeoxyribose 5-phosphate
DescriptionDeoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source.
Structure
Data?1582752172
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001031 (Deoxyribose 5-phosphate)


  Mrv0541 02231218532D          

 13 13  0  0  1  0            999 V2000
   10.8915   -9.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1458   -7.9250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0709   -9.0675    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8994   -8.2605    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2270   -8.4001    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5189   -9.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0340   -8.2286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6414   -6.0153    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9703   -7.5226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5522   -6.4334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0595   -7.1045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6139   -7.8480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3059   -6.7690    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  4  2  1  1  0  0  0
  2 11  1  0  0  0  0
  3  6  1  6  0  0  0
  3  4  1  0  0  0  0
  4 12  1  0  0  0  0
  5  7  1  1  0  0  0
  5 12  1  0  0  0  0
  8 13  1  0  0  0  0
  9 13  1  0  0  0  0
 10 13  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
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3D MOL for HMDB0001031 (Deoxyribose 5-phosphate)

HMDB0001031
     RDKit          3D
Deoxyribose 5-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.8175    1.8754   -0.9575 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1340    0.4155   -0.6670 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5635    0.2792    0.9508 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164   -0.1614   -1.7108 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6714   -0.4222   -0.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7249    0.2407   -0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3960   -0.6935    0.2727 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9076   -0.3470    1.5072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9848    0.4999    1.2134 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5622    1.6488    0.5288 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7065   -0.3699    0.1868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5230   -0.6874   -0.7226 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7005   -1.9247   -1.3166 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1482    1.0137    1.4838 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0735   -0.5064   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    1.1284   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2213    0.5918    0.8342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0108   -1.7355    0.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6059    0.7278    2.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2438    1.8314   -0.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4626    0.1885   -0.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1243   -1.2848    0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3972    0.0803   -1.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4568   -2.3885   -0.8686 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 12  7  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  1
  9 19  1  1
 10 20  1  0
 11 21  1  0
 11 22  1  0
 12 23  1  6
 13 24  1  0
M  END
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3D SDF for HMDB0001031 (Deoxyribose 5-phosphate)


  Mrv0541 02231218532D          

 13 13  0  0  1  0            999 V2000
   10.8915   -9.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1458   -7.9250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0709   -9.0675    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8994   -8.2605    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2270   -8.4001    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5189   -9.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0340   -8.2286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6414   -6.0153    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9703   -7.5226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5522   -6.4334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0595   -7.1045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6139   -7.8480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3059   -6.7690    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  4  2  1  1  0  0  0
  2 11  1  0  0  0  0
  3  6  1  6  0  0  0
  3  4  1  0  0  0  0
  4 12  1  0  0  0  0
  5  7  1  1  0  0  0
  5 12  1  0  0  0  0
  8 13  1  0  0  0  0
  9 13  1  0  0  0  0
 10 13  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001031

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
KKZFLSZAWCYPOC-VPENINKCSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.46469128826616

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.14

> <JCHEM_LOGP>
-1.5251322443333333

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.255762605408527

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2299449119892785

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2560418070675405

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
39.3231

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxyribose-5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001031 (Deoxyribose 5-phosphate)

HMDB0001031
     RDKit          3D
Deoxyribose 5-phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.8175    1.8754   -0.9575 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1340    0.4155   -0.6670 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5635    0.2792    0.9508 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164   -0.1614   -1.7108 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6714   -0.4222   -0.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7249    0.2407   -0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3960   -0.6935    0.2727 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9076   -0.3470    1.5072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9848    0.4999    1.2134 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5622    1.6488    0.5288 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7065   -0.3699    0.1868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5230   -0.6874   -0.7226 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7005   -1.9247   -1.3166 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1482    1.0137    1.4838 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0735   -0.5064   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897    1.1284   -0.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2213    0.5918    0.8342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0108   -1.7355    0.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6059    0.7278    2.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2438    1.8314   -0.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4626    0.1885   -0.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1243   -1.2848    0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3972    0.0803   -1.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4568   -2.3885   -0.8686 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 12  7  1  0
  3 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  1
  9 19  1  1
 10 20  1  0
 11 21  1  0
 11 22  1  0
 12 23  1  6
 13 24  1  0
M  END
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PDB for HMDB0001031 (Deoxyribose 5-phosphate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      20.331 -17.087   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.072 -14.793   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.799 -16.926   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.479 -15.420   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.957 -15.680   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      17.769 -18.070   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      22.463 -15.360   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      16.131 -11.229   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.878 -14.042   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      14.097 -12.009   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      16.911 -13.262   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      19.813 -14.650   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      15.504 -12.635   0.000  0.00  0.00           P+0
CONECT    1    3    5                                                       
CONECT    2    4   11                                                       
CONECT    3    1    6    4                                                  
CONECT    4    2    3   12                                                  
CONECT    5    1    7   12                                                  
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8   13                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11    2   13                                                       
CONECT   12    4    5                                                       
CONECT   13    8    9   10   11                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0001031 (Deoxyribose 5-phosphate)

COMPND    HMDB0001031
HETATM    1  O1  UNL     1       2.818   1.875  -0.958  1.00  0.00           O  
HETATM    2  P1  UNL     1       3.134   0.415  -0.667  1.00  0.00           P  
HETATM    3  O2  UNL     1       3.563   0.279   0.951  1.00  0.00           O  
HETATM    4  O3  UNL     1       4.316  -0.161  -1.711  1.00  0.00           O  
HETATM    5  O4  UNL     1       1.671  -0.422  -0.898  1.00  0.00           O  
HETATM    6  C1  UNL     1       0.725   0.241  -0.102  1.00  0.00           C  
HETATM    7  C2  UNL     1      -0.396  -0.693   0.273  1.00  0.00           C  
HETATM    8  O5  UNL     1      -0.908  -0.347   1.507  1.00  0.00           O  
HETATM    9  C3  UNL     1      -1.985   0.500   1.213  1.00  0.00           C  
HETATM   10  O6  UNL     1      -1.562   1.649   0.529  1.00  0.00           O  
HETATM   11  C4  UNL     1      -2.706  -0.370   0.187  1.00  0.00           C  
HETATM   12  C5  UNL     1      -1.523  -0.687  -0.723  1.00  0.00           C  
HETATM   13  O7  UNL     1      -1.700  -1.925  -1.317  1.00  0.00           O  
HETATM   14  H1  UNL     1       3.148   1.014   1.484  1.00  0.00           H  
HETATM   15  H2  UNL     1       5.074  -0.506  -1.164  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.390   1.128  -0.664  1.00  0.00           H  
HETATM   17  H4  UNL     1       1.221   0.592   0.834  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.011  -1.735   0.310  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.606   0.728   2.087  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.244   1.831  -0.179  1.00  0.00           H  
HETATM   21  H8  UNL     1      -3.463   0.188  -0.380  1.00  0.00           H  
HETATM   22  H9  UNL     1      -3.124  -1.285   0.644  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.397   0.080  -1.505  1.00  0.00           H  
HETATM   24  H11 UNL     1      -2.457  -2.388  -0.869  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   14
CONECT    4   15
CONECT    5    6
CONECT    6    7   16   17
CONECT    7    8   12   18
CONECT    8    9
CONECT    9   10   11   19
CONECT   10   20
CONECT   11   12   21   22
CONECT   12   13   23
CONECT   13   24
END
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SMILES for HMDB0001031 (Deoxyribose 5-phosphate)

O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
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INCHI for HMDB0001031 (Deoxyribose 5-phosphate)

InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Deoxyribose 5-phosphoric acidGenerator
2-Deoxy-alpha-D-ribose 5-phosphateHMDB
2-Deoxy-alpha-delta-ribose 5-phosphateHMDB
2-Deoxy-D-ribose 5-phosphateHMDB
2-Deoxy-D-ribose-5-phosphateHMDB
2-Deoxyribose 5-phosphateHMDB
2-Deoxyribose-5-pHMDB
2-Deoxyribose-5-phosphateHMDB
Deoxy-ribose-5PHMDB
Deoxyribose-5-pHMDB
Deoxyribose-5-phosphateHMDB
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Namedeoxyribose-5-phosphate
CAS Registry Number102916-66-5
SMILES
O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
InChI Identifier
InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1
InChI KeyKKZFLSZAWCYPOC-VPENINKCSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available132.469http://allccs.zhulab.cn/database/detail?ID=AllCCS00000382
Predicted Molecular Properties
PropertyValueSource
Water Solubility37.5 g/LALOGPS
logP-2.1ALOGPS
logP-1.5ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.32 m³·mol⁻¹ChemAxon
Polarizability17.46 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]+146.83631661259
DarkChem[M-H]-141.0631661259
AllCCS[M+H]+146.2632859911
AllCCS[M-H]-138.19132859911
DeepCCS[M+H]+138.5330932474
DeepCCS[M-H]-136.15730932474
DeepCCS[M-2H]-169.84630932474
DeepCCS[M+Na]+144.45430932474
AllCCS[M+H]+146.332859911
AllCCS[M+H-H2O]+142.432859911
AllCCS[M+NH4]+149.932859911
AllCCS[M+Na]+150.932859911
AllCCS[M-H]-138.232859911
AllCCS[M+Na-2H]-139.132859911
AllCCS[M+HCOO]-140.132859911

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, 2022.1.91 minutes32390414
Predicted by Siyang on May 30, 20228.8832 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20228.66 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid381.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid465.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid277.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid46.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid171.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid50.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid269.9 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 Acid236.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)770.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid551.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid40.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid627.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid179.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid239.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate733.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA368.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water427.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Deoxyribose 5-phosphateO[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O12938.8Standard polar33892256
Deoxyribose 5-phosphateO[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O11723.0Standard non polar33892256
Deoxyribose 5-phosphateO[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O11877.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Deoxyribose 5-phosphate,1TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O)O11922.0Semi standard non polar33892256
Deoxyribose 5-phosphate,1TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O1894.2Semi standard non polar33892256
Deoxyribose 5-phosphate,1TMS,isomer #3C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](O)C[C@@H]1O1913.5Semi standard non polar33892256
Deoxyribose 5-phosphate,2TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O)O11923.7Semi standard non polar33892256
Deoxyribose 5-phosphate,2TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O[Si](C)(C)C)O11976.1Semi standard non polar33892256
Deoxyribose 5-phosphate,2TMS,isomer #3C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C1965.2Semi standard non polar33892256
Deoxyribose 5-phosphate,2TMS,isomer #4C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](O)C[C@@H]1O)O[Si](C)(C)C1942.4Semi standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O11970.5Semi standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O11946.9Standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O12431.5Standard polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O12011.9Semi standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O11979.0Standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O12244.6Standard polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #3C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C2011.9Semi standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #3C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1966.1Standard non polar33892256
Deoxyribose 5-phosphate,3TMS,isomer #3C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C2212.8Standard polar33892256
Deoxyribose 5-phosphate,4TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O11990.4Semi standard non polar33892256
Deoxyribose 5-phosphate,4TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O11983.8Standard non polar33892256
Deoxyribose 5-phosphate,4TMS,isomer #1C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O12143.8Standard polar33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O)O12162.8Semi standard non polar33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O2148.4Semi standard non polar33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](O)C[C@@H]1O2161.4Semi standard non polar33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O)O12351.2Semi standard non polar33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O12414.5Semi standard non polar33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C2412.0Semi standard non polar33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C2395.3Semi standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O12613.5Semi standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O12543.6Standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O12692.8Standard polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12625.3Semi standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12548.2Standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12567.2Standard polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2632.6Semi standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2548.2Standard non polar33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2540.0Standard polar33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12831.0Semi standard non polar33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12665.4Standard non polar33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O12551.5Standard polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
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 IDFDB022380
KNApSAcK IDNot Available
Chemspider ID25057464
KEGG Compound IDC00673
BioCyc IDNot Available
BiGG ID35666
Wikipedia LinkNot Available
METLIN ID5956
PubChem Compound45934311
PDB IDAAB
ChEBI ID16132
Food Biomarker OntologyNot Available
VMH ID2DR5P
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMethod of preparing 2-deoxyribose 5-phosphate US Patent #7270992
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available

Enzymes

Enzyme Details
1. Putative deoxyribose-phosphate aldolase
General function:
Involved in catalytic activity
Specific function:
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).
Gene Name:
DERA
Uniprot ID:
Q9Y315
Molecular weight:
35230.395
Enzyme Details
2. Ribokinase
General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
Enzyme Details
3. Phosphoglucomutase-2
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity.
Gene Name:
PGM2
Uniprot ID:
Q96G03
Molecular weight:
68282.765
Reactions
Deoxyribose 1-phosphate → Deoxyribose 5-phosphatedetails