Showing metabocard for Deoxyribose 5-phosphate (MMDBc0029533)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:31:18 UTC
Update Date2022-08-31 13:42:32 UTC
Metabolite IDMMDBc0029533
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923ea84940>


  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
Download

3D MOL for #<Metabolite:0x00007f923ea84940>

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
Download

3D SDF for #<Metabolite:0x00007f923ea84940>


  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>
MMDBc0029533

> <DATABASE_NAME>
MIME

> <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

$$$$
Download

3D-SDF for #<Metabolite:0x00007f923ea84940>

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
Download

PDB for #<Metabolite:0x00007f923ea84940>

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 #<Metabolite:0x00007f923ea84940>

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 #<Metabolite:0x00007f923ea84940>

O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
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INCHI for #<Metabolite:0x00007f923ea84940>

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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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
Molecular FormulaC5H11O7P
Average Mass214.1104
Monoisotopic Mass214.024239218
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