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Showing metabocard for 1-Deoxy-D-xylulose 5-phosphate (HMDB0001213)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:08 UTC
HMDB IDHMDB0001213
Secondary Accession Numbers
  • HMDB01213
Metabolite Identification
Common Name1-Deoxy-D-xylulose 5-phosphate
Description1-Deoxy-D-xylulose 5-phosphate 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. 1-Deoxy-D-xylulose 5-phosphate exists in all living species, ranging from bacteria to plants to humans. 1-Deoxy-D-xylulose 5-phosphate has been detected, but not quantified in, several different foods, such as limes (Citrus aurantiifolia), anises (Pimpinella anisum), european chestnuts (Castanea sativa), yellow bell peppers (Capsicum annuum), and silver lindens (Tilia argentea). This could make 1-deoxy-D-xylulose 5-phosphate a potential biomarker for the consumption of these foods. 1-Deoxy-D-xylulose 5-phosphate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 1-Deoxy-D-xylulose 5-phosphate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

  Mrv1652309042000192D          

 13 12  0  0  1  0            999 V2000
    1.0461   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
M  END
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3D MOL for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

HMDB0001213
     RDKit          3D
1-Deoxy-D-xylulose 5-phosphate
 24 23  0  0  0  0  0  0  0  0999 V2000
   -3.4885   -0.8539    0.3920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1169   -0.7444   -0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5020   -1.7891   -0.3064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764    0.5642   -0.5431 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5168    1.5566   -0.2749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3129    0.9346    0.1834 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0830    2.1924   -0.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8256   -0.0086   -0.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9454    0.5011    0.5896 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2267   -0.5631    0.2930 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8887   -1.5559   -0.7914 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6556   -1.4005    1.6876 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    0.3963   -0.2792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0362   -1.7115   -0.0691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    0.1049    0.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4017   -1.0996    1.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3995    0.6071   -1.6509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8874    1.9712   -1.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5317    1.0924    1.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6502    2.0582   -1.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9940   -0.0325   -1.1698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6639   -1.0237    0.3099 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2449   -2.1543    1.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1205    0.9582   -1.0077 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  1
  7 20  1  0
  8 21  1  0
  8 22  1  0
 12 23  1  0
 13 24  1  0
M  END
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3D SDF for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

  Mrv1652309042000192D          

 13 12  0  0  1  0            999 V2000
    1.0461   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001213

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1

> <INCHI_KEY>
AJPADPZSRRUGHI-RFZPGFLSSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.184616142625956

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.93

> <JCHEM_LOGP>
-1.9430149353333332

> <ALOGPS_LOGS>
-0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.5046605893829295

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4788376412403776

> <JCHEM_PKA_STRONGEST_BASIC>
-3.578076314026042

> <JCHEM_POLAR_SURFACE_AREA>
124.29000000000002

> <JCHEM_REFRACTIVITY>
40.769999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-deoxy-D-xylulose-5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

HMDB0001213
     RDKit          3D
1-Deoxy-D-xylulose 5-phosphate
 24 23  0  0  0  0  0  0  0  0999 V2000
   -3.4885   -0.8539    0.3920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1169   -0.7444   -0.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5020   -1.7891   -0.3064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764    0.5642   -0.5431 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5168    1.5566   -0.2749 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3129    0.9346    0.1834 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0830    2.1924   -0.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8256   -0.0086   -0.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9454    0.5011    0.5896 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2267   -0.5631    0.2930 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.8887   -1.5559   -0.7914 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6556   -1.4005    1.6876 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5226    0.3963   -0.2792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0362   -1.7115   -0.0691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0510    0.1049    0.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4017   -1.0996    1.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3995    0.6071   -1.6509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8874    1.9712   -1.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5317    1.0924    1.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6502    2.0582   -1.1493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9940   -0.0325   -1.1698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6639   -1.0237    0.3099 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2449   -2.1543    1.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1205    0.9582   -1.0077 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  1
  7 20  1  0
  8 21  1  0
  8 22  1  0
 12 23  1  0
 13 24  1  0
M  END
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PDB for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       1.953  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.286  -4.977   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.620  -1.127   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.954  -4.977   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621  -3.437   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0       9.955  -2.667   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      11.288  -1.897   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      10.725  -4.001   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.185  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

COMPND    HMDB0001213
HETATM    1  C1  UNL     1      -3.489  -0.854   0.392  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.117  -0.744  -0.176  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.502  -1.789  -0.306  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.576   0.564  -0.543  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.517   1.557  -0.275  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.313   0.935   0.183  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.083   2.192  -0.329  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.826  -0.009  -0.079  1.00  0.00           C  
HETATM    9  O4  UNL     1       1.945   0.501   0.590  1.00  0.00           O  
HETATM   10  P1  UNL     1       3.227  -0.563   0.293  1.00  0.00           P  
HETATM   11  O5  UNL     1       2.889  -1.556  -0.791  1.00  0.00           O  
HETATM   12  O6  UNL     1       3.656  -1.401   1.688  1.00  0.00           O  
HETATM   13  O7  UNL     1       4.523   0.396  -0.279  1.00  0.00           O  
HETATM   14  H1  UNL     1      -4.036  -1.712  -0.069  1.00  0.00           H  
HETATM   15  H2  UNL     1      -4.051   0.105   0.291  1.00  0.00           H  
HETATM   16  H3  UNL     1      -3.402  -1.100   1.476  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.399   0.607  -1.651  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.887   1.971  -1.080  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.532   1.092   1.249  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.650   2.058  -1.149  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.994  -0.033  -1.170  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.664  -1.024   0.310  1.00  0.00           H  
HETATM   23  H10 UNL     1       4.245  -2.154   1.434  1.00  0.00           H  
HETATM   24  H11 UNL     1       4.120   0.958  -1.008  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3    3    4
CONECT    4    5    6   17
CONECT    5   18
CONECT    6    7    8   19
CONECT    7   20
CONECT    8    9   21   22
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   23
CONECT   13   24
END
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SMILES for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
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INCHI for HMDB0001213 (1-Deoxy-D-xylulose 5-phosphate)

InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Deoxy-D-xylulose 5-phosphoric acidGenerator
1-Deoxy-D-threo-pentulose 5-phosphateHMDB
D-1-Deoxyxylulose-5-PHMDB
Deoxyxylulose-5-phosphateHMDB
DOXPHMDB
DXPHMDB
1-Deoxylulose 5-phosphateMeSH, HMDB
Chemical FormulaC5H11O7P
Average Molecular Weight214.1104
Monoisotopic Molecular Weight214.024239218
IUPAC Name{[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional Name1-deoxy-D-xylulose-5-phosphate
CAS Registry Number190079-18-6
SMILES
CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1
InChI KeyAJPADPZSRRUGHI-RFZPGFLSSA-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-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Alpha-hydroxy ketone
  • Ketone
  • 1,2-diol
  • Secondary alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial application
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]-MetCCS_train_neg134.47730932474
[M-H]-Not Available134.477http://allccs.zhulab.cn/database/detail?ID=AllCCS00000386
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
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 IDDB02496
Phenol Explorer Compound IDNot Available
FooDB IDFDB022494
KNApSAcK IDC00007292
Chemspider ID391473
KEGG Compound IDC11437
BioCyc IDDEOXYXYLULOSE-5P
BiGG IDNot Available
Wikipedia Link1-Deoxy-D-xylulose 5-phosphate
METLIN ID6085
PubChem Compound443201
PDB IDNot Available
ChEBI ID16493
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceBlagg, Brian S. J.; Poulter, C. Dale. Synthesis of 1-Deoxy-D-xylulose and 1-Deoxy-D-xylulose-5-phosphate. Journal of Organic Chemistry (1999), 64(5), 1508-1511.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kuzuyama T, Takagi M, Takahashi S, Seto H: Cloning and characterization of 1-deoxy-D-xylulose 5-phosphate synthase from Streptomyces sp. Strain CL190, which uses both the mevalonate and nonmevalonate pathways for isopentenyl diphosphate biosynthesis. J Bacteriol. 2000 Feb;182(4):891-7. [PubMed:10648511 ]