Showing metabocard for 1-Deoxy-D-xylulose 5-phosphate (MMDBc0029592)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:33:33 UTC
Update Date2022-08-31 13:58:38 UTC
Metabolite IDMMDBc0029592
Metabolite Identification
Common Name1-Deoxy-D-xylulose 5-phosphate
Description1-Deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway. This is an alternative metabolic pathway leading to the formation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis is 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f124126f458>


  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
Download

3D MOL for #<Metabolite:0x00007f124126f458>

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
Download

3D SDF for #<Metabolite:0x00007f124126f458>


  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>
MMDBc0029592

> <DATABASE_NAME>
MIME

> <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

$$$$
Download

3D-SDF for #<Metabolite:0x00007f124126f458>

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
Download

PDB for #<Metabolite:0x00007f124126f458>

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 #<Metabolite:0x00007f124126f458>

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 #<Metabolite:0x00007f124126f458>

CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007f124126f458>

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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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
Molecular FormulaC5H11O7P
Average Mass214.1104
Monoisotopic Mass214.024239218
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