Showing metabocard for D-Xylulose 1-phosphate (MMDBc0047953)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:18:36 UTC
Update Date2024-04-30 20:33:39 UTC
Metabolite IDMMDBc0047953
Metabolite Identification
Common NameD-Xylulose 1-phosphate
DescriptionD-Xylulose 1-phosphate is produced in the hepatocytes and is the product of fructokinase (ketohexokinase, EC 2.7.1.3) phosphorylation of D-xylulose. The cleavage of D-xylulose-1-phosphate glycolaldehyde by aldolase (fructose-bisphosphate aldolase, EC 4.1.2.13) produces glycolaldehyde which is an oxalate precursor. The distribution of both enzymes in human tissues indicates that this reaction sequence occurs mainly in the liver, to a lesser extent in the kidney, and very little in heart, brain and muscle. The kinetic properties of fructokinase show that this enzyme can phosphorylate D-xylulose as readily as D-fructose (PMID: 6458298 , 13898172 , 6284103 , 2996495 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f922c1dea28>


  Mrv1652304092018262D          

 14 13  0  0  0  0            999 V2000
 9988.6266 9988.1094    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9987.9129 9987.6974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9987.6974    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9988.6266 9988.9344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1986 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.9129 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.0578 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.4842 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7735 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.7697 9988.1094    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9986.1832 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.0533 9987.6955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.3583 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f922c1dea28>

HMDB0006534
     RDKit          3D
D-Xylulose 1-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -0.3808    2.1316    0.5781 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0286    1.1067    0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4199    0.6039    0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7042   -0.5701   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2736   -1.0238    0.1218 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.2274   -1.9320    1.3418 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0055   -1.8957   -1.1261 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1382    0.3493    0.5335 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8863    0.3939   -0.8705 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1498   -0.6847   -1.3872 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0227   -0.2234   -0.0688 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7841   -1.0410   -0.9231 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9974    0.8427    0.4213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0674    0.1982    1.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4694    0.4796    1.4735 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.4035    0.1031 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7929   -1.3626   -1.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4591    0.8617   -0.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2773    1.0600   -1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3458   -1.5115   -0.9167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6961   -0.7941    0.8031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1790   -1.8056   -0.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5150    1.5730    1.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4336    1.3176   -0.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9270    0.5228    0.7613 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  6
 10 20  1  0
 11 21  1  1
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f922c1dea28>


  Mrv1652304092018262D          

 14 13  0  0  0  0            999 V2000
 9988.6266 9988.1094    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9987.9129 9987.6974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9987.6974    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9988.6266 9988.9344    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9987.1986 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9987.9129 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.0578 9988.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.3422 9986.8724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9986.4842 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7735 9987.6974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.7697 9988.1094    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9986.1832 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.0533 9987.6955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9985.3583 9988.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047953

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)/t3-,5+/m1/s1

> <INCHI_KEY>
NBOCCPQHBPGYCX-WUJLRWPWSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.109

> <EXACT_MASS>
230.019154312

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.009626265060398

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.80

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208722028772268

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.178619064267565

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9797461037901494

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.472199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f922c1dea28>

HMDB0006534
     RDKit          3D
D-Xylulose 1-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -0.3808    2.1316    0.5781 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0286    1.1067    0.0600 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4199    0.6039    0.3717 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7042   -0.5701   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2736   -1.0238    0.1218 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.2274   -1.9320    1.3418 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0055   -1.8957   -1.1261 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1382    0.3493    0.5335 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8863    0.3939   -0.8705 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1498   -0.6847   -1.3872 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0227   -0.2234   -0.0688 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7841   -1.0410   -0.9231 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9974    0.8427    0.4213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0674    0.1982    1.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4694    0.4796    1.4735 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.4035    0.1031 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7929   -1.3626   -1.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4591    0.8617   -0.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2773    1.0600   -1.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3458   -1.5115   -0.9167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6961   -0.7941    0.8031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1790   -1.8056   -0.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5150    1.5730    1.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4336    1.3176   -0.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9270    0.5228    0.7613 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  6
 10 20  1  0
 11 21  1  1
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

PDB for #<Metabolite:0x00007f922c1dea28>

HEADER    PROTEIN                                 09-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-APR-20         0                                  
HETATM    1  C   UNK     0    8645.4368644.471   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8644.1048643.702   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8646.7728643.702   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8645.4368646.011   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8642.7718644.471   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8644.1048642.162   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8648.1088644.471   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8646.7728642.162   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8641.4378643.702   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8649.4448643.702   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0    8640.1048644.471   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0    8640.8758645.807   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8638.7668643.698   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8639.3368645.807   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2    9                                                       
CONECT    6    2                                                            
CONECT    7    3   10                                                       
CONECT    8    3                                                            
CONECT    9    5   11                                                       
CONECT   10    7                                                            
CONECT   11    9   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for #<Metabolite:0x00007f922c1dea28>

COMPND    HMDB0006534
HETATM    1  O1  UNL     1      -0.381   2.132   0.578  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.029   1.107   0.060  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.420   0.604   0.372  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.704  -0.570  -0.309  1.00  0.00           O  
HETATM    5  P1  UNL     1       3.274  -1.024   0.122  1.00  0.00           P  
HETATM    6  O3  UNL     1       3.227  -1.932   1.342  1.00  0.00           O  
HETATM    7  O4  UNL     1       4.006  -1.896  -1.126  1.00  0.00           O  
HETATM    8  O5  UNL     1       4.138   0.349   0.533  1.00  0.00           O  
HETATM    9  C3  UNL     1      -0.886   0.394  -0.871  1.00  0.00           C  
HETATM   10  O6  UNL     1      -0.150  -0.685  -1.387  1.00  0.00           O  
HETATM   11  C4  UNL     1      -2.023  -0.223  -0.069  1.00  0.00           C  
HETATM   12  O7  UNL     1      -2.784  -1.041  -0.923  1.00  0.00           O  
HETATM   13  C5  UNL     1      -2.997   0.843   0.421  1.00  0.00           C  
HETATM   14  O8  UNL     1      -4.067   0.198   1.084  1.00  0.00           O  
HETATM   15  H1  UNL     1       1.469   0.480   1.474  1.00  0.00           H  
HETATM   16  H2  UNL     1       2.143   1.403   0.103  1.00  0.00           H  
HETATM   17  H3  UNL     1       4.793  -1.363  -1.424  1.00  0.00           H  
HETATM   18  H4  UNL     1       4.459   0.862  -0.242  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.277   1.060  -1.636  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.346  -1.512  -0.917  1.00  0.00           H  
HETATM   21  H7  UNL     1      -1.696  -0.794   0.803  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.179  -1.806  -0.449  1.00  0.00           H  
HETATM   23  H9  UNL     1      -2.515   1.573   1.090  1.00  0.00           H  
HETATM   24  H10 UNL     1      -3.434   1.318  -0.481  1.00  0.00           H  
HETATM   25  H11 UNL     1      -4.927   0.523   0.761  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   15   16
CONECT    4    5
CONECT    5    6    6    7    8
CONECT    7   17
CONECT    8   18
CONECT    9   10   11   19
CONECT   10   20
CONECT   11   12   13   21
CONECT   12   22
CONECT   13   14   23   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x00007f922c1dea28>

OC[C@@H](O)[C@H](O)C(=O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007f922c1dea28>

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)/t3-,5+/m1/s1
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Synonyms
ValueSource
D-Xylulose 1-phosphoric acidGenerator
L-Threo-pentulose 1-phosphateHMDB
Xylulose-1-phosphateHMDB
D-Xylulose-1-phosphateHMDB
D-Xylulose 1-phosphateHMDB
Molecular FormulaC5H11O8P
Average Mass230.109
Monoisotopic Mass230.019154312
IUPAC Name{[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxy}phosphonic acid
Traditional Name[(3S,4R)-3,4,5-trihydroxy-2-oxopentyl]oxyphosphonic acid
CAS Registry Number63323-91-1
SMILES
OC[C@@H](O)[C@H](O)C(=O)COP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)/t3-,5+/m1/s1
InChI KeyNBOCCPQHBPGYCX-WUJLRWPWSA-N