Showing metabocard for Xylulose 5-phosphate (MMDBc0029819)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:43:01 UTC
Update Date2024-10-15 17:07:05 UTC
Metabolite IDMMDBc0029819
Metabolite Identification
Common NameXylulose 5-phosphate
DescriptionXylulose 5-phosphate (Xu-5-P) is a metabolite of the hexose monophosphate pathway that activates protein phosphatase 2A to mediate the acute effects of carbohydrate feeding on the glycolytic pathway, as well as the coordinate long-term control of the enzymes required for fatty acid and triglyceride synthesis. Xu-5-P is the signal for the coordinated control of lipogenesis. Feeding carbohydrates to cells causes levels of glucose, Glucose-6-phosphate (Glc-6-P), and Fructose-6-phosphate (Fru-6-P) to rise. Elevation of Fru-6-P leads to elevation of Xu-5-P in reactions catalyzed by the near-equilibrium isomerases of the nonoxidative portion of the hexose monophosphate pathway (ribulose 5-phosphate (Ru5P) epimerase [EC 5.1.3.1], ribose 5-phosphate (Rib5P) isomerase [EC 5.3.1.6], transaldolase [EC 2.2.1.2], and transketolase [EC 2.2.1.1]). The elevation of Xu-5-P is the coordinating signal that both acutely activates phosphofructokinase [PFK; EC 2.7.1.11] in glycolysis and will increase transcription of the genes for the enzymes of lipogenesis, the hexose monophosphate shunt, and glycolysis, all of which are required for the de novo synthesis of fat. (PMID 12721358 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92099e7d00>


  Mrv1652309042000132D          

 14 13  0  0  1  0            999 V2000
    2.9980   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414   -2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1414   -1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8559   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993   -2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4118   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5868   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f92099e7d00>

HMDB0000868
     RDKit          3D
Xylulose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -1.5545    0.1068   -1.8695 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0338    0.0909   -0.7879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3355    0.7799   -0.4876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3315    1.1622    0.8572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4307   -0.6025    0.3562 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8011   -1.9986    0.1680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0205   -0.5253    0.4570 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5786   -1.1651    1.5662 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8209    0.6383   -0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7575    0.0326   -0.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295    0.2134   -0.4692 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.1385   -0.5502   -1.5343 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9810    1.6900   -0.2404 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5549   -0.7267    0.9997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0646   -0.1166   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5875    1.5761   -1.1690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7584    0.4990    1.4264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9664   -0.3833    1.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3009   -2.3107   -0.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3523   -1.3545   -0.3682 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9034   -0.4520    2.2134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1227    1.2612   -0.6337 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2493    1.2574    0.7420 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4202    2.4690   -0.1558 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9767   -1.5914    0.7544 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
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f92099e7d00>


  Mrv1652309042000132D          

 14 13  0  0  1  0            999 V2000
    2.9980   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414   -2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1414   -1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559   -2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8559   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849   -2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993   -2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4118   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5868   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029819

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5-/m1/s1

> <INCHI_KEY>
FNZLKVNUWIIPSJ-RFZPGFLSSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.05369731874536

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.504370847667953

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4785529591465414

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3276267100529333

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.472199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribulose-5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f92099e7d00>

HMDB0000868
     RDKit          3D
Xylulose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -1.5545    0.1068   -1.8695 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0338    0.0909   -0.7879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3355    0.7799   -0.4876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3315    1.1622    0.8572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4307   -0.6025    0.3562 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8011   -1.9986    0.1680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0205   -0.5253    0.4570 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5786   -1.1651    1.5662 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8209    0.6383   -0.0331 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7575    0.0326   -0.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295    0.2134   -0.4692 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.1385   -0.5502   -1.5343 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9810    1.6900   -0.2404 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5549   -0.7267    0.9997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0646   -0.1166   -0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5875    1.5761   -1.1690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7584    0.4990    1.4264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9664   -0.3833    1.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3009   -2.3107   -0.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3523   -1.3545   -0.3682 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9034   -0.4520    2.2134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1227    1.2612   -0.6337 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2493    1.2574    0.7420 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4202    2.4690   -0.1558 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9767   -1.5914    0.7544 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
  2  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  0
  9 23  1  0
 13 24  1  0
 14 25  1  0
M  END
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PDB for #<Metabolite:0x00007f92099e7d00>

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  O   UNK     0       5.596  -4.771   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.930  -4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.264  -4.771   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.264  -6.311   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.597  -4.001   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.597  -2.461   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      10.931  -4.771   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.931  -6.311   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      12.265  -4.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      13.598  -4.771   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      14.932  -4.001   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      16.266  -3.231   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      15.702  -5.335   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      14.162  -2.667   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   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:0x00007f92099e7d00>

COMPND    HMDB0000868
HETATM    1  O1  UNL     1      -1.554   0.107  -1.869  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.034   0.091  -0.788  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.336   0.780  -0.488  1.00  0.00           C  
HETATM    4  O2  UNL     1      -3.331   1.162   0.857  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.431  -0.602   0.356  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.801  -1.999   0.168  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.021  -0.525   0.457  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.579  -1.165   1.566  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.821   0.638  -0.033  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.758   0.033  -0.895  1.00  0.00           O  
HETATM   11  P1  UNL     1       3.329   0.213  -0.469  1.00  0.00           P  
HETATM   12  O6  UNL     1       4.139  -0.550  -1.534  1.00  0.00           O  
HETATM   13  O7  UNL     1       3.981   1.690  -0.240  1.00  0.00           O  
HETATM   14  O8  UNL     1       3.555  -0.727   1.000  1.00  0.00           O  
HETATM   15  H1  UNL     1      -4.065  -0.117  -0.561  1.00  0.00           H  
HETATM   16  H2  UNL     1      -3.587   1.576  -1.169  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.758   0.499   1.426  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.966  -0.383   1.334  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.301  -2.311  -0.626  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.352  -1.355  -0.368  1.00  0.00           H  
HETATM   21  H7  UNL     1       0.903  -0.452   2.213  1.00  0.00           H  
HETATM   22  H8  UNL     1       0.123   1.261  -0.634  1.00  0.00           H  
HETATM   23  H9  UNL     1       1.249   1.257   0.742  1.00  0.00           H  
HETATM   24  H10 UNL     1       3.420   2.469  -0.156  1.00  0.00           H  
HETATM   25  H11 UNL     1       3.977  -1.591   0.754  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    5
CONECT    3    4   15   16
CONECT    4   17
CONECT    5    6    7   18
CONECT    6   19
CONECT    7    8    9   20
CONECT    8   21
CONECT    9   10   22   23
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x00007f92099e7d00>

OCC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007f92099e7d00>

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5-/m1/s1
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Synonyms
ValueSource
5-O-Phosphono-D-threo-pentos-2-uloseChEBI
5-O-Phosphono-D-xyluloseChEBI
D-Xylulose-5-phosphateChEBI
D-Xylulose-5-phosphoric acidGenerator
Xylulose 5-phosphoric acidGenerator
D-Xylulose 5-phosphateHMDB
D-Xylulose 5-PO4HMDB
D-Xylulose-5-PHMDB
Xu-5-PHMDB
Xylulose-PHMDB
Xylulose-phosphateHMDB
Xylulose-5-phosphateMeSH, HMDB
Xylulose-5-phosphate, (D)-isomerMeSH, HMDB
Xylulose 5-phosphateHMDB
keto-D-Xylulose 5-phosphateHMDB
Molecular FormulaC5H11O8P
Average Mass230.1098
Monoisotopic Mass230.01915384
IUPAC Name{[(2R,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional Nameribulose-5-phosphate
CAS Registry Number4212-65-1
SMILES
OCC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5-/m1/s1
InChI KeyFNZLKVNUWIIPSJ-RFZPGFLSSA-N