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Showing metabocard for alpha-D-xylose 1-phosphate (HMDB0304536)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 10:31:41 UTC
Update Date2021-09-24 10:31:41 UTC
HMDB IDHMDB0304536
Secondary Accession NumbersNone
Metabolite Identification
Common Namealpha-D-xylose 1-phosphate
Description3,4,5-trihydroxyoxan-2-yl phosphate belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn. Based on a literature review very few articles have been published on 3,4,5-trihydroxyoxan-2-yl phosphate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304536 (alpha-D-xylose 1-phosphate)


  Mrv1533005141513052D          

 14 14  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0164   -2.3645    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.9355    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  4  9  1  0  0  0  0
  3 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  CHG  2  12  -1  13  -1
M  END
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3D MOL for HMDB0304536 (alpha-D-xylose 1-phosphate)

HMDB0304536
     RDKit          3D
alpha-D-xylose 1-phosphate
 23 23  0  0  0  0  0  0  0  0999 V2000
    3.7169   -0.7242    0.0492 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2921    0.6355   -0.4871 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9514    0.8107   -2.0504 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.8990    1.8912    0.4700 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.6225    0.7114   -0.6479 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9538    0.0279    0.3711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    0.9947    1.0581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7825    1.4118    0.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9221    0.4313    0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9621    0.6585   -0.5123 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3601   -0.9485    0.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1637   -1.6722   -0.6098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0441   -1.0119   -0.2289 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5576   -2.2822    0.1217 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6757   -0.4260    1.0797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0933    2.4539    0.3813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4463    1.3546   -0.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2690    0.5880    1.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7323    1.0281    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4085   -1.4964    1.2898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1854   -1.1115   -1.4376 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0745   -0.9388   -1.3359 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -2.3858    1.0849 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
 11 13  1  0
 13 14  1  0
 13  6  1  0
  6 15  1  0
  8 16  1  0
  8 17  1  0
  9 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
M  CHG  2   3  -1   4  -1
M  END
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3D SDF for HMDB0304536 (alpha-D-xylose 1-phosphate)


  Mrv1533005141513052D          

 14 14  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0164   -2.3645    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.9355    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  4  9  1  0  0  0  0
  3 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  CHG  2  12  -1  13  -1
M  END
> <DATABASE_ID>
HMDB0304536

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1COC(OP([O-])([O-])=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-2-1-12-5(4(8)3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/p-2

> <INCHI_KEY>
ILXHFXFPPZGENN-UHFFFAOYSA-L

> <FORMULA>
C5H9O8P

> <MOLECULAR_WEIGHT>
228.094

> <EXACT_MASS>
228.004601408

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.49347242527385

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5-trihydroxyoxan-2-yl phosphate

> <ALOGPS_LOGP>
-2.09

> <JCHEM_LOGP>
-2.425770307333333

> <ALOGPS_LOGS>
-0.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.2202268460405445

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1565307698131155

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526611513944256

> <JCHEM_POLAR_SURFACE_AREA>
142.34

> <JCHEM_REFRACTIVITY>
38.5904

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.53e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4,5-trihydroxyoxan-2-yl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304536 (alpha-D-xylose 1-phosphate)

HMDB0304536
     RDKit          3D
alpha-D-xylose 1-phosphate
 23 23  0  0  0  0  0  0  0  0999 V2000
    3.7169   -0.7242    0.0492 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2921    0.6355   -0.4871 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9514    0.8107   -2.0504 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.8990    1.8912    0.4700 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.6225    0.7114   -0.6479 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9538    0.0279    0.3711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    0.9947    1.0581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7825    1.4118    0.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9221    0.4313    0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9621    0.6585   -0.5123 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3601   -0.9485    0.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1637   -1.6722   -0.6098 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0441   -1.0119   -0.2289 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5576   -2.2822    0.1217 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6757   -0.4260    1.0797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0933    2.4539    0.3813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4463    1.3546   -0.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2690    0.5880    1.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7323    1.0281    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4085   -1.4964    1.2898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1854   -1.1115   -1.4376 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0745   -0.9388   -1.3359 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -2.3858    1.0849 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
 11 13  1  0
 13 14  1  0
 13  6  1  0
  6 15  1  0
  8 16  1  0
  8 17  1  0
  9 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 13 22  1  0
 14 23  1  0
M  CHG  2   3  -1   4  -1
M  END
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PDB for HMDB0304536 (alpha-D-xylose 1-phosphate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       2.667  -3.080   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       4.001  -3.850   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       1.897  -4.414   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       3.437  -1.746   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    4                                                            
CONECT   10    3   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   28    0
END
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3D PDB for HMDB0304536 (alpha-D-xylose 1-phosphate)

COMPND    HMDB0304536
HETATM    1  O1  UNL     1       3.717  -0.724   0.049  1.00  0.00           O  
HETATM    2  P1  UNL     1       3.292   0.635  -0.487  1.00  0.00           P  
HETATM    3  O2  UNL     1       3.951   0.811  -2.050  1.00  0.00           O1-
HETATM    4  O3  UNL     1       3.899   1.891   0.470  1.00  0.00           O1-
HETATM    5  O4  UNL     1       1.623   0.711  -0.648  1.00  0.00           O  
HETATM    6  C1  UNL     1       0.954   0.028   0.371  1.00  0.00           C  
HETATM    7  O5  UNL     1       0.217   0.995   1.058  1.00  0.00           O  
HETATM    8  C2  UNL     1      -0.782   1.412   0.178  1.00  0.00           C  
HETATM    9  C3  UNL     1      -1.922   0.431   0.376  1.00  0.00           C  
HETATM   10  O6  UNL     1      -2.962   0.658  -0.512  1.00  0.00           O  
HETATM   11  C4  UNL     1      -1.360  -0.948   0.303  1.00  0.00           C  
HETATM   12  O7  UNL     1      -2.164  -1.672  -0.610  1.00  0.00           O  
HETATM   13  C5  UNL     1       0.044  -1.012  -0.229  1.00  0.00           C  
HETATM   14  O8  UNL     1       0.558  -2.282   0.122  1.00  0.00           O  
HETATM   15  H1  UNL     1       1.676  -0.426   1.080  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.093   2.454   0.381  1.00  0.00           H  
HETATM   17  H3  UNL     1      -0.446   1.355  -0.891  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.269   0.588   1.437  1.00  0.00           H  
HETATM   19  H5  UNL     1      -3.732   1.028   0.000  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.409  -1.496   1.290  1.00  0.00           H  
HETATM   21  H7  UNL     1      -2.185  -1.112  -1.438  1.00  0.00           H  
HETATM   22  H8  UNL     1       0.075  -0.939  -1.336  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.321  -2.386   1.085  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    5    6
CONECT    6    7   13   15
CONECT    7    8
CONECT    8    9   16   17
CONECT    9   10   11   18
CONECT   10   19
CONECT   11   12   13   20
CONECT   12   21
CONECT   13   14   22
CONECT   14   23
END
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SMILES for HMDB0304536 (alpha-D-xylose 1-phosphate)

OC1COC(OP([O-])([O-])=O)C(O)C1O
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INCHI for HMDB0304536 (alpha-D-xylose 1-phosphate)

InChI=1S/C5H11O8P/c6-2-1-12-5(4(8)3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3,4,5-Trihydroxyoxan-2-yl phosphoric acidGenerator
Β-L-arabinose 1-phosphoric acidGenerator
Α-D-xylose 1-phosphoric acidGenerator
Chemical FormulaC5H9O8P
Average Molecular Weight228.094
Monoisotopic Molecular Weight228.004601408
IUPAC Name3,4,5-trihydroxyoxan-2-yl phosphate
Traditional Name3,4,5-trihydroxyoxan-2-yl phosphate
CAS Registry NumberNot Available
SMILES
OC1COC(OP([O-])([O-])=O)C(O)C1O
InChI Identifier
InChI=1S/C5H11O8P/c6-2-1-12-5(4(8)3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/p-2
InChI KeyILXHFXFPPZGENN-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-2.1ALOGPS
logP-2.4ChemAxon
logS-0.44ALOGPS
pKa (Strongest Acidic)1.16ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area142.34 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity38.59 m³·mol⁻¹ChemAxon
Polarizability17.49 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+148.9632859911
AllCCS[M+H-H2O]+144.9732859911
AllCCS[M+Na]+153.73932859911
AllCCS[M+NH4]+152.6732859911
AllCCS[M-H]-133.80632859911
AllCCS[M+Na-2H]-134.13232859911
AllCCS[M+HCOO]-134.56932859911
DeepCCS[M+H]+139.1630932474
DeepCCS[M-H]-136.80230932474
DeepCCS[M-2H]-170.45930932474
DeepCCS[M+Na]+145.30830932474

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB031272
KNApSAcK IDNot Available
Chemspider ID11625640
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound23431615
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available