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Showing metabocard for D-Arabinose 5-phosphate (HMDB0011734)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-03-03 10:37:18 UTC
Update Date2021-09-14 15:07:02 UTC
HMDB IDHMDB0011734
Secondary Accession Numbers
  • HMDB11734
Metabolite Identification
Common NameD-Arabinose 5-phosphate
DescriptionD-Arabinose 5-phosphate, also known as 5-O-phosphono-D-arabinose or D-a-5-p, 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. D-Arabinose 5-phosphate exists in all living organisms, ranging from bacteria to humans. D-Arabinose 5-phosphate has been detected, but not quantified in, several different foods, such as kumquats (Fortunella), brassicas, winter savories (Satureja montana), soft-necked garlics (Allium sativum L. var. sativum), and plains prickly pears (Opuntia macrorhiza). This could make D-arabinose 5-phosphate a potential biomarker for the consumption of these foods. D-Arabinose 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 D-Arabinose 5-phosphate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011734 (D-Arabinose 5-phosphate)

  Mrv1652309042000342D          

 14 13  0  0  1  0            999 V2000
   12.4149  -18.4154    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   11.7005  -18.8279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8274  -19.1299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0024  -17.7009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8439  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -18.0029    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2728  -18.4154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9873  -18.0029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7018  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1294  -18.0029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7018  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9873  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2728  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 11  9  2  0  0  0  0
  8 12  1  6  0  0  0
  7 13  1  6  0  0  0
  6 14  1  1  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0011734 (D-Arabinose 5-phosphate)

HMDB0011734
     RDKit          3D
D-Arabinose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -2.4512    2.2362   -0.9198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515    1.2661   -0.5367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6331    0.3730    0.5478 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7113   -0.4982    0.8876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.5011    0.1231 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2114   -1.3356    1.2509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2757    0.3270   -0.1757 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3091    1.1291   -1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207   -0.4957   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0499    0.4256   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5721   -0.2400   -0.3005 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.6828   -1.4353   -1.1976 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6330    0.9573   -0.9109 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1743   -0.6529    1.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9924    1.0634   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3212    0.9175    1.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5648   -0.7284    1.8404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7474   -1.1135   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160   -2.2139    1.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0861    1.0166    0.7095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485    0.5895   -2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0724   -1.1722    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635   -1.0766   -1.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2389    1.8609   -0.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694   -0.6986    1.9113 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
  3  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
  2 15  1  0
  3 16  1  1
  4 17  1  0
  5 18  1  6
  6 19  1  0
  7 20  1  1
  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 HMDB0011734 (D-Arabinose 5-phosphate)

  Mrv1652309042000342D          

 14 13  0  0  1  0            999 V2000
   12.4149  -18.4154    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   11.7005  -18.8279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8274  -19.1299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0024  -17.7009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8439  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -18.0029    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2728  -18.4154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9873  -18.0029    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7018  -18.4154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1294  -18.0029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7018  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9873  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2728  -19.2404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5583  -17.1779    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 11  9  2  0  0  0  0
  8 12  1  6  0  0  0
  7 13  1  6  0  0  0
  6 14  1  1  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011734

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1

> <INCHI_KEY>
PPQRONHOSHZGFQ-WDCZJNDASA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.998594047608492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.64

> <JCHEM_LOGP>
-3.0615916523333335

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.51682044808608

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4910102081094525

> <JCHEM_PKA_STRONGEST_BASIC>
-3.544450846242131

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.256

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arabinose 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0011734 (D-Arabinose 5-phosphate)

HMDB0011734
     RDKit          3D
D-Arabinose 5-phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
   -2.4512    2.2362   -0.9198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0515    1.2661   -0.5367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6331    0.3730    0.5478 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7113   -0.4982    0.8876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.5011    0.1231 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2114   -1.3356    1.2509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2757    0.3270   -0.1757 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3091    1.1291   -1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207   -0.4957   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0499    0.4256   -0.2388 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5721   -0.2400   -0.3005 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.6828   -1.4353   -1.1976 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6330    0.9573   -0.9109 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1743   -0.6529    1.2352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9924    1.0634   -1.0708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3212    0.9175    1.4523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5648   -0.7284    1.8404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7474   -1.1135   -0.7375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6160   -2.2139    1.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0861    1.0166    0.7095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4485    0.5895   -2.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0724   -1.1722    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635   -1.0766   -1.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2389    1.8609   -0.7799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694   -0.6986    1.9113 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
  3  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
  2 15  1  0
  3 16  1  1
  4 17  1  0
  5 18  1  6
  6 19  1  0
  7 20  1  1
  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 HMDB0011734 (D-Arabinose 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  P   UNK     0      23.174 -34.375   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      21.841 -35.145   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      23.944 -35.709   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      22.404 -33.042   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      25.842 -34.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.175 -33.605   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.509 -34.375   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.843 -33.605   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.177 -34.375   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      24.508 -33.605   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      31.177 -35.915   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      29.843 -32.065   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      28.509 -35.915   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      27.175 -32.065   0.000  0.00  0.00           O+0
CONECT    1    2    3    4   10                                             
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    6   10                                                       
CONECT    6    5    7   14                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   11                                                       
CONECT   10    5    1                                                       
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    7                                                            
CONECT   14    6                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0011734 (D-Arabinose 5-phosphate)

COMPND    HMDB0011734
HETATM    1  O1  UNL     1      -2.451   2.236  -0.920  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.052   1.266  -0.537  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.633   0.373   0.548  1.00  0.00           C  
HETATM    4  O2  UNL     1      -3.711  -0.498   0.888  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.457  -0.501   0.123  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.211  -1.336   1.251  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.276   0.327  -0.176  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.309   1.129  -1.279  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.021  -0.496  -0.235  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.050   0.426  -0.239  1.00  0.00           O  
HETATM   11  P1  UNL     1       3.572  -0.240  -0.300  1.00  0.00           P  
HETATM   12  O6  UNL     1       3.683  -1.435  -1.198  1.00  0.00           O  
HETATM   13  O7  UNL     1       4.633   0.957  -0.911  1.00  0.00           O  
HETATM   14  O8  UNL     1       4.174  -0.653   1.235  1.00  0.00           O  
HETATM   15  H1  UNL     1      -3.992   1.063  -1.071  1.00  0.00           H  
HETATM   16  H2  UNL     1      -2.321   0.917   1.452  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.565  -0.728   1.840  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.747  -1.113  -0.737  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.616  -2.214   1.044  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.086   1.017   0.710  1.00  0.00           H  
HETATM   21  H7  UNL     1      -0.449   0.589  -2.083  1.00  0.00           H  
HETATM   22  H8  UNL     1       1.072  -1.172   0.647  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.963  -1.077  -1.183  1.00  0.00           H  
HETATM   24  H10 UNL     1       4.239   1.861  -0.780  1.00  0.00           H  
HETATM   25  H11 UNL     1       3.469  -0.699   1.911  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   15
CONECT    3    4    5   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 HMDB0011734 (D-Arabinose 5-phosphate)

O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C=O
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INCHI for HMDB0011734 (D-Arabinose 5-phosphate)

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-O-Phosphono-D-arabinoseChEBI
D-a-5-pChEBI
D-Arabinose 5-phosphoric acidGenerator
Arabinose-5-PHMDB
Arabinose-5PHMDB
Arabinose 5-phosphate, di-li saltMeSH, HMDB
Arabinose 5-phosphateMeSH, HMDB
Arabinose 5-phosphate, (beta-D)-isomerMeSH, HMDB
Chemical FormulaC5H11O8P
Average Molecular Weight230.1098
Monoisotopic Molecular Weight230.01915384
IUPAC Name{[(2R,3R,4S)-2,3,4-trihydroxy-5-oxopentyl]oxy}phosphonic acid
Traditional Namearabinose 5-phosphate
CAS Registry Number13137-52-5
SMILES
O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C=O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
InChI KeyPPQRONHOSHZGFQ-WDCZJNDASA-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 phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Beta-hydroxy aldehyde
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Aldehyde
  • Organic oxide
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue Locations
  • Prostate
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 IDFDB028414
KNApSAcK IDNot Available
Chemspider ID163687
KEGG Compound IDC01112
BioCyc IDARABINOSE-5P
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound188324
PDB IDNot Available
ChEBI ID16241
Food Biomarker OntologyNot Available
VMH IDARA5P
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]