MiMeDB: Showing metabocard for D-Ribulose 1,5-bisphosphate (MMDBc0030059)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:23 UTC

Update Date

2022-08-31 17:39:21 UTC

Metabolite ID

MMDBc0030059

Metabolite Identification

Common Name

D-Ribulose 1,5-bisphosphate

Description

D-ribulose 1,5-bisphosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribulose 1,5-bisphosphate is invovled in the Calvin reductive pentose phosphate cycle. The Calvin Cycle is the primary conduit for the fixation of carbon dioxide into the biosphere; ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the rate-limiting fixation step. (PMID 16423843 ) Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. (PMID 19557347 )

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0304322
     RDKit          3D
D-ribulose-1,5-bisphosphate
 30 29  0  0  0  0  0  0  0  0999 V2000
    0.1789    1.6278    1.2140 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4643    1.2267    0.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6041    0.2844   -0.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1920    0.0030    1.1682 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4726   -1.0548    0.9816 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9572   -2.4752    0.9289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5371   -0.9636    2.2994 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3020   -0.6762   -0.4624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3300    1.6832   -1.0560 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3242    2.5530   -0.6371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9998    0.4892   -1.7198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7526    0.9314   -2.8183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   -0.1485   -0.7628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3105   -0.6115    0.3501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3778   -1.3318    1.4409 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.6678   -1.5480    2.7486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7691   -0.3973    1.6536 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8003   -2.8498    0.8051 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3584    0.7740   -0.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2784   -0.6519   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4739   -0.8694    1.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7807    0.1725   -0.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3133    2.2036   -1.8041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0378    2.9798    0.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2640   -0.2456   -2.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9240    1.9063   -2.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4510   -1.0050   -1.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7515    0.5925   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4950    0.5548    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6830   -3.1539    1.1034 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
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  3 19  1  0
  3 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  6
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  0
 13 28  1  0
 17 29  1  0
 18 30  1  0
M  END


  Mrv1652303062018502D          

 18 17  0  0  1  0            999 V2000
    7.1463  -18.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8597  -19.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5920  -18.9281    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.3055  -19.3423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0190  -18.9316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4328  -19.3462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8597  -20.1747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5920  -18.1031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3055  -20.1673    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0190  -18.1066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7085  -18.9133    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.3051  -19.6455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9950  -18.4991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1227  -18.1998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7325  -17.6957    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.3217  -16.9823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4460  -17.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1433  -18.4093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  2  1  1  0  0  0  0
 11  6  1  0  0  0  0
  7  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  8  1  6  0  0  0
  4  3  1  0  0  0  0
  4  9  1  1  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
 15 10  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 14 11  1  0  0  0  0
 16 15  2  0  0  0  0
 17 15  1  0  0  0  0
 18 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030059

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1

> <INCHI_KEY>
YAHZABJORDUQGO-NQXXGFSBSA-N

> <FORMULA>
C5H12O11P2

> <MOLECULAR_WEIGHT>
310.0897

> <EXACT_MASS>
309.98548425

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.437500389577625

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-2.8838290126666664

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.6549995885319904

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0021606343762866

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5803636984429508

> <JCHEM_POLAR_SURFACE_AREA>
191.04999999999995

> <JCHEM_REFRACTIVITY>
53.345099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.21e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribulose-1,5-bisphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304322
     RDKit          3D
D-ribulose-1,5-bisphosphate
 30 29  0  0  0  0  0  0  0  0999 V2000
    0.1789    1.6278    1.2140 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4643    1.2267    0.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6041    0.2844   -0.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1920    0.0030    1.1682 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4726   -1.0548    0.9816 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9572   -2.4752    0.9289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5371   -0.9636    2.2994 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3020   -0.6762   -0.4624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3300    1.6832   -1.0560 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3242    2.5530   -0.6371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9998    0.4892   -1.7198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7526    0.9314   -2.8183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   -0.1485   -0.7628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3105   -0.6115    0.3501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3778   -1.3318    1.4409 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.6678   -1.5480    2.7486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7691   -0.3973    1.6536 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8003   -2.8498    0.8051 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3584    0.7740   -0.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2784   -0.6519   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4739   -0.8694    1.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7807    0.1725   -0.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3133    2.2036   -1.8041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0378    2.9798    0.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2640   -0.2456   -2.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9240    1.9063   -2.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4510   -1.0050   -1.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7515    0.5925   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4950    0.5548    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6830   -3.1539    1.1034 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
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  3 19  1  0
  3 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  6
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  0
 13 28  1  0
 17 29  1  0
 18 30  1  0
M  END

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0      13.340 -35.346   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.671 -36.119   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.038 -35.332   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.370 -36.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.702 -35.339   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.008 -36.113   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      14.671 -37.659   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      16.038 -33.792   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      17.370 -37.646   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      18.702 -33.799   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      10.656 -35.305   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       9.903 -36.672   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.324 -34.532   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      11.429 -33.973   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      20.034 -33.032   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      19.267 -31.700   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      21.366 -32.265   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      20.801 -34.364   0.000  0.00  0.00           O+0
CONECT    1    6    2                                                       
CONECT    2    1    7    3                                                  
CONECT    3    2    8    4                                                  
CONECT    4    3    9    5                                                  
CONECT    5    4   10                                                       
CONECT    6    1   11                                                       
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5   15                                                       
CONECT   11    6   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   10   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

COMPND    HMDB0304322
HETATM    1  O1  UNL     1       0.179   1.628   1.214  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.464   1.227   0.110  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.604   0.284  -0.062  1.00  0.00           C  
HETATM    4  O2  UNL     1       2.192   0.003   1.168  1.00  0.00           O  
HETATM    5  P1  UNL     1       3.473  -1.055   0.982  1.00  0.00           P  
HETATM    6  O3  UNL     1       2.957  -2.475   0.929  1.00  0.00           O  
HETATM    7  O4  UNL     1       4.537  -0.964   2.299  1.00  0.00           O  
HETATM    8  O5  UNL     1       4.302  -0.676  -0.462  1.00  0.00           O  
HETATM    9  C3  UNL     1      -0.330   1.683  -1.056  1.00  0.00           C  
HETATM   10  O6  UNL     1      -1.324   2.553  -0.637  1.00  0.00           O  
HETATM   11  C4  UNL     1      -1.000   0.489  -1.720  1.00  0.00           C  
HETATM   12  O7  UNL     1      -1.753   0.931  -2.818  1.00  0.00           O  
HETATM   13  C5  UNL     1      -1.974  -0.148  -0.763  1.00  0.00           C  
HETATM   14  O8  UNL     1      -1.311  -0.611   0.350  1.00  0.00           O  
HETATM   15  P2  UNL     1      -2.378  -1.332   1.441  1.00  0.00           P  
HETATM   16  O9  UNL     1      -1.668  -1.548   2.749  1.00  0.00           O  
HETATM   17  O10 UNL     1      -3.769  -0.397   1.654  1.00  0.00           O  
HETATM   18  O11 UNL     1      -2.800  -2.850   0.805  1.00  0.00           O  
HETATM   19  H1  UNL     1       2.358   0.774  -0.721  1.00  0.00           H  
HETATM   20  H2  UNL     1       1.278  -0.652  -0.572  1.00  0.00           H  
HETATM   21  H3  UNL     1       5.474  -0.869   1.987  1.00  0.00           H  
HETATM   22  H4  UNL     1       4.781   0.173  -0.324  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.313   2.204  -1.804  1.00  0.00           H  
HETATM   24  H6  UNL     1      -1.038   2.980   0.217  1.00  0.00           H  
HETATM   25  H7  UNL     1      -0.264  -0.246  -2.045  1.00  0.00           H  
HETATM   26  H8  UNL     1      -1.924   1.906  -2.683  1.00  0.00           H  
HETATM   27  H9  UNL     1      -2.451  -1.005  -1.307  1.00  0.00           H  
HETATM   28  H10 UNL     1      -2.751   0.592  -0.464  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.495   0.555   1.692  1.00  0.00           H  
HETATM   30  H12 UNL     1      -3.683  -3.154   1.103  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   19   20
CONECT    4    5
CONECT    5    6    6    7    8
CONECT    7   21
CONECT    8   22
CONECT    9   10   11   23
CONECT   10   24
CONECT   11   12   13   25
CONECT   12   26
CONECT   13   14   27   28
CONECT   14   15
CONECT   15   16   16   17   18
CONECT   17   29
CONECT   18   30
END

HMDB0304322
     RDKit          3D
D-ribulose-1,5-bisphosphate
 30 29  0  0  0  0  0  0  0  0999 V2000
    0.1789    1.6278    1.2140 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4643    1.2267    0.1099 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6041    0.2844   -0.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1920    0.0030    1.1682 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4726   -1.0548    0.9816 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9572   -2.4752    0.9289 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5371   -0.9636    2.2994 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3020   -0.6762   -0.4624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3300    1.6832   -1.0560 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3242    2.5530   -0.6371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9998    0.4892   -1.7198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7526    0.9314   -2.8183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   -0.1485   -0.7628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3105   -0.6115    0.3501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3778   -1.3318    1.4409 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.6678   -1.5480    2.7486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7691   -0.3973    1.6536 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8003   -2.8498    0.8051 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3584    0.7740   -0.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2784   -0.6519   -0.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4739   -0.8694    1.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7807    0.1725   -0.3244 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3133    2.2036   -1.8041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0378    2.9798    0.2166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2640   -0.2456   -2.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9240    1.9063   -2.6832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4510   -1.0050   -1.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7515    0.5925   -0.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4950    0.5548    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6830   -3.1539    1.1034 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
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  3 19  1  0
  3 20  1  0
  7 21  1  0
  8 22  1  0
  9 23  1  6
 10 24  1  0
 11 25  1  6
 12 26  1  0
 13 27  1  0
 13 28  1  0
 17 29  1  0
 18 30  1  0
M  END

Synonyms

Value	Source
RIBULOSE-1,5-diphosphATE	ChEBI
RIBULOSE-1,5-diphosphoric acid	Generator
D-Ribulose 1,5-bisphosphoric acid	Generator
D-Ribulose-1,5-bisphosphoric acid	Generator
Ribulose-1,5 diphosphate	MeSH
Ribulose-1,5 diphosphate, (D)-isomer	MeSH
Ribulose-1,5-bisphosphate	MeSH

Molecular Formula

C₅H₁₂O₁₁P₂

Average Mass

310.0897

Monoisotopic Mass

309.98548425

IUPAC Name

{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid

Traditional Name

ribulose-1,5-bisphosphate

CAS Registry Number

24218-00-6

SMILES

O[C@H](COP(O)(O)=O)[C@@H](O)C(=O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1

InChI Key

YAHZABJORDUQGO-NQXXGFSBSA-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose-5-phosphate
Pentose phosphate
Glycerone phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Alpha-hydroxy ketone
Ketone
1,2-diol
Secondary alcohol
Carbonyl group
Hydrocarbon derivative
Alcohol
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose phosphate (CHEBI:16710 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.1 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-2.9	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	191.05 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	53.35 m³·mol⁻¹	ChemAxon
Polarizability	22.44 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	118	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	30	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	6	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	5	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces; Human	Metabolic reconstruction
Bacteria	Proteobacteria	15	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	2	Human feces; Human	Metabolic reconstruction
Bacteria	nah	3
Bacteria/Eubacteria	Cyanobacteria	34	Human
Archaea/Archaea	Euryarchaeota	11
Bacteria/Eubacteria	Verrucomicrobia	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Blood	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	31557052

External Links

HMDB ID

HMDB0304322

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Ribulose-1,5-bisphosphate

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

16710

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-Ribulose 1,5-bisphosphate (MMDBc0030059)

MOL for #<Metabolite:0x00007f9202327198>

3D MOL for #<Metabolite:0x00007f9202327198>

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3D-SDF for #<Metabolite:0x00007f9202327198>

PDB for #<Metabolite:0x00007f9202327198>

3D PDB for #<Metabolite:0x00007f9202327198>

SMILES for #<Metabolite:0x00007f9202327198>

INCHI for #<Metabolite:0x00007f9202327198>

Structure for #<Metabolite:0x00007f9202327198>

3D Structure for #<Metabolite:0x00007f9202327198>