MiMeDB: Showing metabocard for TDP-alpha-D-glucose (MMDBc0056325)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:50 UTC

Update Date

2022-08-12 20:09:40 UTC

Metabolite ID

MMDBc0056325

Metabolite Identification

Common Name

TDP-alpha-D-glucose

Description

Thymidine 5'-(trihydrogen diphosphate), P'-(alpha-D-glucopyranosyl) ester, also known as TDP-alpha-D-glucose, belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. Based on a literature review very few articles have been published on Thymidine 5'-(trihydrogen diphosphate), P'-(alpha-D-glucopyranosyl) ester.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 46 48  0  0  1  0            999 V2000
   -4.4522    4.7466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1468    5.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9024    9.2852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0231    6.9486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6318    4.6604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2893    9.8372    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7615    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4608   10.6442    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    7.1786    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8477   11.1962    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0964    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0631   10.9413    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2962    3.9067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414    5.9090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8916   10.1343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9908    4.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4757    3.8205    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3264    5.2416    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6870    9.5401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2454   10.8991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0192   12.0032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8810    6.9486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4500   11.4933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7811    3.2393    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1703    4.4017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7243    8.7951    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2342    7.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1284    9.2439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424    8.9009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1946    7.7556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    5.9090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5047    9.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1069    9.8794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    8.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9793    8.0105    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9354    9.0724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.0739   10.0922    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6324    7.5085    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6323   11.4512    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1640    7.5531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6762   10.3893    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    6.1103    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2346   11.7483    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    5.1739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785   10.6864    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  3  1  1  0  0  0
  7  4  1  1  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  5  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  1  0  0  0  0
 17 13  2  0  0  0  0
 17 16  1  0  0  0  0
 18  2  1  0  0  0  0
 14 18  1  1  0  0  0
 18 16  1  0  0  0  0
 19  3  1  0  0  0  0
  8 20  1  6  0  0  0
  9 21  1  6  0  0  0
 10 22  1  6  0  0  0
 11 23  1  6  0  0  0
 12 24  1  6  0  0  0
 25 13  1  0  0  0  0
 26 16  2  0  0  0  0
 31  4  1  0  0  0  0
 32  7  1  0  0  0  0
 32 14  1  0  0  0  0
 33  6  1  0  0  0  0
 33 15  1  0  0  0  0
 15 34  1  6  0  0  0
 36 27  1  0  0  0  0
 36 28  2  0  0  0  0
 36 31  1  0  0  0  0
 36 35  1  0  0  0  0
 37 29  1  0  0  0  0
 37 30  2  0  0  0  0
 37 34  1  0  0  0  0
 37 35  1  0  0  0  0
  6 38  1  6  0  0  0
  7 39  1  6  0  0  0
  8 40  1  1  0  0  0
  9 41  1  1  0  0  0
 10 42  1  6  0  0  0
 11 43  1  1  0  0  0
 12 44  1  1  0  0  0
 14 45  1  6  0  0  0
 15 46  1  1  0  0  0
M  CHG  2  25  -1  27  -1
M  END


  Mrv1652306172222222D          

 46 48  0  0  1  0            999 V2000
   -4.4522    4.7466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1468    5.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9024    9.2852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0231    6.9486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6318    4.6604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2893    9.8372    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7615    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4608   10.6442    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    7.1786    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8477   11.1962    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0964    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0631   10.9413    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2962    3.9067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414    5.9090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8916   10.1343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9908    4.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4757    3.8205    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3264    5.2416    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6870    9.5401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2454   10.8991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0192   12.0032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8810    6.9486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4500   11.4933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7811    3.2393    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1703    4.4017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7243    8.7951    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2342    7.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1284    9.2439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424    8.9009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1946    7.7556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    5.9090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5047    9.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1069    9.8794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    8.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9793    8.0105    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9354    9.0724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.0739   10.0922    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6324    7.5085    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6323   11.4512    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1640    7.5531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6762   10.3893    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    6.1103    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2346   11.7483    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    5.1739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785   10.6864    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  3  1  1  0  0  0
  7  4  1  1  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  5  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  1  0  0  0  0
 17 13  2  0  0  0  0
 17 16  1  0  0  0  0
 18  2  1  0  0  0  0
 14 18  1  1  0  0  0
 18 16  1  0  0  0  0
 19  3  1  0  0  0  0
  8 20  1  6  0  0  0
  9 21  1  6  0  0  0
 10 22  1  6  0  0  0
 11 23  1  6  0  0  0
 12 24  1  6  0  0  0
 25 13  1  0  0  0  0
 26 16  2  0  0  0  0
 31  4  1  0  0  0  0
 32  7  1  0  0  0  0
 32 14  1  0  0  0  0
 33  6  1  0  0  0  0
 33 15  1  0  0  0  0
 15 34  1  6  0  0  0
 36 27  1  0  0  0  0
 36 28  2  0  0  0  0
 36 31  1  0  0  0  0
 36 35  1  0  0  0  0
 37 29  1  0  0  0  0
 37 30  2  0  0  0  0
 37 34  1  0  0  0  0
 37 35  1  0  0  0  0
  6 38  1  6  0  0  0
  7 39  1  6  0  0  0
  8 40  1  1  0  0  0
  9 41  1  1  0  0  0
 10 42  1  6  0  0  0
 11 43  1  1  0  0  0
 12 44  1  1  0  0  0
 14 45  1  6  0  0  0
 15 46  1  1  0  0  0
M  CHG  2  25  -1  27  -1
M  END
> <DATABASE_ID>
MMDBc0056325

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)O[C@@]([H])(N2C=C(C)C([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C16H26N2O17P2/c1-5-2-18(16(26)17-13(5)25)14-11(23)9(21)7(32-14)4-31-36(27,28)35-37(29,30)34-15-12(24)10(22)8(20)6(3-19)33-15/h2,6-12,14-15,19-24H,3-4H2,1H3,(H,27,28)(H,29,30)(H,17,25,26)/p-2/t6-,7-,8-,9-,10+,11-,12-,14-,15-/m1/s1

> <INCHI_KEY>
PNFJZOCDYNFHQC-ZATQAWDKSA-L

> <FORMULA>
C16H24N2O17P2

> <MOLECULAR_WEIGHT>
578.314

> <EXACT_MASS>
578.056118477

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
47.50877656383706

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-5-methyl-2-oxo-1,2-dihydropyrimidin-4-olate

> <JCHEM_LOGP>
-4.233556785

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.176306409982704

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7325996076788206

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6484093801081894

> <JCHEM_POLAR_SURFACE_AREA>
300.69000000000005

> <JCHEM_REFRACTIVITY>
120.5632

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-5-methyl-2-oxopyrimidin-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -8.311   8.860   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.874   9.945   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.151  17.332   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.043  12.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.779   8.699   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.007  18.363   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.421  12.495   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.327  19.869   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667  13.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.182  20.900   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.913  12.495   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.718  20.424   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.153   7.293   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.437  11.030   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.398  18.917   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.716   8.377   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.621   7.132   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -4.343   9.784   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0      10.616  17.808   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.791  20.345   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.667  14.940   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       7.503  22.406   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -5.378  12.971   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.573  21.454   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -7.058   6.047   0.000  0.00  0.00           O-1
HETATM   26  O   UNK     0      -2.185   8.216   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       1.352  16.418   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0       2.304  13.488   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.106  17.255   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       5.119  16.615   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.363  14.477   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -1.897  11.030   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       6.542  17.887   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.933  18.442   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       3.293  15.429   0.000  0.00  0.00           O+0
HETATM   36  P   UNK     0       1.828  14.953   0.000  0.00  0.00           P+0
HETATM   37  P   UNK     0       3.613  16.935   0.000  0.00  0.00           P+0
HETATM   38  H   UNK     0       9.471  18.839   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      -1.181  14.016   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       8.647  21.376   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -4.040  14.099   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       6.862  19.393   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0      -5.002  11.406   0.000  0.00  0.00           H+0
HETATM   44  H   UNK     0       6.038  21.930   0.000  0.00  0.00           H+0
HETATM   45  H   UNK     0      -2.738   9.658   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0       4.253  19.948   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    5   18                                                       
CONECT    3    6   19                                                       
CONECT    4    7   31                                                       
CONECT    5    1    2   13                                                  
CONECT    6    3    8   33   38                                             
CONECT    7    4    9   32   39                                             
CONECT    8    6   10   20   40                                             
CONECT    9    7   11   21   41                                             
CONECT   10    8   12   22   42                                             
CONECT   11    9   14   23   43                                             
CONECT   12   10   15   24   44                                             
CONECT   13    5   17   25                                                  
CONECT   14   11   18   32   45                                             
CONECT   15   12   33   34   46                                             
CONECT   16   17   18   26                                                  
CONECT   17   13   16                                                       
CONECT   18    2   14   16                                                  
CONECT   19    3                                                            
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   13                                                            
CONECT   26   16                                                            
CONECT   27   36                                                            
CONECT   28   36                                                            
CONECT   29   37                                                            
CONECT   30   37                                                            
CONECT   31    4   36                                                       
CONECT   32    7   14                                                       
CONECT   33    6   15                                                       
CONECT   34   15   37                                                       
CONECT   35   36   37                                                       
CONECT   36   27   28   31   35                                             
CONECT   37   29   30   34   35                                             
CONECT   38    6                                                            
CONECT   39    7                                                            
CONECT   40    8                                                            
CONECT   41    9                                                            
CONECT   42   10                                                            
CONECT   43   11                                                            
CONECT   44   12                                                            
CONECT   45   14                                                            
CONECT   46   15                                                            
MASTER        0    0    0    0    0    0    0    0   46    0   96    0
END

Synonyms

Value	Source
TDP-alpha-D-Glucose	ChEBI
TDP-a-D-Glucose	Generator
TDP-Α-D-glucose	Generator
Thymidine 5'-(trihydrogen diphosphate), p'-(a-D-glucopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphate), p'-(α-D-glucopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(a-D-glucopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(alpha-D-glucopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(α-D-glucopyranosyl) ester	Generator

Molecular Formula

C₁₆H₂₄N₂O₁₇P₂

Average Mass

578.314

Monoisotopic Mass

578.056118477

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-5-methyl-2-oxo-1,2-dihydropyrimidin-4-olate

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-5-methyl-2-oxopyrimidin-4-olate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)O[C@@]([H])(N2C=C(C)C([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C16H26N2O17P2/c1-5-2-18(16(26)17-13(5)25)14-11(23)9(21)7(32-14)4-31-36(27,28)35-37(29,30)34-15-12(24)10(22)8(20)6(3-19)33-15/h2,6-12,14-15,19-24H,3-4H2,1H3,(H,27,28)(H,29,30)(H,17,25,26)/p-2/t6-,7-,8-,9-,10+,11-,12-,14-,15-/m1/s1

InChI Key

PNFJZOCDYNFHQC-ZATQAWDKSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine ribonucleoside diphosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	300.69 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	120.56 m³·mol⁻¹	ChemAxon
Polarizability	47.51 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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	Actinobacteria	16	Human ; Cattle

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

17600383

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16667347

PDB ID

Not Available

ChEBI ID

137931

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 TDP-alpha-D-glucose (MMDBc0056325)

MOL for #<Metabolite:0x00007fece001e0d0>

3D MOL for #<Metabolite:0x00007fece001e0d0>

3D SDF for #<Metabolite:0x00007fece001e0d0>

3D-SDF for #<Metabolite:0x00007fece001e0d0>

PDB for #<Metabolite:0x00007fece001e0d0>

3D PDB for #<Metabolite:0x00007fece001e0d0>

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Structure for #<Metabolite:0x00007fece001e0d0>

3D Structure for #<Metabolite:0x00007fece001e0d0>