NP-MRD: Showing NP-Card for Cytidine diphosphate ribitol (NP0004768)

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Record Information

Version

1.0

Created at

2020-12-09 02:11:17 UTC

Updated at

2021-07-15 16:50:06 UTC

NP-MRD ID

NP0004768

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cytidine diphosphate ribitol

Provided By

NPAtlas

Description

CDP-ribitol is also known as CDP ribitol. Cytidine diphosphate ribitol is found in Lactobacillus. It was first documented in 1956 (PMID: 13382807). Based on a literature review a significant number of articles have been published on CDP-ribitol (PMID: 34015330) (PMID: 33819634) (PMID: 32441338) (PMID: 32210362) (PMID: 32188898) (PMID: 31988979).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118093D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306242118093D          

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    4.8782    1.2271    1.1142 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9587    1.7394    2.3987 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2510   -1.0081    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3969   -0.8686    2.0577 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2696   -1.4292    0.0447 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0400   -2.7461   -2.8294 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2118   -1.6907   -2.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8126   -1.4264   -2.9056 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9224   -0.6424   -1.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -0.6517    2.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5943    0.3274    2.1511 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8631   -0.1028   -0.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7881    0.7175    0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3859   -2.2213    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5700   -0.1479    1.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7414    2.5697   -0.8928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0536    2.1087    0.7891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2089    2.5857   -0.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2120    0.5743   -2.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7999   -0.4144   -0.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6860    0.0539    1.8172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3091    1.3561   -0.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6251   -0.3147   -2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2153   -0.5564    1.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5193   -0.7099    0.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0359   -2.5962    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4525    1.5530   -0.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348    2.5973    2.1384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6233    1.6769    0.4238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8714    2.1488    2.4905 H   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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  1  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 15 14  1  6  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
  8 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
  5 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34  2  2  0  0  0  0
 30  6  1  0  0  0  0
  1 35  1  0  0  0  0
  1 36  1  0  0  0  0
  3 37  1  0  0  0  0
  4 38  1  0  0  0  0
  6 39  1  1  0  0  0
  8 40  1  1  0  0  0
  9 41  1  0  0  0  0
  9 42  1  0  0  0  0
 13 43  1  0  0  0  0
 17 44  1  0  0  0  0
 19 45  1  0  0  0  0
 19 46  1  0  0  0  0
 20 47  1  6  0  0  0
 21 48  1  0  0  0  0
 22 49  1  1  0  0  0
 23 50  1  0  0  0  0
 24 51  1  1  0  0  0
 25 52  1  0  0  0  0
 26 53  1  0  0  0  0
 26 54  1  0  0  0  0
 27 55  1  0  0  0  0
 28 56  1  6  0  0  0
 29 57  1  0  0  0  0
 30 58  1  6  0  0  0
 31 59  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004768

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]([H])(O[H])[C@]([H])(O[H])[C@]([H])(O[H])C([H])([H])O[P@@](=O)(O[H])O[P@](=O)(O[H])OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=C([H])C(=NC2=O)N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8+,10-,11+,12+,13+/m0/s1

> <INCHI_KEY>
DPJKHFICSGCNIR-HRENORGGSA-N

> <FORMULA>
C14H25N3O15P2

> <MOLECULAR_WEIGHT>
537.3069

> <EXACT_MASS>
537.076090169

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
45.86551042633326

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(2R,3S,4S)-2,3,4,5-tetrahydroxypentyl]oxy})phosphoryl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.66

> <JCHEM_LOGP>
-5.546027910000001

> <ALOGPS_LOGS>
-1.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2716914228409646

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.863228048328863

> <JCHEM_PKA_STRONGEST_BASIC>
-0.032010534264323987

> <JCHEM_POLAR_SURFACE_AREA>
291.5899999999999

> <JCHEM_REFRACTIVITY>
104.95270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cdp ribitol

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 59 60  0  0  0  0  0  0  0  0999 V2000
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    2.7800    0.1969    1.0784 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5535   -0.0590    0.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6353    1.6645   -0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6770    1.4110   -2.0314 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3502    0.5283    0.0399 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3825    0.6536    1.4065 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7719    0.4029   -0.4629 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.8504    0.2711   -1.8331 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4332   -0.7251    0.2828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8151   -1.9111   -0.0663 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4753    1.4568    0.5905 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8923    2.5809    1.1785 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8782    1.2271    1.1142 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9587    1.7394    2.3987 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2510   -1.0081    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3969   -0.8686    2.0577 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2696   -1.4292    0.0447 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0400   -2.7461   -2.8294 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2118   -1.6907   -2.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1926   -0.6517    2.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5943    0.3274    2.1511 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8631   -0.1028   -0.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7881    0.7175    0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3859   -2.2213    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5700   -0.1479    1.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7414    2.5697   -0.8928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0536    2.1087    0.7891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2089    2.5857   -0.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2120    0.5743   -2.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7999   -0.4144   -0.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6860    0.0539    1.8172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3091    1.3561   -0.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6251   -0.3147   -2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2153   -0.5564    1.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5193   -0.7099    0.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0359   -2.5962    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4525    1.5530   -0.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348    2.5973    2.1384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6233    1.6769    0.4238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8714    2.1488    2.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 11 10  1  1
 11 12  2  0
 11 13  1  0
 11 14  1  0
 15 14  1  6
 15 16  2  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  8 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
  5 32  1  0
 32 33  2  0
 32 34  1  0
 34  2  2  0
 30  6  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  0
  6 39  1  1
  8 40  1  1
  9 41  1  0
  9 42  1  0
 13 43  1  0
 17 44  1  0
 19 45  1  0
 19 46  1  0
 20 47  1  6
 21 48  1  0
 22 49  1  1
 23 50  1  0
 24 51  1  1
 25 52  1  0
 26 53  1  0
 26 54  1  0
 27 55  1  0
 28 56  1  6
 29 57  1  0
 30 58  1  6
 31 59  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0       9.232  -2.036  -2.097  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.151  -1.590  -1.286  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.917  -1.300  -1.837  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.881  -0.869  -1.031  0.00  0.00           C+0
HETATM    5  N   UNK     0       6.036  -0.717   0.308  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.961  -0.266   1.171  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.730  -0.773   0.797  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.780   0.197   1.078  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.554  -0.059   0.268  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.026  -1.312   0.570  0.00  0.00           O+0
HETATM   11  P   UNK     0      -0.369  -1.633  -0.333  0.00  0.00           P+0
HETATM   12  O   UNK     0       0.054  -2.588  -1.448  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.440  -2.461   0.647  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.000  -0.281  -1.065  0.00  0.00           O+0
HETATM   15  P   UNK     0      -1.877   0.731  -0.095  0.00  0.00           P+0
HETATM   16  O   UNK     0      -1.494   2.186  -0.237  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.785   0.346   1.547  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.507   0.605  -0.540  0.00  0.00           O+0
HETATM   19  C   UNK     0      -4.202   1.779  -0.259  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.635   1.665  -0.651  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.677   1.411  -2.031  0.00  0.00           O+0
HETATM   22  C   UNK     0      -6.350   0.528   0.040  0.00  0.00           C+0
HETATM   23  O   UNK     0      -6.383   0.654   1.407  0.00  0.00           O+0
HETATM   24  C   UNK     0      -7.772   0.403  -0.463  0.00  0.00           C+0
HETATM   25  O   UNK     0      -7.850   0.271  -1.833  0.00  0.00           O+0
HETATM   26  C   UNK     0      -8.433  -0.725   0.283  0.00  0.00           C+0
HETATM   27  O   UNK     0      -7.815  -1.911  -0.066  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.475   1.457   0.591  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.892   2.581   1.179  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.878   1.227   1.114  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.959   1.739   2.399  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.251  -1.008   0.817  0.00  0.00           C+0
HETATM   33  O   UNK     0       7.397  -0.869   2.058  0.00  0.00           O+0
HETATM   34  N   UNK     0       8.270  -1.429   0.045  0.00  0.00           N+0
HETATM   35  H   UNK     0       9.040  -2.746  -2.829  0.00  0.00           H+0
HETATM   36  H   UNK     0      10.212  -1.691  -2.001  0.00  0.00           H+0
HETATM   37  H   UNK     0       6.813  -1.426  -2.906  0.00  0.00           H+0
HETATM   38  H   UNK     0       4.922  -0.642  -1.456  0.00  0.00           H+0
HETATM   39  H   UNK     0       5.193  -0.652   2.188  0.00  0.00           H+0
HETATM   40  H   UNK     0       2.594   0.327   2.151  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.863  -0.103  -0.805  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.788   0.718   0.341  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.386  -2.221   1.599  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.570  -0.148   1.844  0.00  0.00           H+0
HETATM   45  H   UNK     0      -3.741   2.570  -0.893  0.00  0.00           H+0
HETATM   46  H   UNK     0      -4.054   2.109   0.789  0.00  0.00           H+0
HETATM   47  H   UNK     0      -6.209   2.586  -0.482  0.00  0.00           H+0
HETATM   48  H   UNK     0      -5.212   0.574  -2.267  0.00  0.00           H+0
HETATM   49  H   UNK     0      -5.800  -0.414  -0.227  0.00  0.00           H+0
HETATM   50  H   UNK     0      -5.686   0.054   1.817  0.00  0.00           H+0
HETATM   51  H   UNK     0      -8.309   1.356  -0.187  0.00  0.00           H+0
HETATM   52  H   UNK     0      -8.625  -0.315  -2.027  0.00  0.00           H+0
HETATM   53  H   UNK     0      -8.215  -0.556   1.372  0.00  0.00           H+0
HETATM   54  H   UNK     0      -9.519  -0.710   0.077  0.00  0.00           H+0
HETATM   55  H   UNK     0      -8.036  -2.596   0.637  0.00  0.00           H+0
HETATM   56  H   UNK     0       3.453   1.553  -0.502  0.00  0.00           H+0
HETATM   57  H   UNK     0       3.135   2.597   2.138  0.00  0.00           H+0
HETATM   58  H   UNK     0       5.623   1.677   0.424  0.00  0.00           H+0
HETATM   59  H   UNK     0       5.871   2.149   2.490  0.00  0.00           H+0
CONECT    1    2   35   36                                                  
CONECT    2    1    3   34                                                  
CONECT    3    2    4   37                                                  
CONECT    4    3    5   38                                                  
CONECT    5    4    6   32                                                  
CONECT    6    5    7   30   39                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   28   40                                             
CONECT    9    8   10   41   42                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11   43                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15   44                                                       
CONECT   18   15   19                                                       
CONECT   19   18   20   45   46                                             
CONECT   20   19   21   22   47                                             
CONECT   21   20   48                                                       
CONECT   22   20   23   24   49                                             
CONECT   23   22   50                                                       
CONECT   24   22   25   26   51                                             
CONECT   25   24   52                                                       
CONECT   26   24   27   53   54                                             
CONECT   27   26   55                                                       
CONECT   28    8   29   30   56                                             
CONECT   29   28   57                                                       
CONECT   30   28   31    6   58                                             
CONECT   31   30   59                                                       
CONECT   32    5   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    2                                                       
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    3                                                            
CONECT   38    4                                                            
CONECT   39    6                                                            
CONECT   40    8                                                            
CONECT   41    9                                                            
CONECT   42    9                                                            
CONECT   43   13                                                            
CONECT   44   17                                                            
CONECT   45   19                                                            
CONECT   46   19                                                            
CONECT   47   20                                                            
CONECT   48   21                                                            
CONECT   49   22                                                            
CONECT   50   23                                                            
CONECT   51   24                                                            
CONECT   52   25                                                            
CONECT   53   26                                                            
CONECT   54   26                                                            
CONECT   55   27                                                            
CONECT   56   28                                                            
CONECT   57   29                                                            
CONECT   58   30                                                            
CONECT   59   31                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  120    0
END

RDKit          3D

59 60  0  0  0  0  0  0  0  0999 V2000
    9.2319   -2.0358   -2.0970 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1512   -1.5902   -1.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9174   -1.2999   -1.8367 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8812   -0.8685   -1.0308 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0363   -0.7173    0.3082 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9610   -0.2658    1.1709 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7297   -0.7732    0.7972 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7800    0.1969    1.0784 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5535   -0.0590    0.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0256   -1.3115    0.5699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3688   -1.6332   -0.3333 P   0  0  1  0  0  5  0  0  0  0  0  0
    0.0543   -2.5883   -1.4478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4399   -2.4612    0.6465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9998   -0.2810   -1.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8771    0.7312   -0.0952 P   0  0  2  0  0  5  0  0  0  0  0  0
   -1.4940    2.1862   -0.2371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7847    0.3455    1.5468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5072    0.6046   -0.5399 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2015    1.7785   -0.2593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6353    1.6645   -0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6770    1.4110   -2.0314 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3502    0.5283    0.0399 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3825    0.6536    1.4065 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7719    0.4029   -0.4629 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.8504    0.2711   -1.8331 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4332   -0.7251    0.2828 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8151   -1.9111   -0.0663 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4753    1.4568    0.5905 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8923    2.5809    1.1785 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8782    1.2271    1.1142 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9587    1.7394    2.3987 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2510   -1.0081    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3969   -0.8686    2.0577 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2696   -1.4292    0.0447 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0400   -2.7461   -2.8294 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2118   -1.6907   -2.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8126   -1.4264   -2.9056 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9224   -0.6424   -1.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -0.6517    2.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5943    0.3274    2.1511 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8631   -0.1028   -0.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7881    0.7175    0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3859   -2.2213    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5700   -0.1479    1.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7414    2.5697   -0.8928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0536    2.1087    0.7891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2089    2.5857   -0.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2120    0.5743   -2.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7999   -0.4144   -0.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6860    0.0539    1.8172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3091    1.3561   -0.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6251   -0.3147   -2.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2153   -0.5564    1.3716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5193   -0.7099    0.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0359   -2.5962    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4525    1.5530   -0.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1348    2.5973    2.1384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6233    1.6769    0.4238 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8714    2.1488    2.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 11 10  1  1
 11 12  2  0
 11 13  1  0
 11 14  1  0
 15 14  1  6
 15 16  2  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  8 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
  5 32  1  0
 32 33  2  0
 32 34  1  0
 34  2  2  0
 30  6  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  0
  6 39  1  1
  8 40  1  1
  9 41  1  0
  9 42  1  0
 13 43  1  0
 17 44  1  0
 19 45  1  0
 19 46  1  0
 20 47  1  6
 21 48  1  0
 22 49  1  1
 23 50  1  0
 24 51  1  1
 25 52  1  0
 26 53  1  0
 26 54  1  0
 27 55  1  0
 28 56  1  6
 29 57  1  0
 30 58  1  6
 31 59  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
CDP 5-Ester with D-ribitol	ChEBI
CDP Ribitol	ChEBI
CDP-L-Ribitol	ChEBI
CDPribitol	ChEBI
Cytidine 5'-(trihydrogen diphosphate), p'-5-ester with D-ribitol	ChEBI
Cytidine diphosphate ribitol	ChEBI
Cytidine 5'-(trihydrogen diphosphoric acid), p'-5-ester with D-ribitol	Generator
Cytidine diphosphoric acid ribitol	Generator

Chemical Formula

C₁₄H₂₅N₃O₁₅P₂

Average Mass

537.3069 Da

Monoisotopic Mass

537.07609 Da

IUPAC Name

{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(2R,3S,4S)-2,3,4,5-tetrahydroxypentyl]oxy})phosphoryl]oxy})phosphinic acid

Traditional Name

cdp ribitol

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8+,10-,11+,12+,13+/m0/s1

InChI Key

DPJKHFICSGCNIR-HRENORGGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Lactobacillus	NPAtlas	13382807

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nucleotide-alditol (CHEBI:16022 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-5.5	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.032	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	291.59 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	104.95 m³·mol⁻¹	ChemAxon
Polarizability	45.87 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA006986

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

144770

KEGG Compound ID

C00789

BioCyc ID

CPD-1111

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

16022

Good Scents ID

Not Available

References

General References

BADDILEY J, BUCHANAN JG, CARSS B, MATHIAS AP, SANDERSON AR: The isolation of cytidine diphosphate glycerol, cytidine diphosphate ribitol and mannitol 1-phosphate from Lactobacillus arabinosus. Biochem J. 1956 Dec;64(4):599-603. doi: 10.1042/bj0640599. [PubMed:13382807 ]
Ury B, Potelle S, Caligiore F, Whorton MR, Bommer GT: The promiscuous binding pocket of SLC35A1 ensures redundant transport of CDP-ribitol to the Golgi. J Biol Chem. 2021 Jan-Jun;296:100789. doi: 10.1016/j.jbc.2021.100789. Epub 2021 May 18. [PubMed:34015330 ]
Li FKK, Gale RT, Petrotchenko EV, Borchers CH, Brown ED, Strynadka NCJ: Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis. J Struct Biol. 2021 Jun;213(2):107733. doi: 10.1016/j.jsb.2021.107733. Epub 2021 Apr 2. [PubMed:33819634 ]
Haskovic M, Coelho AI, Lindhout M, Zijlstra F, Veizaj R, Vos R, Vanoevelen JM, Bierau J, Lefeber DJ, Rubio-Gozalbo ME: Nucleotide sugar profiles throughout development in wildtype and galt knockout zebrafish. J Inherit Metab Dis. 2020 Sep;43(5):994-1001. doi: 10.1002/jimd.12265. Epub 2020 Jun 5. [PubMed:32441338 ]
Leonard A, Mohlis K, Schluter R, Taylor E, Lalk M, Methling K: Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. J Antibiot (Tokyo). 2020 Jul;73(7):441-454. doi: 10.1038/s41429-020-0296-3. Epub 2020 Mar 24. [PubMed:32210362 ]
Lu PJ, Tucker JD, Branch EK, Guo F, Blaeser AR, Lu QL: Ribitol enhances matriglycan of alpha-dystroglycan in breast cancer cells without affecting cell growth. Sci Rep. 2020 Mar 18;10(1):4935. doi: 10.1038/s41598-020-61747-z. [PubMed:32188898 ]
Cataldi MP, Blaeser A, Lu P, Leroy V, Lu QL: ISPD Overexpression Enhances Ribitol-Induced Glycosylation of alpha-Dystroglycan in Dystrophic FKRP Mutant Mice. Mol Ther Methods Clin Dev. 2019 Dec 24;17:271-280. doi: 10.1016/j.omtm.2019.12.005. eCollection 2020 Jun 12. [PubMed:31988979 ]
van Tol W, van Scherpenzeel M, Alsady M, Riemersma M, Hermans E, Kragt E, Tasca G, Kamsteeg EJ, Pennings M, van Beusekom E, Vermeulen JR, van Bokhoven H, Voermans NC, Willemsen MA, Ashikov A, Lefeber DJ: Cytidine Diphosphate-Ribitol Analysis for Diagnostics and Treatment Monitoring of Cytidine Diphosphate-l-Ribitol Pyrophosphorylase A Muscular Dystrophy. Clin Chem. 2019 Oct;65(10):1295-1306. doi: 10.1373/clinchem.2019.305391. Epub 2019 Aug 2. [PubMed:31375477 ]
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Showing NP-Card for Cytidine diphosphate ribitol (NP0004768)

MOL for NP0004768 (Cytidine diphosphate ribitol)

3D MOL for NP0004768 (Cytidine diphosphate ribitol)

3D SDF for NP0004768 (Cytidine diphosphate ribitol)

3D-SDF for NP0004768 (Cytidine diphosphate ribitol)

PDB for NP0004768 (Cytidine diphosphate ribitol)

3D PDB for NP0004768 (Cytidine diphosphate ribitol)

SMILES for NP0004768 (Cytidine diphosphate ribitol)

INCHI for NP0004768 (Cytidine diphosphate ribitol)

Structure for NP0004768 (Cytidine diphosphate ribitol)

3D Structure for NP0004768 (Cytidine diphosphate ribitol)