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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 07:43:01 UTC

Update Date

2021-09-24 07:43:01 UTC

HMDB ID

HMDB0304166

Secondary Accession Numbers

None

Metabolite Identification

Common Name

4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol

Description

4-diphosphocytidyl-2-c-methyl-d-erythritol is a member of the class of compounds known as pyrimidine ribonucleoside diphosphates. Pyrimidine ribonucleoside diphosphates are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. 4-diphosphocytidyl-2-c-methyl-d-erythritol is soluble (in water) and a moderately acidic compound (based on its pKa). 4-diphosphocytidyl-2-c-methyl-d-erythritol can be found in a number of food items such as pepper (c. chinense), pistachio, chestnut, and lupine, which makes 4-diphosphocytidyl-2-c-methyl-d-erythritol a potential biomarker for the consumption of these food products. 4-diphosphocytidyl-2-c-methyl-d-erythritol may be a unique E.coli metabolite.

Structure

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


  Mrv0541 08131209252D          

 38 39  0  0  0  0            999 V2000
    7.7729    4.7407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0717    2.8941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8125    4.2110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2432    3.7011    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0278    3.9561    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9840    5.0180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6301    4.2531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2828    3.1714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8563    3.1491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  4  1  1  0  0  0
  8  5  1  0  0  0  0
  9  2  1  0  0  0  0
 10  7  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 14  1  1  1  0  0  0
 14  6  1  0  0  0  0
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 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 16 13  2  0  0  0  0
 17  3  1  0  0  0  0
 12 17  1  1  0  0  0
 17 13  1  0  0  0  0
 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
 11 21  1  6  0  0  0
 22 13  1  0  0  0  0
 14 23  1  1  0  0  0
 28  4  1  0  0  0  0
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 30  7  1  0  0  0  0
 30 12  1  0  0  0  0
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 33 29  1  0  0  0  0
 33 31  1  0  0  0  0
  7 34  1  6  0  0  0
  8 35  1  6  0  0  0
 10 36  1  1  0  0  0
 11 37  1  1  0  0  0
 12 38  1  6  0  0  0
M  END

HMDB0304166
     RDKit          3D
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
 58 59  0  0  0  0  0  0  0  0999 V2000
   -6.6369    0.0680    1.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9499    0.7954    0.2197 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.6705    1.9944    0.5542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9652    0.0832   -0.6800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1610   -0.0642    0.0039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7725    1.2691   -0.5224 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.1532    1.8922   -1.7443 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5703    0.4537   -0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1768   -0.2514    0.5548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7437   -0.9289    0.0799 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.9607   -1.9725   -0.9672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7519    0.3545   -0.5824 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7538   -1.5894    1.2974 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3079   -1.8456    0.5076 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.5681   -3.0608   -0.4550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1086   -0.4658   -0.5380 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1253   -2.0473    1.2626 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9028   -0.8936    0.8721 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0245   -1.3756    0.0242 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7353   -0.3472   -0.5241 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1036   -0.6164   -0.3415 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7510    0.6884   -0.3114 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0570    1.7692    0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6347    3.0173    0.1722 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9284    3.1762   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4725    4.3761   -0.2775 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5693    2.1086   -0.7319 N   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9295   -2.3500    0.6862 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2059   -3.3870   -0.2430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5362   -1.0491    1.3522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4514    0.2282    2.2144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7323    0.4714    1.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0087    2.6867    0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6288   -0.9030   -1.0313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1210    0.7207   -1.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3109   -0.8809    0.4779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4267    2.2170    0.0603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4721    2.5213   -2.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6899    1.1374   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5388   -0.3222   -1.4489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6724    1.0218    0.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182   -0.6602   -1.3018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019   -0.1524    0.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3935   -0.5128    1.8470 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5904   -1.9389   -0.8877 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3918   -1.2321   -1.2483 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0537    1.6063    0.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1043    3.8831    0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9069    5.1507    0.0718 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.0350   -3.1408    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5485   -2.7374    1.6262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3605   -3.8646   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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  2  4  1  0
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  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
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 13 14  1  0
 14 15  2  0
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 14 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  3
 25 27  1  0
 27 28  2  0
 28 29  1  0
 21 30  1  0
 30 31  1  0
 30 32  1  0
 32 33  1  0
 32 19  1  0
 28 22  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  0
  4 39  1  0
  5 40  1  0
  6 41  1  1
  7 42  1  0
  8 43  1  0
  8 44  1  0
 12 45  1  0
 16 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  6
 21 50  1  6
 23 51  1  0
 24 52  1  0
 26 53  1  0
 29 54  1  0
 30 55  1  1
 31 56  1  0
 32 57  1  1
 33 58  1  0
M  END


  Mrv0541 08131209252D          

 38 39  0  0  0  0            999 V2000
    7.7729    4.7407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0717    2.8941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8125    4.2110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2432    3.7011    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0278    3.9561    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9840    5.0180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6301    4.2531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2828    3.1714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4143   -0.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9044    1.5549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9225    1.6607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3086    2.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2871    2.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9440    1.0253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1594    0.7703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.1155    1.8322    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8563    3.1491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  4  1  1  0  0  0
  8  5  1  0  0  0  0
  9  2  1  0  0  0  0
 10  7  1  0  0  0  0
 11 10  1  0  0  0  0
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 14  1  1  1  0  0  0
 14  6  1  0  0  0  0
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 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 16 13  2  0  0  0  0
 17  3  1  0  0  0  0
 12 17  1  1  0  0  0
 17 13  1  0  0  0  0
 18  6  1  0  0  0  0
  8 19  1  6  0  0  0
 10 20  1  6  0  0  0
 11 21  1  6  0  0  0
 22 13  1  0  0  0  0
 14 23  1  1  0  0  0
 28  4  1  0  0  0  0
 29  5  1  0  0  0  0
 30  7  1  0  0  0  0
 30 12  1  0  0  0  0
 32 24  1  0  0  0  0
 32 25  2  0  0  0  0
 32 28  1  0  0  0  0
 32 31  1  0  0  0  0
 33 26  1  0  0  0  0
 33 27  2  0  0  0  0
 33 29  1  0  0  0  0
 33 31  1  0  0  0  0
  7 34  1  6  0  0  0
  8 35  1  6  0  0  0
 10 36  1  1  0  0  0
 11 37  1  1  0  0  0
 12 38  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0304166

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](O)(COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)[C@@](C)(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1

> <INCHI_KEY>
YFAUKWZNPVBCFF-XHIBXCGHSA-N

> <FORMULA>
C14H25N3O14P2

> <MOLECULAR_WEIGHT>
521.3075

> <EXACT_MASS>
521.081175547

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
44.2308836200152

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphinic acid

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-5.256357834182517

> <ALOGPS_LOGS>
-1.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.244482545586397

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7735335724974854

> <JCHEM_PKA_STRONGEST_BASIC>
3.343686373109885

> <JCHEM_POLAR_SURFACE_AREA>
272.34999999999997

> <JCHEM_REFRACTIVITY>
115.04089999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-cdp-2-C-methyl-D-erythritol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304166
     RDKit          3D
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
 58 59  0  0  0  0  0  0  0  0999 V2000
   -6.6369    0.0680    1.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9499    0.7954    0.2197 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.6705    1.9944    0.5542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9652    0.0832   -0.6800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1610   -0.0642    0.0039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7725    1.2691   -0.5224 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.1532    1.8922   -1.7443 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5703    0.4537   -0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1768   -0.2514    0.5548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7437   -0.9289    0.0799 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.9607   -1.9725   -0.9672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7519    0.3545   -0.5824 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7538   -1.5894    1.2974 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3079   -1.8456    0.5076 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.5681   -3.0608   -0.4550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1086   -0.4658   -0.5380 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1253   -2.0473    1.2626 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9028   -0.8936    0.8721 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0245   -1.3756    0.0242 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7353   -0.3472   -0.5241 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1036   -0.6164   -0.3415 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7510    0.6884   -0.3114 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0570    1.7692    0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6347    3.0173    0.1722 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9284    3.1762   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4725    4.3761   -0.2775 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5693    2.1086   -0.7319 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9823    0.8669   -0.7428 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7441   -0.2020   -1.2225 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2065   -1.4785    0.8553 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2393   -2.3922    0.8332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9295   -2.3500    0.6862 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2059   -3.3870   -0.2430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5362   -1.0491    1.3522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4514    0.2282    2.2144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7323    0.4714    1.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0087    2.6867    0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6288   -0.9030   -1.0313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1210    0.7207   -1.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3109   -0.8809    0.4779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4267    2.2170    0.0603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4721    2.5213   -2.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6899    1.1374   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5388   -0.3222   -1.4489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6724    1.0218    0.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182   -0.6602   -1.3018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019   -0.1524    0.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3935   -0.5128    1.8470 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5904   -1.9389   -0.8877 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3918   -1.2321   -1.2483 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0537    1.6063    0.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1043    3.8831    0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9069    5.1507    0.0718 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0359   -0.9360   -0.6035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0873   -0.9588    1.8044 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0350   -3.1408    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5485   -2.7374    1.6262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3605   -3.8646   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  3
 25 27  1  0
 27 28  2  0
 28 29  1  0
 21 30  1  0
 30 31  1  0
 30 32  1  0
 32 33  1  0
 32 19  1  0
 28 22  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  0
  4 39  1  0
  5 40  1  0
  6 41  1  1
  7 42  1  0
  8 43  1  0
  8 44  1  0
 12 45  1  0
 16 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  6
 21 50  1  6
 23 51  1  0
 24 52  1  0
 26 53  1  0
 29 54  1  0
 30 55  1  1
 31 56  1  0
 32 57  1  1
 33 58  1  0
M  END

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   33  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   34  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2    3    9                                                       
CONECT    3    2   17                                                       
CONECT    4    7   28                                                       
CONECT    5    8   29                                                       
CONECT    6   14   18                                                       
CONECT    7    4   10   30   34                                             
CONECT    8    5   14   19   35                                             
CONECT    9    2   15   16                                                  
CONECT   10    7   11   20   36                                             
CONECT   11   10   12   21   37                                             
CONECT   12   11   17   30   38                                             
CONECT   13   16   17   22                                                  
CONECT   14    1    6    8   23                                             
CONECT   15    9                                                            
CONECT   16    9   13                                                       
CONECT   17    3   12   13                                                  
CONECT   18    6                                                            
CONECT   19    8                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
CONECT   24   32                                                            
CONECT   25   32                                                            
CONECT   26   33                                                            
CONECT   27   33                                                            
CONECT   28    4   32                                                       
CONECT   29    5   33                                                       
CONECT   30    7   12                                                       
CONECT   31   32   33                                                       
CONECT   32   24   25   28   31                                             
CONECT   33   26   27   29   31                                             
CONECT   34    7                                                            
CONECT   35    8                                                            
CONECT   36   10                                                            
CONECT   37   11                                                            
CONECT   38   12                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   78    0
END

COMPND    HMDB0304166
HETATM    1  C1  UNL     1      -6.637   0.068   1.456  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.950   0.795   0.220  1.00  0.00           C  
HETATM    3  O1  UNL     1      -7.670   1.994   0.554  1.00  0.00           O  
HETATM    4  C3  UNL     1      -7.965   0.083  -0.680  1.00  0.00           C  
HETATM    5  O2  UNL     1      -9.161  -0.064   0.004  1.00  0.00           O  
HETATM    6  C4  UNL     1      -5.772   1.269  -0.522  1.00  0.00           C  
HETATM    7  O3  UNL     1      -6.153   1.892  -1.744  1.00  0.00           O  
HETATM    8  C5  UNL     1      -4.570   0.454  -0.648  1.00  0.00           C  
HETATM    9  O4  UNL     1      -4.177  -0.251   0.555  1.00  0.00           O  
HETATM   10  P1  UNL     1      -2.744  -0.929   0.080  1.00  0.00           P  
HETATM   11  O5  UNL     1      -2.961  -1.972  -0.967  1.00  0.00           O  
HETATM   12  O6  UNL     1      -1.752   0.354  -0.582  1.00  0.00           O  
HETATM   13  O7  UNL     1      -1.754  -1.589   1.297  1.00  0.00           O  
HETATM   14  P2  UNL     1      -0.308  -1.846   0.508  1.00  0.00           P  
HETATM   15  O8  UNL     1      -0.568  -3.061  -0.455  1.00  0.00           O  
HETATM   16  O9  UNL     1      -0.109  -0.466  -0.538  1.00  0.00           O  
HETATM   17  O10 UNL     1       1.125  -2.047   1.263  1.00  0.00           O  
HETATM   18  C6  UNL     1       1.903  -0.894   0.872  1.00  0.00           C  
HETATM   19  C7  UNL     1       3.025  -1.376   0.024  1.00  0.00           C  
HETATM   20  O11 UNL     1       3.735  -0.347  -0.524  1.00  0.00           O  
HETATM   21  C8  UNL     1       5.104  -0.616  -0.342  1.00  0.00           C  
HETATM   22  N1  UNL     1       5.751   0.688  -0.311  1.00  0.00           N  
HETATM   23  C9  UNL     1       5.057   1.769   0.155  1.00  0.00           C  
HETATM   24  C10 UNL     1       5.635   3.017   0.172  1.00  0.00           C  
HETATM   25  C11 UNL     1       6.928   3.176  -0.287  1.00  0.00           C  
HETATM   26  N2  UNL     1       7.472   4.376  -0.277  1.00  0.00           N  
HETATM   27  N3  UNL     1       7.569   2.109  -0.732  1.00  0.00           N  
HETATM   28  C12 UNL     1       6.982   0.867  -0.743  1.00  0.00           C  
HETATM   29  O12 UNL     1       7.744  -0.202  -1.223  1.00  0.00           O  
HETATM   30  C13 UNL     1       5.206  -1.478   0.855  1.00  0.00           C  
HETATM   31  O13 UNL     1       6.239  -2.392   0.833  1.00  0.00           O  
HETATM   32  C14 UNL     1       3.929  -2.350   0.686  1.00  0.00           C  
HETATM   33  O14 UNL     1       4.206  -3.387  -0.243  1.00  0.00           O  
HETATM   34  H1  UNL     1      -6.536  -1.049   1.352  1.00  0.00           H  
HETATM   35  H2  UNL     1      -7.451   0.228   2.214  1.00  0.00           H  
HETATM   36  H3  UNL     1      -5.732   0.471   1.946  1.00  0.00           H  
HETATM   37  H4  UNL     1      -7.009   2.687   0.747  1.00  0.00           H  
HETATM   38  H5  UNL     1      -7.629  -0.903  -1.031  1.00  0.00           H  
HETATM   39  H6  UNL     1      -8.121   0.721  -1.596  1.00  0.00           H  
HETATM   40  H7  UNL     1      -9.311  -0.881   0.478  1.00  0.00           H  
HETATM   41  H8  UNL     1      -5.427   2.217   0.060  1.00  0.00           H  
HETATM   42  H9  UNL     1      -5.472   2.521  -2.054  1.00  0.00           H  
HETATM   43  H10 UNL     1      -3.690   1.137  -0.923  1.00  0.00           H  
HETATM   44  H11 UNL     1      -4.539  -0.322  -1.449  1.00  0.00           H  
HETATM   45  H12 UNL     1      -1.672   1.022   0.188  1.00  0.00           H  
HETATM   46  H13 UNL     1       0.418  -0.660  -1.302  1.00  0.00           H  
HETATM   47  H14 UNL     1       1.302  -0.152   0.443  1.00  0.00           H  
HETATM   48  H15 UNL     1       2.393  -0.513   1.847  1.00  0.00           H  
HETATM   49  H16 UNL     1       2.590  -1.939  -0.888  1.00  0.00           H  
HETATM   50  H17 UNL     1       5.392  -1.232  -1.248  1.00  0.00           H  
HETATM   51  H18 UNL     1       4.054   1.606   0.512  1.00  0.00           H  
HETATM   52  H19 UNL     1       5.104   3.883   0.527  1.00  0.00           H  
HETATM   53  H20 UNL     1       6.907   5.151   0.072  1.00  0.00           H  
HETATM   54  H21 UNL     1       8.036  -0.936  -0.604  1.00  0.00           H  
HETATM   55  H22 UNL     1       5.087  -0.959   1.804  1.00  0.00           H  
HETATM   56  H23 UNL     1       6.035  -3.141   0.169  1.00  0.00           H  
HETATM   57  H24 UNL     1       3.549  -2.737   1.626  1.00  0.00           H  
HETATM   58  H25 UNL     1       3.361  -3.865  -0.466  1.00  0.00           H  
CONECT    1    2   34   35   36
CONECT    2    3    4    6
CONECT    3   37
CONECT    4    5   38   39
CONECT    5   40
CONECT    6    7    8   41
CONECT    7   42
CONECT    8    9   43   44
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   45
CONECT   13   14
CONECT   14   15   15   16   17
CONECT   16   46
CONECT   17   18
CONECT   18   19   47   48
CONECT   19   20   32   49
CONECT   20   21
CONECT   21   22   30   50
CONECT   22   23   28
CONECT   23   24   24   51
CONECT   24   25   52
CONECT   25   26   26   27
CONECT   26   53
CONECT   27   28   28
CONECT   28   29
CONECT   29   54
CONECT   30   31   32   55
CONECT   31   56
CONECT   32   33   57
CONECT   33   58
END

HMDB0304166
     RDKit          3D
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
 58 59  0  0  0  0  0  0  0  0999 V2000
   -6.6369    0.0680    1.4560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9499    0.7954    0.2197 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.6705    1.9944    0.5542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9652    0.0832   -0.6800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1610   -0.0642    0.0039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7725    1.2691   -0.5224 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.1532    1.8922   -1.7443 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5703    0.4537   -0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1768   -0.2514    0.5548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7437   -0.9289    0.0799 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.9607   -1.9725   -0.9672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7519    0.3545   -0.5824 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7538   -1.5894    1.2974 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3079   -1.8456    0.5076 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.5681   -3.0608   -0.4550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1086   -0.4658   -0.5380 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1253   -2.0473    1.2626 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9028   -0.8936    0.8721 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0245   -1.3756    0.0242 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7353   -0.3472   -0.5241 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1036   -0.6164   -0.3415 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7510    0.6884   -0.3114 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0570    1.7692    0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6347    3.0173    0.1722 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9284    3.1762   -0.2873 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4725    4.3761   -0.2775 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5693    2.1086   -0.7319 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9823    0.8669   -0.7428 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7441   -0.2020   -1.2225 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2065   -1.4785    0.8553 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2393   -2.3922    0.8332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9295   -2.3500    0.6862 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2059   -3.3870   -0.2430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5362   -1.0491    1.3522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4514    0.2282    2.2144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7323    0.4714    1.9460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0087    2.6867    0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6288   -0.9030   -1.0313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1210    0.7207   -1.5959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3109   -0.8809    0.4779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4267    2.2170    0.0603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4721    2.5213   -2.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6899    1.1374   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5388   -0.3222   -1.4489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6724    1.0218    0.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182   -0.6602   -1.3018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3019   -0.1524    0.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3935   -0.5128    1.8470 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5904   -1.9389   -0.8877 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3918   -1.2321   -1.2483 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0537    1.6063    0.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1043    3.8831    0.5266 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9069    5.1507    0.0718 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0359   -0.9360   -0.6035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0873   -0.9588    1.8044 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0350   -3.1408    0.1688 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5485   -2.7374    1.6262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3605   -3.8646   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  1
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  3
 25 27  1  0
 27 28  2  0
 28 29  1  0
 21 30  1  0
 30 31  1  0
 30 32  1  0
 32 33  1  0
 32 19  1  0
 28 22  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  4 38  1  0
  4 39  1  0
  5 40  1  0
  6 41  1  1
  7 42  1  0
  8 43  1  0
  8 44  1  0
 12 45  1  0
 16 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  6
 21 50  1  6
 23 51  1  0
 24 52  1  0
 26 53  1  0
 29 54  1  0
 30 55  1  1
 31 56  1  0
 32 57  1  1
 33 58  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₄H₂₅N₃O₁₄P₂

Average Molecular Weight

521.3075

Monoisotopic Molecular Weight

521.081175547

IUPAC Name

[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphinic acid

Traditional Name

4-cdp-2-C-methyl-D-erythritol

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=CC(=N)N=C2O)[C@]([H])(O)[C@]1([H])O)[C@@](C)(O)CO

InChI Identifier

InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1

InChI Key

YFAUKWZNPVBCFF-XHIBXCGHSA-N

Chemical Taxonomy

Description

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

alditol 4-phosphate (CHEBI:16578 )
tetritol phosphate (CHEBI:16578 )
nucleotide-alditol (CHEBI:16578 )

Ontology

Not Available

Exogenous (HMDB: HMDB0304166)

Herbs and Spices (FooDB: FOOD00866)

Nut

Almond (FooDB: FOOD00148)
Brazil nut (FooDB: FOOD00024)
Cashew nut (FooDB: FOOD00011)
Chestnut (FooDB: FOOD00045)
Hazelnut (FooDB: FOOD00376)
Peanut (FooDB: FOOD00016)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)

Tropical fruit

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
American cranberry (FooDB: FOOD00192)
Common grape (FooDB: FOOD00204)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)
Jujube (FooDB: FOOD00388)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)

Fruits (FooDB: FOOD00871)

Vegetable

Shoot vegetable

Fruit vegetable

Eggplant (FooDB: FOOD00174)
Avocado (FooDB: FOOD00130)
Groundcherry (FooDB: FOOD00371)
Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)

Root vegetable

Cabbage

Leaf vegetable

Lettuce (FooDB: FOOD00095)
Swiss chard (FooDB: FOOD00237)
Garden cress (FooDB: FOOD00099)
Endive (FooDB: FOOD00048)
Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)

Mushroom

Tuber

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Other vegetable

Okra (FooDB: FOOD00420)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Tree fern (FooDB: FOOD00797)
Chinese water chestnut (FooDB: FOOD00332)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)

Stalk vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Other soy product (FooDB: FOOD00271)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Gourd

Chayote (FooDB: FOOD00325)
Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Secondary Metabolites: Methylerythritol Phosphate and Polyisoprenoid Biosynthesis (PathBank: SMP0121325)
Secondary Metabolites: Isoprenoid Biosynthesis (Nonmevalonate Pathway) (PathBank: SMP0121328)
MEP/DOXP Pathway (PathBank: SMP0121208)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.8	ALOGPS
logP	-5.3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	3.34	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	272.35 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	115.04 m³·mol⁻¹	ChemAxon
Polarizability	44.23 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	203.853	32859911
AllCCS	[M+H-H2O]+	202.35	32859911
AllCCS	[M+Na]+	205.596	32859911
AllCCS	[M+NH4]+	205.212	32859911
AllCCS	[M-H]-	202.534	32859911
AllCCS	[M+Na-2H]-	203.6	32859911
AllCCS	[M+HCOO]-	204.91	32859911
DeepCCS	[M+H]+	190.707	30932474
DeepCCS	[M-H]-	188.761	30932474
DeepCCS	[M-2H]-	222.65	30932474
DeepCCS	[M+Na]+	196.62	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	10.8239 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	9.72 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	457.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	255.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	24.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	183.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	69.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	345.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	286.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	905.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	592.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	59.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	684.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	196.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	385.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	813.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	603.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	668.0 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Positive-QTOF	splash10-03di-0900010000-dd055cf6bd442a418647	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Positive-QTOF	splash10-03di-2900000000-4e622642413e6ebd8477	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Positive-QTOF	splash10-03di-6900000000-74e9c9a2a9edbdec480f	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Negative-QTOF	splash10-024i-8921880000-a4764a7c92b71559f802	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Negative-QTOF	splash10-01t9-9873300000-13a6ee53acf7e6b82639	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Negative-QTOF	splash10-0bvl-5900000000-5fb1217b0273b9eb07ed	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Positive-QTOF	splash10-0f79-0002980000-b0c2dd0f91aa67816b82	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Positive-QTOF	splash10-08ou-0689210000-ce579339d5226e7cf795	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Positive-QTOF	splash10-0gvp-4975000000-183cd21e1b0b0bbffbdd	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 10V, Negative-QTOF	splash10-00di-0000090000-641c25f0d0828a8b13d8	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 20V, Negative-QTOF	splash10-00fr-4211970000-3141df7963d44155286b	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 40V, Negative-QTOF	splash10-004i-9134000000-c51a8f7c77198cc212bd	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB03687

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443199

PDB ID

Not Available

ChEBI ID

16578

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (HMDB0304166)

MOL for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D MOL for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D SDF for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D-SDF for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

PDB for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D PDB for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

SMILES for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

INCHI for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

Structure for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D Structure for HMDB0304166 (4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra