NP-MRD: Showing NP-Card for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (NP0055045)

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Record Information

Version

2.0

Created at

2022-04-28 01:12:22 UTC

Updated at

2022-04-28 01:12:22 UTC

NP-MRD ID

NP0055045

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

{[(2R,3S,4S,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphoryl}oxy)phosphinic acid belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol is found in Arabidopsis thaliana, Aureococcus anaphagefferens, Chamaemelum nobile , Glycine max , Laurencia dendroidea, Matricaria recutita , Phaeodactylum tricornutum, Sertia mussotii and Thalassiosiria pseudonana. Based on a literature review very few articles have been published on {[(2R,3S,4S,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphoryl}oxy)phosphinic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282203122D          

 33 34  0  0  1  0            999 V2000
   -2.1434    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 P   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1270    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9684    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 O   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  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 24 27  1  0  0  0  0
 19 28  1  0  0  0  0
 14 28  1  0  0  0  0
 10 29  1  6  0  0  0
  7 30  1  1  0  0  0
  2 31  1  6  0  0  0
  2 32  1  6  0  0  0
  1 33  1  0  0  0  0
M  END

     RDKit          3D

 58 59  0  0  0  0  0  0  0  0999 V2000
    7.6838    0.6960   -2.2513 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6191    0.9102   -1.1721 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5430    1.6127   -1.7080 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3147    1.6672   -0.0630 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7795    2.8721   -0.6369 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2366   -0.4540   -0.6847 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7223   -1.2267   -1.7339 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2836   -0.4404    0.4887 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0504    0.0874    0.1664 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1045    0.0303    1.5868 P   0  0  2  0  0  5  0  0  0  0  0  0
    3.6291    1.1144    2.5314 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3319   -1.4610    2.3486 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4819    0.3124    1.2440 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6070   -1.0658    1.7059 P   0  0  1  0  0  5  0  0  0  0  0  0
    0.7944   -2.0856    0.5944 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -1.6817    3.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0299   -0.7653    1.8457 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6660   -0.6181    0.6354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1340   -0.3496    0.7921 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7975   -0.1972   -0.3933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0449   -0.8053   -0.3057 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.0606    0.0175   -0.8728 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7371    0.7718   -1.9474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6468    1.6017   -2.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9484    1.6802   -2.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9188    2.5227   -2.7008 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2367    0.9171   -1.0206 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3226    0.1159   -0.4359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6446   -0.5723    0.5564 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2634   -1.2364    1.0960 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.9278   -2.4553    1.2098 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8294   -1.4968    1.5370 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7678   -1.3168    2.9093 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5754    0.2638   -1.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9213    1.6579   -2.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3153    0.0175   -3.0410 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5438    1.4281   -2.6953 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1562    1.0286    0.2742 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6205    1.8950    0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6025    3.5996    0.0254 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1656   -0.9565   -0.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8616   -2.1885   -1.6063 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2115   -1.4964    0.8359 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7491    0.1426    1.3074 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5891   -1.3567    3.3011 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7545   -1.4834    3.9298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5765   -1.5546    0.0140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    0.2130    0.0542 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3203    0.5542    1.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9570   -1.7453   -0.9294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7234    0.7505   -2.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3860    2.2075   -3.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3384    3.2741   -2.1175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2419    2.4456   -3.6871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6548   -0.4596    1.7746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7666   -2.7849    2.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4577   -2.4772    1.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8966   -1.6762    3.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  6
  2  4  1  0
  4  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
 10  9  1  6
 10 12  1  0
 10 11  2  0
 10 13  1  0
 14 13  1  6
 14 16  1  0
 14 15  2  0
 14 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 30  1  0
 30 31  1  0
 30 32  1  0
 32 33  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  1  0
 25 27  2  0
 27 28  1  0
 28 29  2  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  1
 21 50  1  6
 30 55  1  1
 31 56  1  0
 32 57  1  1
 33 58  1  0
 23 51  1  0
 24 52  1  0
 26 53  1  0
 26 54  1  0
M  END


  Mrv1652304282203122D          

 33 34  0  0  1  0            999 V2000
   -2.1434    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 P   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1270    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9684    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    5.7750    0.0000 O   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  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 24 27  1  0  0  0  0
 19 28  1  0  0  0  0
 14 28  1  0  0  0  0
 10 29  1  6  0  0  0
  7 30  1  1  0  0  0
  2 31  1  6  0  0  0
  2 32  1  6  0  0  0
  1 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055045

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@@H]([C@@H](O)[C@@H]1O)N1C=CC(N)=NC1=O

> <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-OIOYKEMMSA-N

> <FORMULA>
C14H25N3O14P2

> <MOLECULAR_WEIGHT>
521.309

> <EXACT_MASS>
521.081176493

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
43.92324215963468

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.31

> <JCHEM_LOGP>
-4.635116299666668

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2716485952664

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.863190577548116

> <JCHEM_PKA_STRONGEST_BASIC>
-0.03201102607457429

> <JCHEM_POLAR_SURFACE_AREA>
271.35999999999996

> <JCHEM_REFRACTIVITY>
103.6284

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5S)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R,3S)-2,3,4-trihydroxy-3-methylbutoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -4.001  10.010   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -5.335   6.160   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0      -1.334   3.850   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      -2.104   2.516   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   3.080   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0       0.000   1.540   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      -1.540   1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.044  -2.739   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -0.342  -5.926   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.816  -7.494   0.000  0.00  0.00           O+0
HETATM   23  N   UNK     0      -0.620  -8.578   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.778  -7.011   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -3.057  -9.663   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -0.564   5.184   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.461   8.470   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -5.541   8.470   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -5.335  10.780   0.000  0.00  0.00           O+0
CONECT    1    2   33                                                       
CONECT    2    1    3   31   32                                             
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   30                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12   29                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   28                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   28                                                  
CONECT   20   19   21   26                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   20                                                       
CONECT   27   24                                                            
CONECT   28   19   14                                                       
CONECT   29   10                                                            
CONECT   30    7                                                            
CONECT   31    2                                                            
CONECT   32    2                                                            
CONECT   33    1                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

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

Chemical Formula

C₁₄H₂₅N₃O₁₄P₂

Average Mass

521.3090 Da

Monoisotopic Mass

521.08118 Da

IUPAC Name

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

Traditional Name

[(2R,3S,4S,5S)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R,3S)-2,3,4-trihydroxy-3-methylbutoxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@@H]([C@@H](O)[C@@H]1O)N1C=CC(N)=NC1=O

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-OIOYKEMMSA-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
Arabidopsis thaliana	Plant	KNApSAcK
Aureococcus anaphagefferens	Chromista	KNApSAcK
Chamaemelum nobile	Plant	KNApSAcK
Glycine max	Plant	KNApSAcK
Laurencia dendroidea	-	KNApSAcK
Matricaria recutita	Plant	KNApSAcK
Phaeodactylum tricornutum	Chromalveolata	KNApSAcK
Sertia mussotii	-	KNApSAcK
Thalassiosiria pseudonana	-	KNApSAcK

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-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Hydroxypyrimidine
Monoalkyl phosphate
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Tertiary alcohol
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
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-1.3	ALOGPS
logP	-4.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.032	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	271.36 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	103.63 m³·mol⁻¹	ChemAxon
Polarizability	43.92 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163067983

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (NP0055045)

MOL for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D MOL for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D SDF for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D-SDF for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

PDB for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D PDB for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

SMILES for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

INCHI for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

Structure for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)

3D Structure for NP0055045 (4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol)