NP-MRD: Showing NP-Card for {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid (NP0236111)

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Record Information

Version

1.0

Created at

2022-09-06 18:55:54 UTC

Updated at

2022-09-06 18:55:55 UTC

NP-MRD ID

NP0236111

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid

Description

[({[3,4-Dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]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. {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid is found in Helianthus tuberosus. [({[3,4-Dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004261502162D          

 36 38  0  0  0  0            999 V2000
    1.5151    3.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0454    3.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -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  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5757    4.0752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1060    4.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9185    4.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4488    5.1960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2007    3.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0131    3.6455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6704    3.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9525    2.3815    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  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 21 27  1  0  0  0  0
 27 28  2  0  0  0  0
  3 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END

     RDKit          3D

 60 62  0  0  0  0  0  0  0  0999 V2000
    9.8808   -0.6034    1.0628 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7098   -0.3806    0.6366 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4564   -0.1151   -0.7045 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1628    0.1222   -1.1246 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1100    0.1088   -0.2796 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8077    0.3656   -0.8058 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8153   -0.4417   -0.2084 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6782    0.1896   -0.6348 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4017   -0.4076   -0.1442 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2605   -0.4305    1.2193 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2575   -1.1493    1.5438 P   0  0  1  0  0  5  0  0  0  0  0  0
   -0.2151   -2.6322    1.2594 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5853   -0.9716    3.1964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4886   -0.4084    0.6811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2162   -1.4582   -0.4252 P   0  0  1  0  0  5  0  0  0  0  0  0
   -1.2937   -1.4944   -1.6490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2448   -3.0397    0.1763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7030   -0.9268   -0.9458 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6564   -0.8081    0.0268 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.9606   -2.1143    0.7409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4136   -3.0298   -0.1820 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2427    0.1592    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9981    1.3061    0.9051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0782    1.8905   -0.5028 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.7680    3.0956   -0.4140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8681    0.9225   -1.3339 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.1898    1.3911   -1.5147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9626   -0.4083   -0.6656 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.0544   -0.5533    0.1662 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8922    1.6087   -0.1937 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8078    1.7527    1.1842 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3737    1.7973   -0.5519 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5087    2.4803   -1.7560 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3847   -0.1508    1.0116 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4342   -0.1700    1.8154 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6428   -0.3881    1.4579 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3089   -0.1042   -1.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9941    0.3286   -2.1879 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7844    0.1110   -1.8829 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6620    0.1801   -1.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3297   -1.4371   -0.5201 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5677    0.2096   -0.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767   -0.1434    3.5646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4306   -3.6583   -0.5600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1569   -2.4566    1.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8316   -1.8793    1.4211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8394   -3.8118   -0.3105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0088    1.1812    1.3333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4851    2.0635    1.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0594    2.0168   -0.8857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4105    3.5937    0.3696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4338    0.8290   -2.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4559    2.0077   -0.7883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0895   -1.1754   -1.4846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8637   -0.8682   -0.3344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2962    2.3410   -0.7537 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6616    2.0222    1.6063 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9385    2.2445    0.2741 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7343    1.8860   -2.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8339   -0.5887    2.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
 21 20  1  0
 20 19  1  0
 19 18  1  6
 15 18  1  6
 15 17  1  0
 15 16  2  0
 15 14  1  0
 11 14  1  6
 11 13  1  0
 11 12  2  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6 32  1  0
 32 33  1  0
 32 30  1  0
 30 31  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 36  1  0
 36 34  1  0
 34 35  2  0
 19 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28 19  1  0
 30  8  1  0
 34  5  1  0
 21 47  1  0
 20 45  1  0
 20 46  1  0
 17 44  1  0
 13 43  1  0
  9 41  1  0
  9 42  1  0
  8 40  1  6
  6 39  1  6
 32 58  1  1
 33 59  1  0
 30 56  1  6
 31 57  1  0
  4 38  1  0
  3 37  1  0
 36 60  1  0
 23 48  1  0
 23 49  1  0
 24 50  1  6
 25 51  1  0
 26 52  1  6
 27 53  1  0
 28 54  1  6
 29 55  1  0
M  END


  Mrv1533004261502162D          

 36 38  0  0  0  0            999 V2000
    1.5151    3.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0454    3.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -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  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5757    4.0752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1060    4.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9185    4.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4488    5.1960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2007    3.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0131    3.6455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6704    3.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9525    2.3815    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  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 21 27  1  0  0  0  0
 27 28  2  0  0  0  0
  3 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0236111

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)OCC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H24N2O17P2/c18-5-15(12(24)9(21)6(19)3-30-15)33-36(28,29)34-35(26,27)31-4-7-10(22)11(23)13(32-7)17-2-1-8(20)16-14(17)25/h1-2,6-7,9-13,18-19,21-24H,3-5H2,(H,26,27)(H,28,29)(H,16,20,25)

> <INCHI_KEY>
XFMLHGCQNDDNPW-UHFFFAOYSA-N

> <FORMULA>
C15H24N2O17P2

> <MOLECULAR_WEIGHT>
566.302

> <EXACT_MASS>
566.055021317

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
46.12051870916612

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.03

> <JCHEM_LOGP>
-4.822068178666668

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.16252964493022

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.709102366594132

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5272119945774927

> <JCHEM_POLAR_SURFACE_AREA>
291.53999999999996

> <JCHEM_REFRACTIVITY>
106.8932

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.54e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxyphosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  O   UNK     0       2.828   7.072   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.818   5.893   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0       4.001   3.850   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0       4.771   2.516   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.231   5.184   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.667   3.080   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0       2.667   1.540   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0       4.207   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.127   1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667  -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  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       4.808   7.607   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       5.798   8.787   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.315   8.519   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       8.304   9.699   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       7.841   7.072   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       9.358   6.805   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.851   5.893   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       7.378   4.445   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   29   35                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   14   20                                                  
CONECT   20   19                                                            
CONECT   21   16   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   21   28                                                  
CONECT   28   27                                                            
CONECT   29    3   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Value	Source
[({[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy})phosphinate	Generator

Chemical Formula

C₁₅H₂₄N₂O₁₇P₂

Average Mass

566.3020 Da

Monoisotopic Mass

566.05502 Da

IUPAC Name

[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acid

Traditional Name

{[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy[3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxyphosphinic acid

CAS Registry Number

Not Available

SMILES

OCC1(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)OCC(O)C(O)C1O

InChI Identifier

InChI=1S/C15H24N2O17P2/c18-5-15(12(24)9(21)6(19)3-30-15)33-36(28,29)34-35(26,27)31-4-7-10(22)11(23)13(32-7)17-2-1-8(20)16-14(17)25/h1-2,6-7,9-13,18-19,21-24H,3-5H2,(H,26,27)(H,28,29)(H,16,20,25)

InChI Key

XFMLHGCQNDDNPW-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Helianthus tuberosus	LOTUS Database	35616633

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
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Polyol
Azacycle
Oxacycle
Primary alcohol
Organonitrogen compound
Organic nitrogen compound
Organooxygen compound
Alcohol
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
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	ALOGPS
logP	-4.8	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	291.54 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	106.89 m³·mol⁻¹	ChemAxon
Polarizability	46.12 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid (NP0236111)

MOL for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D MOL for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D SDF for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D-SDF for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

PDB for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D PDB for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

SMILES for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

INCHI for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

Structure for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)

3D Structure for NP0236111 ({[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([3,4,5-trihydroxy-2-(hydroxymethyl)oxan-2-yl]oxy)phosphinic acid)