NP-MRD: Showing NP-Card for Park nucleotide (NP0062863)

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Record Information

Version

2.0

Created at

2022-04-28 07:24:29 UTC

Updated at

2022-04-28 07:24:29 UTC

NP-MRD ID

NP0062863

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Park nucleotide

Description

(2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}pentyl]-C-hydroxycarbonimidoyl}-2-{[(2R)-2-{[(2S)-2-{[(2R,3R,4R,5S,6S)-2-({[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-hydroxypropylidene]amino}butanoic acid belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. Park nucleotide is found in Escherichia coli. Based on a literature review very few articles have been published on (2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}pentyl]-C-hydroxycarbonimidoyl}-2-{[(2R)-2-{[(2S)-2-{[(2R,3R,4R,5S,6S)-2-({[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-hydroxypropylidene]amino}butanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282209242D          

 77 79  0  0  1  0            999 V2000
   -1.0901   -9.2864    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3756   -9.6989    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3756  -10.5239    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0901  -10.9364    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8046  -10.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8046   -9.6989    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5190   -9.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5190   -8.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0901  -11.7614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8046  -12.1739    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3921  -12.8883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2171  -11.4594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5190  -12.5864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5190  -13.4114    0.0000 P   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3440  -13.4114    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5190  -14.2364    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2335  -14.6489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2335  -15.4739    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5661  -15.9588    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7814  -15.7038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8210  -16.7434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3361  -17.4108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6460  -16.7434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1309  -17.4108    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7954  -18.1645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2803  -18.8319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1008  -18.7457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5857  -19.4132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4363  -17.9920    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9514  -17.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2870  -16.5709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9009  -15.9588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6940  -13.4114    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3388  -10.9364    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3388  -11.7614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533  -12.1739    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3756  -12.1739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3388   -9.2864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533   -9.6989    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7678   -9.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7678   -8.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4823   -9.6989    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1967   -9.2864    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9112   -9.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9112  -10.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6257   -9.2864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3401   -9.6989    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0546   -9.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7691   -9.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4836   -9.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4836   -8.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1980   -9.6989    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9125   -9.2864    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.9125   -8.4614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1980   -8.0489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1980   -7.2239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4836   -6.8114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4836   -5.9864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.6270   -9.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6270  -10.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3414   -9.2864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.0559   -9.6989    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.7704   -9.2864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7704   -8.4614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.4849   -9.6989    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1993   -9.2864    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.9138   -9.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9138  -10.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6283   -9.2864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1993   -8.4614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0559  -10.5239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3401  -10.5239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0546  -10.9364    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6257  -10.9364    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1967   -8.4614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0533  -10.5239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0901   -8.4614    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  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  4  9  1  1  0  0  0
 10  9  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  6  0  0  0
 10 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 24 30  1  0  0  0  0
 30 31  2  0  0  0  0
 23 32  1  0  0  0  0
 18 32  1  0  0  0  0
 14 33  1  1  0  0  0
  3 34  1  1  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
  2 38  1  6  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 40 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 44 46  1  0  0  0  0
 47 46  1  1  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  2  0  0  0  0
 50 52  1  0  0  0  0
 53 52  1  6  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 53 59  1  0  0  0  0
 59 60  2  0  0  0  0
 59 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  2  0  0  0  0
 63 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  2  0  0  0  0
 67 69  1  0  0  0  0
 66 70  1  1  0  0  0
 62 71  1  6  0  0  0
 47 72  1  0  0  0  0
 72 73  2  0  0  0  0
 72 74  1  0  0  0  0
 43 75  1  6  0  0  0
 39 76  1  6  0  0  0
  1 77  1  1  0  0  0
M  END

     RDKit          3D

142144  0  0  0  0  0  0  0  0999 V2000
   -5.9715   -4.4348   -2.4117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4064   -3.0611   -2.4588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1530   -2.5303   -3.5468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1524   -2.3492   -1.2527 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6025   -1.0139   -1.1635 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3862   -0.0206   -0.4295 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.7584   -0.2885   -0.7825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3501    0.7973   -1.8906 P   0  0  2  0  0  5  0  0  0  0  0  0
   -6.2906    1.0957   -2.9593 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8435    2.2549   -1.2150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6222    0.0550   -2.7347 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3890   -1.0005   -1.6482 P   0  0  2  0  0  5  0  0  0  0  0  0
   -8.4325   -1.5992   -0.6408 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1284   -2.2819   -2.4985 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5959   -0.1151   -0.8672 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8402   -0.6923    0.3859 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9260    0.0796    1.1230 C   0  0  2  0  0  0  0  0  0  0  0  0
  -13.1154    0.0578    0.4046 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.8666    1.0426    1.0798 C   0  0  2  0  0  0  0  0  0  0  0  0
  -15.1211    1.2844    0.4346 N   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1439    1.7697    1.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.3675    2.0349    0.6466 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.5528    1.7979   -0.7047 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.6330    2.0029   -1.3051 O   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5198    1.3178   -1.4163 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3340    1.0689   -0.8575 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3817    0.6200   -1.5641 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9054    2.2236    0.9908 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.9110    2.7241   -0.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5949    1.5493    1.2421 C   0  0  2  0  0  0  0  0  0  0  0  0
  -10.5986    1.9286    0.3370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2932    0.0797    0.8951 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4018   -0.6452    1.5973 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1479   -1.6299    2.4742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2754   -2.4051    3.2519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2189   -1.2492    0.8961 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2925   -2.6429    1.1546 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1660   -1.0801   -0.5521 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5745    0.1026   -0.9126 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9665    0.1885   -2.1046 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5231    1.2834   -2.9395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4858    0.0790   -2.2200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0038    0.5906   -3.2950 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2977   -0.5273   -1.2724 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0842   -1.1333   -0.3266 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4382   -1.4520    0.9787 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4878   -0.6877   -0.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2139   -0.5137   -1.1141 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0039   -0.4773    1.1730 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4324   -0.1233    1.3598 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7378    1.3058    1.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2087    1.5572    1.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1023    0.7136    0.4750 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7418    0.0846   -0.5439 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4661    0.5788    0.8405 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.4233   -0.2266    0.0840 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.3994   -1.6891    0.5082 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9527   -2.0710    1.7946 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4543   -1.5489    3.0636 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1774   -2.1362    4.2823 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0301   -3.5495    4.4068 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.7579    0.3276    0.0430 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0001    1.3519    0.7612 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7926   -0.2004   -0.7418 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1288    0.4047   -0.7040 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.2162   -0.5825   -0.9678 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1440    1.4909   -1.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1739    1.6631   -2.5165 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2444    2.3648   -1.7913 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2793    3.4344   -2.7504 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282209242D          

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 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
  2 38  1  6  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 40 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 44 46  1  0  0  0  0
 47 46  1  1  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  2  0  0  0  0
 50 52  1  0  0  0  0
 53 52  1  6  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 53 59  1  0  0  0  0
 59 60  2  0  0  0  0
 59 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  2  0  0  0  0
 63 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  2  0  0  0  0
 67 69  1  0  0  0  0
 66 70  1  1  0  0  0
 62 71  1  6  0  0  0
 47 72  1  0  0  0  0
 72 73  2  0  0  0  0
 72 74  1  0  0  0  0
 43 75  1  6  0  0  0
 39 76  1  6  0  0  0
  1 77  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0062863

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](CCCCN)NC(=O)CC[C@H](NC(=O)[C@@H](C)NC(=O)[C@H](C)O[C@H]1[C@H](O)[C@H](CO)O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@@H]2O[C@@H]([C@H](O)[C@@H]2O)N2C=CC(=O)NC2=O)[C@@H]1NC(C)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C40H65N9O26P2/c1-16(32(57)44-18(3)37(61)62)43-35(60)21(8-6-7-12-41)46-25(52)10-9-22(38(63)64)47-33(58)17(2)42-34(59)19(4)71-31-27(45-20(5)51)39(73-23(14-50)29(31)55)74-77(68,69)75-76(66,67)70-15-24-28(54)30(56)36(72-24)49-13-11-26(53)48-40(49)65/h11,13,16-19,21-24,27-31,36,39,50,54-56H,6-10,12,14-15,41H2,1-5H3,(H,42,59)(H,43,60)(H,44,57)(H,45,51)(H,46,52)(H,47,58)(H,61,62)(H,63,64)(H,66,67)(H,68,69)(H,48,53,65)/t16-,17+,18-,19-,21+,22-,23-,24-,27+,28+,29+,30+,31+,36-,39+/m0/s1

> <INCHI_KEY>
PFMVORMCVGOQKR-RDVYADALSA-N

> <FORMULA>
C40H65N9O26P2

> <MOLECULAR_WEIGHT>
1149.945

> <EXACT_MASS>
1149.351597245

> <JCHEM_ACCEPTOR_COUNT>
24

> <JCHEM_ATOM_COUNT>
142

> <JCHEM_AVERAGE_POLARIZABILITY>
104.34765259348717

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]carbamoyl}ethyl]carbamoyl}pentyl]carbamoyl}-2-[(2R)-2-[(2S)-2-{[(2R,3R,4R,5S,6S)-2-({[({[(2S,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}propanamido]propanamido]butanoic acid

> <ALOGPS_LOGP>
-0.53

> <JCHEM_LOGP>
-9.013748472961193

> <ALOGPS_LOGS>
-2.66

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.8258910278359393

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7165247900482177

> <JCHEM_PKA_STRONGEST_BASIC>
10.317140778810288

> <JCHEM_POLAR_SURFACE_AREA>
535.5299999999999

> <JCHEM_REFRACTIVITY>
247.4764000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
30

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]carbamoyl}ethyl]carbamoyl}pentyl]carbamoyl}-2-[(2R)-2-[(2S)-2-{[(2R,3R,4R,5S,6S)-2-[({[(2S,3S,4R,5S)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}propanamido]propanamido]butanoic 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      -2.035 -17.335   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.701 -18.105   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.701 -19.645   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.035 -20.415   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.369 -19.645   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.369 -18.105   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.702 -17.335   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.702 -15.795   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.035 -21.955   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0      -3.369 -22.725   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      -2.599 -24.058   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -4.139 -21.391   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.702 -23.495   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      -4.702 -25.035   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      -6.242 -25.035   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -4.702 -26.575   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -6.036 -27.345   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.036 -28.885   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.790 -29.790   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.325 -29.314   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -5.266 -31.254   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.361 -32.500   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -6.806 -31.254   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -7.711 -32.500   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      -7.085 -33.907   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.990 -35.153   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -9.521 -34.992   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0     -10.427 -36.238   0.000  0.00  0.00           O+0
HETATM   29  N   UNK     0     -10.148 -33.585   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -9.243 -32.339   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -9.869 -30.932   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -7.282 -29.790   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -3.162 -25.035   0.000  0.00  0.00           O+0
HETATM   34  N   UNK     0       0.633 -20.415   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       0.633 -21.955   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       1.966 -22.725   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -0.701 -22.725   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       0.633 -17.335   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       1.966 -18.105   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.300 -17.335   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       3.300 -15.795   0.000  0.00  0.00           O+0
HETATM   42  N   UNK     0       4.634 -18.105   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0       5.967 -17.335   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       7.301 -18.105   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0       7.301 -19.645   0.000  0.00  0.00           O+0
HETATM   46  N   UNK     0       8.635 -17.335   0.000  0.00  0.00           N+0
HETATM   47  C   UNK     0       9.968 -18.105   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      11.302 -17.335   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      12.636 -18.105   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      13.969 -17.335   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      13.969 -15.795   0.000  0.00  0.00           O+0
HETATM   52  N   UNK     0      15.303 -18.105   0.000  0.00  0.00           N+0
HETATM   53  C   UNK     0      16.637 -17.335   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      16.637 -15.795   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      15.303 -15.025   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      15.303 -13.485   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      13.969 -12.715   0.000  0.00  0.00           C+0
HETATM   58  N   UNK     0      13.969 -11.175   0.000  0.00  0.00           N+0
HETATM   59  C   UNK     0      17.970 -18.105   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      17.970 -19.645   0.000  0.00  0.00           O+0
HETATM   61  N   UNK     0      19.304 -17.335   0.000  0.00  0.00           N+0
HETATM   62  C   UNK     0      20.638 -18.105   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      21.971 -17.335   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      21.971 -15.795   0.000  0.00  0.00           O+0
HETATM   65  N   UNK     0      23.305 -18.105   0.000  0.00  0.00           N+0
HETATM   66  C   UNK     0      24.639 -17.335   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      25.972 -18.105   0.000  0.00  0.00           C+0
HETATM   68  O   UNK     0      25.972 -19.645   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      27.306 -17.335   0.000  0.00  0.00           O+0
HETATM   70  C   UNK     0      24.639 -15.795   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      20.638 -19.645   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0       9.968 -19.645   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0      11.302 -20.415   0.000  0.00  0.00           O+0
HETATM   74  O   UNK     0       8.635 -20.415   0.000  0.00  0.00           O+0
HETATM   75  C   UNK     0       5.967 -15.795   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0       1.966 -19.645   0.000  0.00  0.00           C+0
HETATM   77  O   UNK     0      -2.035 -15.795   0.000  0.00  0.00           O+0
CONECT    1    2    6   77                                                  
CONECT    2    1    3   38                                                  
CONECT    3    2    4   34                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15   16   33                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   32                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   32                                                  
CONECT   24   23   25   30                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   24   31                                                  
CONECT   31   30                                                            
CONECT   32   23   18                                                       
CONECT   33   14                                                            
CONECT   34    3   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
CONECT   38    2   39                                                       
CONECT   39   38   40   76                                                  
CONECT   40   39   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   43                                                       
CONECT   43   42   44   75                                                  
CONECT   44   43   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47                                                       
CONECT   47   46   48   72                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   53                                                       
CONECT   53   52   54   59                                                  
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57                                                            
CONECT   59   53   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   62                                                       
CONECT   62   61   63   71                                                  
CONECT   63   62   64   65                                                  
CONECT   64   63                                                            
CONECT   65   63   66                                                       
CONECT   66   65   67   70                                                  
CONECT   67   66   68   69                                                  
CONECT   68   67                                                            
CONECT   69   67                                                            
CONECT   70   66                                                            
CONECT   71   62                                                            
CONECT   72   47   73   74                                                  
CONECT   73   72                                                            
CONECT   74   72                                                            
CONECT   75   43                                                            
CONECT   76   39                                                            
CONECT   77    1                                                            
MASTER        0    0    0    0    0    0    0    0   77    0  158    0
END

View in JSmol

Synonyms

Value

Source

Generator

Chemical Formula

C₄₀H₆₅N₉O₂₆P₂

Average Mass

1149.9450 Da

Monoisotopic Mass

1149.35160 Da

IUPAC Name

(2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]carbamoyl}ethyl]carbamoyl}pentyl]carbamoyl}-2-[(2R)-2-[(2S)-2-{[(2R,3R,4R,5S,6S)-2-({[({[(2S,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}propanamido]propanamido]butanoic acid

Traditional Name

(2S)-4-{[(1R)-5-amino-1-{[(1S)-1-{[(1S)-1-carboxyethyl]carbamoyl}ethyl]carbamoyl}pentyl]carbamoyl}-2-[(2R)-2-[(2S)-2-{[(2R,3R,4R,5S,6S)-2-[({[(2S,3S,4R,5S)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}propanamido]propanamido]butanoic acid

CAS Registry Number

Not Available

SMILES

C[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](CCCCN)NC(=O)CC[C@H](NC(=O)[C@@H](C)NC(=O)[C@H](C)O[C@H]1[C@H](O)[C@H](CO)O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@@H]2O[C@@H]([C@H](O)[C@@H]2O)N2C=CC(=O)NC2=O)[C@@H]1NC(C)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C40H65N9O26P2/c1-16(32(57)44-18(3)37(61)62)43-35(60)21(8-6-7-12-41)46-25(52)10-9-22(38(63)64)47-33(58)17(2)42-34(59)19(4)71-31-27(45-20(5)51)39(73-23(14-50)29(31)55)74-77(68,69)75-76(66,67)70-15-24-28(54)30(56)36(72-24)49-13-11-26(53)48-40(49)65/h11,13,16-19,21-24,27-31,36,39,50,54-56H,6-10,12,14-15,41H2,1-5H3,(H,42,59)(H,43,60)(H,44,57)(H,45,51)(H,46,52)(H,47,58)(H,61,62)(H,63,64)(H,66,67)(H,68,69)(H,48,53,65)/t16-,17+,18-,19-,21+,22-,23-,24-,27+,28+,29+,30+,31+,36-,39+/m0/s1

InChI Key

PFMVORMCVGOQKR-RDVYADALSA-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
Escherichia coli	Bacteria	KNApSAcK

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine ribonucleoside diphosphate
Alpha peptide
Pentose-5-phosphate
Pentose phosphate
N-acyl-alpha-hexosamine
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Alanine or derivatives
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Alpha-amino acid or derivatives
Hydroxypyrimidine
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Dicarboxylic acid or derivatives
Heteroaromatic compound
Tetrahydrofuran
Amino acid
Secondary alcohol
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
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	-0.53	ALOGPS
logP	-9	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	1.72	ChemAxon
pKa (Strongest Basic)	10.32	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	24	ChemAxon
Hydrogen Donor Count	16	ChemAxon
Polar Surface Area	535.53 Å²	ChemAxon
Rotatable Bond Count	30	ChemAxon
Refractivity	247.48 m³·mol⁻¹	ChemAxon
Polarizability	104.35 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

163105501

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Park nucleotide (NP0062863)

MOL for NP0062863 (Park nucleotide)

3D MOL for NP0062863 (Park nucleotide)

3D SDF for NP0062863 (Park nucleotide)

3D-SDF for NP0062863 (Park nucleotide)

PDB for NP0062863 (Park nucleotide)

3D PDB for NP0062863 (Park nucleotide)

SMILES for NP0062863 (Park nucleotide)

INCHI for NP0062863 (Park nucleotide)

Structure for NP0062863 (Park nucleotide)

3D Structure for NP0062863 (Park nucleotide)