NP-MRD: Showing NP-Card for (2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid (NP0161616)

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Record Information

Version

2.0

Created at

2022-09-02 19:50:39 UTC

Updated at

2022-09-02 19:50:40 UTC

NP-MRD ID

NP0161616

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid

Description

Mildiomycin D belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. Based on a literature review very few articles have been published on Mildiomycin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022221502D          

 35 36  0  0  1  0            999 V2000
   -1.4289    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1105   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  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   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 13  8  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 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
 16 24  1  0  0  0  0
 24 25  1  0  0  0  0
 15 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 13 28  1  0  0  0  0
 28 29  1  6  0  0  0
 29 30  2  0  0  0  0
 30 31  1  4  0  0  0
 30 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END

     RDKit          3D

 65 66  0  0  0  0  0  0  0  0999 V2000
    1.7416   -6.6093    1.1814 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5068   -6.0135    0.7991 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3025   -4.7328    0.7463 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1614   -4.1551    1.1586 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9312   -2.8335    1.1121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3037   -2.3216    1.5713 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8758   -2.0107    0.6305 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6133   -0.5712    0.5856 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1845    0.0168   -0.6697 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7942    1.2691   -0.9481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8422    1.8806    0.0522 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5781    2.3618    1.1530 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1993    3.4513    1.2290 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8537    3.6505    2.4935 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3631    4.5311    0.2598 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7398    4.3862   -1.0019 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8974    5.8780    0.8297 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4960    6.0498    2.0756 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2112    0.8550    0.4508 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4052    0.9112   -0.4770 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8831    2.2226   -0.6041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5588    0.1283    0.1388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7145    0.2432   -0.8629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8823   -0.5172   -0.2949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5637   -1.9030   -0.0937 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5589   -2.7539    0.4391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6921   -2.2330    1.1167 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4484   -4.0217    0.3153 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1160   -4.7196    0.6667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0845    0.4153   -1.8299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6531   -0.7487   -2.0203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2555    1.2349   -2.9291 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2318   -0.4265    0.5392 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0302   -2.5151    0.2050 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2603   -3.8708    0.2552 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5432   -4.4524   -0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3666   -3.4399   -0.6671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1706   -2.8308    1.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0664   -0.1238    1.4949 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8555   -0.4883   -1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1462    1.7792   -1.8284 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3092    2.6755   -0.4640 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8484    3.8549    2.3925 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4746    4.6311    0.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9109    4.9609   -1.1820 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3784    4.2698   -1.8061 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2680    6.6965    0.1747 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8108    5.9420    0.8732 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4068    6.4030    1.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5286    1.1679    1.4873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6486    2.6252   -1.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2447   -0.9135    0.2618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8637    0.6360    1.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9712    1.3065   -1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4087   -0.1648   -1.8483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1550   -0.0785    0.6887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7852   -0.4032   -0.9367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6334   -2.2764   -0.3304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8362   -2.4806    2.1114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3592   -1.6175    0.6212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1345    0.9575   -3.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8063   -1.8494   -0.1857 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3287   -5.2020   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9909   -4.9980    0.6491 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9562   -3.1156    0.0507 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 15  1  0
 15 17  1  0
 17 18  1  0
 15 13  1  0
 13 14  1  0
 13 12  2  0
 12 11  1  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
  8 33  1  0
 33 19  1  0
 19 20  1  0
 20 21  1  6
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  2  0
 20 30  1  0
 30 32  1  0
 30 31  2  0
  8  7  1  0
  7 34  1  0
 34 35  2  0
 35 36  1  0
 36 37  1  0
 35  3  1  0
  3  2  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
 19 11  1  0
  5  7  1  0
 16 45  1  0
 16 46  1  0
 15 44  1  6
 17 47  1  0
 17 48  1  0
 18 49  1  0
 14 43  1  0
 11 42  1  6
 10 41  1  0
  9 40  1  0
  8 39  1  1
 19 50  1  1
 21 51  1  0
 22 52  1  0
 22 53  1  0
 23 54  1  0
 23 55  1  0
 24 56  1  0
 24 57  1  0
 25 58  1  0
 27 59  1  0
 27 60  1  0
 28 29  1  0
 32 61  1  0
 34 62  1  0
 36 63  1  0
 36 64  1  0
 37 65  1  0
  2  1  1  0
  6 38  1  0
M  END


  Mrv1652309022221502D          

 35 36  0  0  1  0            999 V2000
   -1.4289    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1105   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  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   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 13  8  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 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
 16 24  1  0  0  0  0
 24 25  1  0  0  0  0
 15 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 13 28  1  0  0  0  0
 28 29  1  6  0  0  0
 29 30  2  0  0  0  0
 30 31  1  4  0  0  0
 30 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0161616

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CO)C(O)=N[C@H]1C=C[C@@H](O[C@@H]1[C@](O)(CCCNC(N)=N)C(O)=O)N1C=C(CO)C(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C19H30N8O8/c20-10(8-29)15(30)25-11-2-3-12(27-6-9(7-28)14(21)26-18(27)33)35-13(11)19(34,16(31)32)4-1-5-24-17(22)23/h2-3,6,10-13,28-29,34H,1,4-5,7-8,20H2,(H,25,30)(H,31,32)(H2,21,26,33)(H4,22,23,24)/t10-,11-,12+,13-,19+/m0/s1

> <INCHI_KEY>
GVLLATLXQPLOAJ-LGSFDMRSSA-N

> <FORMULA>
C19H30N8O8

> <MOLECULAR_WEIGHT>
498.497

> <EXACT_MASS>
498.218659958

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
49.298742543770494

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2S,3S,6R)-3-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid

> <ALOGPS_LOGP>
-3.12

> <JCHEM_LOGP>
-7.1758406241873

> <ALOGPS_LOGS>
-3.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
3.413316959977454

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7805706598854294

> <JCHEM_PKA_STRONGEST_BASIC>
11.925448384910199

> <JCHEM_POLAR_SURFACE_AREA>
287.41

> <JCHEM_REFRACTIVITY>
141.4345

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[(2S,3S,6R)-3-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  N   UNK     0      -2.667   6.160   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000   6.160   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.206  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.874  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.644  -2.104   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.644   0.564   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       8.002  -7.700   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       5.335  -7.700   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      -1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   13                                             
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    8   14   28                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   26                                                  
CONECT   16   15   17   24                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   16   25                                                  
CONECT   25   24                                                            
CONECT   26   15   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   13   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₃₀N₈O₈

Average Mass

498.4970 Da

Monoisotopic Mass

498.21866 Da

IUPAC Name

(2R)-2-[(2S,3S,6R)-3-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid

Traditional Name

(2R)-2-[(2S,3S,6R)-3-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CO)C(O)=N[C@H]1C=C[C@@H](O[C@@H]1[C@](O)(CCCNC(N)=N)C(O)=O)N1C=C(CO)C(=N)N=C1O

InChI Identifier

InChI=1S/C19H30N8O8/c20-10(8-29)15(30)25-11-2-3-12(27-6-9(7-28)14(21)26-18(27)33)35-13(11)19(34,16(31)32)4-1-5-24-17(22)23/h2-3,6,10-13,28-29,34H,1,4-5,7-8,20H2,(H,25,30)(H,31,32)(H2,21,26,33)(H4,22,23,24)/t10-,11-,12+,13-,19+/m0/s1

InChI Key

GVLLATLXQPLOAJ-LGSFDMRSSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Gamma amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid amide
Serine or derivatives
Gamma amino acid or derivatives
Alpha-amino acid or derivatives
Aminopyrimidine
Pyrimidone
Alpha-hydroxy acid
Hydropyrimidine
Hydroxy acid
Pyran
Pyrimidine
Imidolactam
Heteroaromatic compound
Tertiary alcohol
Secondary carboxylic acid amide
Carboxamide group
Amino acid
Guanidine
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Carboxylic acid
Monocarboxylic acid or derivatives
Aromatic alcohol
Organic oxygen compound
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Primary amine
Organic oxide
Alcohol
Amine
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	-3.1	ALOGPS
logP	-7.2	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	2.78	ChemAxon
pKa (Strongest Basic)	11.93	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	287.41 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	141.43 m³·mol⁻¹	ChemAxon
Polarizability	49.3 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

2330097

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3070418

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid (NP0161616)

MOL for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

3D MOL for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

3D SDF for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

3D-SDF for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

PDB for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

3D PDB for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

SMILES for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

INCHI for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

Structure for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)

3D Structure for NP0161616 ((2r)-2-[(2s,3s,6r)-3-{[(2s)-2-amino-1,3-dihydroxypropylidene]amino}-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2-hydroxypentanoic acid)