NP-MRD: Showing NP-Card for (r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0170313)

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Record Information

Version

1.0

Created at

2022-09-03 06:27:24 UTC

Updated at

2022-09-03 06:27:24 UTC

NP-MRD ID

NP0170313

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid

Description

Nikkomycin z, also known as neopolyoxin C, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. (r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid is found in Streptomyces tendae. It was first documented in 2022 (PMID: 35893139). Based on a literature review a significant number of articles have been published on nikkomycin z (PMID: 35788183) (PMID: 35648145) (PMID: 35601106) (PMID: 35533026).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032208272D          

 35 37  0  0  1  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    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   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5253   -5.4349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -6.2195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7553   -6.8870    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5758   -6.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0607   -7.4682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7252   -8.2219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2101   -8.8893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9047   -8.3081    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4197   -7.6407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5993   -7.7269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -6.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9605   -6.8870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -5.4349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4058   -5.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
    0.0000    0.0000    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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  4  0  0  0
  5  7  2  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 12  8  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  2  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 12 25  1  0  0  0  0
 25 26  1  6  0  0  0
  2 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 29 35  1  0  0  0  0
M  END

     RDKit          3D

 60 62  0  0  0  0  0  0  0  0999 V2000
    1.8924    1.0839    0.5368 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053   -0.0099    1.0710 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9376   -1.1427    1.5534 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6907   -2.2501    2.0809 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9717   -1.5523    0.5064 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.3011   -1.4647    0.6603 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1616   -1.8963   -0.4355 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9979   -3.3601   -0.5449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3116   -3.9960    0.3094 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5550   -4.1257   -1.5476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5999   -1.6123   -0.0673 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7650   -0.2192    0.1736 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1381   -0.1177    0.3589 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6005    1.2517    0.2196 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0731    2.1073   -0.6626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5730    3.3853   -0.7263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5988    3.8174    0.0866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0994    5.1311    0.0081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1030    2.9300    0.9599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6016    1.6820    1.0092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1169    0.8765    1.8580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7835   -1.0362   -0.6289 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.5277   -1.9784    0.0476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5701   -1.7866   -1.2056 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9100   -3.1080   -1.4660 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8281   -0.4677    0.0843 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5840   -1.4692    0.7136 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8093    0.6202   -0.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0358    0.3139   -0.7979 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9305    1.2976   -1.0944 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6279    2.6183   -0.8432 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5389    3.6331   -1.1439 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4067    2.9116   -0.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5480    1.9188   -0.0087 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3028    2.0954    0.7580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9433    1.0145    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6583    0.9464   -0.5366 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3261    0.4794    1.9517 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3701   -0.7162    2.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9419   -2.9774    1.4037 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4571   -1.9653    2.6946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0638   -2.8652   -0.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8498   -1.3937   -1.3470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9506   -4.4151   -2.3033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9356   -2.2032    0.7818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3301   -0.4152    1.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2685    1.7610   -1.2969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1564    4.0898   -1.4354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3828    5.8624   -0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3402   -0.5220   -1.4261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0993   -1.6408    0.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2738   -1.2333   -2.1135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2976   -3.1064   -2.3964 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4444   -0.8746   -0.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9148   -2.1442    0.0668 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2947   -0.7296   -1.0049 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8848    1.0449   -1.5298 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4649    4.0319   -2.0800 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1280    3.9396   -0.0747 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 21 22  2  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
  2 27  1  0
 27 28  1  0
 27 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  0
 32 33  1  0
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 34 35  2  0
 25 12  1  0
 21 15  1  0
 35 29  1  0
  1 36  1  0
  1 37  1  0
  1 38  1  0
  2 39  1  1
  3 40  1  1
  4 41  1  0
  4 42  1  0
  6 43  1  0
  8 44  1  6
 12 46  1  1
 14 47  1  1
 23 51  1  6
 24 52  1  0
 25 53  1  6
 26 54  1  0
 16 48  1  0
 17 49  1  0
 19 50  1  0
 11 45  1  0
 27 55  1  6
 28 56  1  0
 30 57  1  0
 31 58  1  0
 33 59  1  0
 34 60  1  0
M  END


  Mrv1652309032208272D          

 35 37  0  0  1  0            999 V2000
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    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   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5253   -5.4349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -6.2195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7553   -6.8870    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5758   -6.8007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0607   -7.4682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7252   -8.2219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2101   -8.8893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9047   -8.3081    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4197   -7.6407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5993   -7.7269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -6.2195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9605   -6.8870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904   -5.4349    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4058   -5.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
    0.0000    0.0000    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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  4  0  0  0
  5  7  2  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 12  8  1  1  0  0  0
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 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  2  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 12 25  1  0  0  0  0
 25 26  1  6  0  0  0
  2 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 29 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0170313

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H](N)C(O)=N[C@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(O)=NC1=O)C(O)=O)[C@H](O)C1=CC=C(O)C=N1

> <INCHI_IDENTIFIER>
InChI=1S/C20H25N5O10/c1-7(13(28)9-3-2-8(26)6-22-9)11(21)17(31)24-12(19(32)33)16-14(29)15(30)18(35-16)25-5-4-10(27)23-20(25)34/h2-7,11-16,18,26,28-30H,21H2,1H3,(H,24,31)(H,32,33)(H,23,27,34)/t7-,11-,12+,13-,14-,15+,16+,18+/m0/s1

> <INCHI_KEY>
WWJFFVUVFNBJTN-JKEIIPFCSA-N

> <FORMULA>
C20H25N5O10

> <MOLECULAR_WEIGHT>
495.445

> <EXACT_MASS>
495.160142025

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
46.012581124866934

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-{[(2S,3S,4S)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}-2-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetic acid

> <ALOGPS_LOGP>
-1.65

> <JCHEM_LOGP>
-5.188007336841811

> <ALOGPS_LOGS>
-3.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.119300297604386

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4315708328301024

> <JCHEM_PKA_STRONGEST_BASIC>
9.72125452719228

> <JCHEM_POLAR_SURFACE_AREA>
251.84999999999997

> <JCHEM_REFRACTIVITY>
112.67899999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.52e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-{[(2S,3S,4S)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       4.001  -6.930   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.581 -10.145   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.105 -11.610   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       7.010 -12.856   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       8.541 -12.695   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.447 -13.941   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.820 -15.347   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       9.725 -16.593   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0       7.289 -15.508   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       6.384 -14.263   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.852 -14.424   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.565 -11.610   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.660 -12.856   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.089 -10.145   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.624  -9.669   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13   25                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   23                                                  
CONECT   15   14   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   15   22                                                  
CONECT   22   21                                                            
CONECT   23   14   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   12   26                                                  
CONECT   26   25                                                            
CONECT   27    2   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   35                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   29                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Value	Source
Neopolyoxin C	MeSH
Nikkomycin	MeSH

Chemical Formula

C₂₀H₂₅N₅O₁₀

Average Mass

495.4450 Da

Monoisotopic Mass

495.16014 Da

IUPAC Name

(2R)-2-{[(2S,3S,4S)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}-2-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetic acid

Traditional Name

(R)-{[(2S,3S,4S)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H](N)C(O)=N[C@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(O)=NC1=O)C(O)=O)[C@H](O)C1=CC=C(O)C=N1

InChI Identifier

InChI=1S/C20H25N5O10/c1-7(13(28)9-3-2-8(26)6-22-9)11(21)17(31)24-12(19(32)33)16-14(29)15(30)18(35-16)25-5-4-10(27)23-20(25)34/h2-7,11-16,18,26,28-30H,21H2,1H3,(H,24,31)(H,32,33)(H,23,27,34)/t7-,11-,12+,13-,14-,15+,16+,18+/m0/s1

InChI Key

WWJFFVUVFNBJTN-JKEIIPFCSA-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
Streptomyces tendae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
5'-deoxyribonucleoside
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Glycosyl compound
N-glycosyl compound
Alpha-amino acid or derivatives
Hydroxypyridine
Pyrimidone
Aralkylamine
Fatty amide
Hydropyrimidine
N-acyl-amine
Pyridine
Pyrimidine
Fatty acyl
Oxolane
Vinylogous amide
Heteroaromatic compound
1,3-aminoalcohol
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Urea
Carboxamide group
Lactam
Amino acid
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Alcohol
Organic oxide
Primary aliphatic amine
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organonitrogen compound
Aromatic alcohol
Organooxygen compound
Primary amine
Organic oxygen compound
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	-1.6	ALOGPS
logP	-5.2	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	2.43	ChemAxon
pKa (Strongest Basic)	9.72	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	251.85 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	112.68 m³·mol⁻¹	ChemAxon
Polarizability	46.01 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

8111154

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9935526

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Poester VR, Munhoz LS, Benelli JL, Melo AM, Al-Hatmi AMS, Larwood DJ, Martinez M, Stevens DA, Xavier MO: Initial Results of the International Efforts in Screening New Agents against Candida auris. J Fungi (Basel). 2022 Jul 25;8(8):771. doi: 10.3390/jof8080771. [PubMed:35893139 ]
Ren Z, Chhetri A, Guan Z, Suo Y, Yokoyama K, Lee SY: Structural basis for inhibition and regulation of a chitin synthase from Candida albicans. Nat Struct Mol Biol. 2022 Jul;29(7):653-664. doi: 10.1038/s41594-022-00791-x. Epub 2022 Jul 4. [PubMed:35788183 ]
Khatoon R, Sharma S, Prasad R, Lynn AM, Prakash A, Banerjee A: Genome-wide analysis of PTR transporters in Candida species and their functional characterization in Candida auris. Appl Microbiol Biotechnol. 2022 Jun;106(11):4223-4235. doi: 10.1007/s00253-022-11998-9. Epub 2022 Jun 1. [PubMed:35648145 ]
Brandt P, Gerwien F, Wagner L, Kruger T, Ramirez-Zavala B, Mirhakkak MH, Schauble S, Kniemeyer O, Panagiotou G, Brakhage AA, Morschhauser J, Vylkova S: Candida albicans SR-Like Protein Kinases Regulate Different Cellular Processes: Sky1 Is Involved in Control of Ion Homeostasis, While Sky2 Is Important for Dipeptide Utilization. Front Cell Infect Microbiol. 2022 May 6;12:850531. doi: 10.3389/fcimb.2022.850531. eCollection 2022. [PubMed:35601106 ]
Khalfe Y, Rosen T: Future Fungal Fighters in Dermatology: Novel Antifungal Drug Pipeline. J Drugs Dermatol. 2022 May 1;21(5):496-501. doi: 10.36849/JDD.6373. [PubMed:35533026 ]
LOTUS database [Link]

Showing NP-Card for (r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0170313)

MOL for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D MOL for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D SDF for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D-SDF for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

PDB for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D PDB for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

SMILES for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

INCHI for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

Structure for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D Structure for NP0170313 ((r)-{[(2s,3s,4s)-2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)