NP-MRD: Showing NP-Card for {[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0274375)

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Record Information

Version

1.0

Created at

2022-09-08 21:44:58 UTC

Updated at

2022-09-08 21:44:58 UTC

NP-MRD ID

NP0274375

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[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 hydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing at least hydroxyl group. {[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid is found in Streptomyces cacaoi. Nikkomycin z is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161505252D          

 35 37  0  0  0  0            999 V2000
    6.2728   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -3.8684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0028   -3.2448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2728   -2.4652    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -3.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9226   -4.1802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6525   -2.7770    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8424   -2.9329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3023   -2.3093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4803   -2.3797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1594   -1.6197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7830   -1.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7126   -0.2576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4894   -1.5058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2494   -1.1849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3559   -1.4326    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7921   -2.0349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0114   -1.8478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2511   -1.0584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0547   -0.8713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3126   -0.4561    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1161   -0.6432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6799   -0.0409    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
    4.1124   -4.3361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7622   -3.8684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3530   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -2.9329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -4.3361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7032   -4.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2433   -4.8039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9732   -5.5834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5133   -6.2071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1631   -5.7393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -5.1157    0.0000 N   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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 16  1  0  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  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  2  0  0  0  0
  8 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  2 27  1  0  0  0  0
 27 28  1  0  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
    3.4023   -2.4818   -1.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4070   -1.2525   -0.3000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6774   -0.4755   -0.4698 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7994   -1.2686   -0.1254 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6873    0.7178    0.4387 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4863    1.9936   -0.0360 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5008    3.0660    0.8303 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7207    2.8211    2.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7303    3.9227    3.0259 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9192    1.5581    2.6385 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8961    0.5469    1.7571 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1774   -0.4493   -0.6151 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2004   -0.0777   -2.0005 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9436   -1.1804   -0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8108   -1.5551    0.9486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0905   -1.4729   -1.1642 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2815   -2.1893   -0.7593 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3915   -3.4182   -1.5822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5108   -3.6492   -2.4447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4211   -4.3444   -1.4589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4818   -1.3353   -1.0722 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4648   -0.0986   -0.4201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7888    0.3434   -0.6454 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0616    1.5659    0.0436 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1589    2.2594   -0.2690 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4696    3.4608    0.3763 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6275    3.9291    1.3468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8310    5.0111    1.9850 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5265    3.2124    1.6453 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2461    2.0436    1.0012 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2238    1.3669    1.2702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5783   -0.8348   -0.1268 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5211   -0.7636    1.2763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7581   -2.0102   -0.6165 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5076   -2.9019    0.4367 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3315   -3.0539   -0.9414 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4223   -2.1236   -2.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5529   -3.1332   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3269   -1.5746    0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8287   -0.1770   -1.5202 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1607   -1.7338   -0.9188 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3190    2.1712   -1.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3403    4.0444    0.4224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6341    4.3635    3.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0921    1.3840    3.7066 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1488    0.5007   -0.0212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0306    0.4981   -2.1862 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3419    0.4520   -2.2906 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0527   -1.1440   -2.1539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1954   -2.4213    0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2566   -5.2400   -1.0421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5122   -1.1392   -2.1508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9351    0.4486   -1.7376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8488    1.9263   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3497    4.0303    0.1351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8895    3.5644    2.3779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6131   -0.8554   -0.4927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7430   -1.2634    1.6279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2702   -2.5041   -1.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3867   -3.0794    0.8583 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 21  1  0
 21 22  1  0
 22 23  1  0
 23 32  1  0
 32 33  1  0
 32 34  1  0
 34 35  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  2  0
 27 29  1  0
 29 30  1  0
 30 31  2  0
 17 18  1  0
 18 20  1  0
 18 19  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 34 21  1  0
 30 24  1  0
 11  5  1  0
  1 36  1  0
  1 37  1  0
  1 38  1  0
  2 39  1  1
 12 46  1  1
 13 47  1  0
 13 48  1  0
 16 49  1  0
 17 50  1  1
 21 52  1  6
 23 53  1  6
 32 57  1  1
 33 58  1  0
 34 59  1  6
 35 60  1  0
 25 54  1  0
 26 55  1  0
 29 56  1  0
 20 51  1  0
  3 40  1  6
  4 41  1  0
  6 42  1  0
  7 43  1  0
  9 44  1  0
 10 45  1  0
M  END


  Mrv1533004161505252D          

 35 37  0  0  0  0            999 V2000
    6.2728   -4.6480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -3.8684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0028   -3.2448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2728   -2.4652    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -3.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9226   -4.1802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6525   -2.7770    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8424   -2.9329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3023   -2.3093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4803   -2.3797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1594   -1.6197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7830   -1.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7126   -0.2576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4894   -1.5058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2494   -1.1849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3559   -1.4326    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7921   -2.0349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0114   -1.8478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2511   -1.0584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0547   -0.8713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3126   -0.4561    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1161   -0.6432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6799   -0.0409    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
    4.1124   -4.3361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7622   -3.8684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3530   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -2.9329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -4.3361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7032   -4.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2433   -4.8039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9732   -5.5834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5133   -6.2071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1631   -5.7393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -5.1157    0.0000 N   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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 16  1  0  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  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  2  0  0  0  0
  8 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  2 27  1  0  0  0  0
 27 28  1  0  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>
NP0274375

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C(N)C(=O)NC(C1OC(C(O)C1O)N1C=CC(=O)NC1=O)C(O)=O)C(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)

> <INCHI_KEY>
WWJFFVUVFNBJTN-UHFFFAOYSA-N

> <FORMULA>
C20H25N5O10

> <MOLECULAR_WEIGHT>
495.445

> <EXACT_MASS>
495.160142025

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
46.02586145644875

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanamido]-2-[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <ALOGPS_LOGP>
-1.21

> <JCHEM_LOGP>
-5.649640293748052

> <ALOGPS_LOGS>
-2.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.762563337801057

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6059540645366353

> <JCHEM_PKA_STRONGEST_BASIC>
7.7681436275681355

> <JCHEM_POLAR_SURFACE_AREA>
244.86999999999995

> <JCHEM_REFRACTIVITY>
111.83559999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanamido][5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0      11.709  -8.676   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.213  -7.221   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.205  -6.057   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      11.709  -4.602   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       9.693  -6.348   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.189  -7.803   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       8.685  -5.184   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       7.172  -5.475   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.164  -4.311   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.630  -4.442   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.031  -3.023   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.195  -2.015   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.064  -0.481   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.514  -2.811   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.932  -2.212   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       2.531  -2.674   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.479  -3.798   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.021  -3.449   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.469  -1.976   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.969  -1.627   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       0.584  -0.851   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.083  -1.201   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.136  -0.076   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       7.677  -8.094   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.156  -7.221   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      13.726  -6.930   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      14.230  -5.475   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      14.734  -8.094   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      16.246  -7.803   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      17.254  -8.967   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      16.750 -10.422   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      17.758 -11.587   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      15.238 -10.713   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      14.230  -9.549   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   24                                                  
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    9   15                                                  
CONECT   15   14                                                            
CONECT   16   11   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   16   23                                                  
CONECT   23   22                                                            
CONECT   24    8   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
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
Nikkomycin Z	MeSH
2-{[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetate	Generator

Chemical Formula

C₂₀H₂₅N₅O₁₀

Average Mass

495.4450 Da

Monoisotopic Mass

495.16014 Da

IUPAC Name

2-[2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanamido]-2-[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

Traditional Name

[2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanamido][5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

CC(C(N)C(=O)NC(C1OC(C(O)C1O)N1C=CC(=O)NC1=O)C(O)=O)C(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)

InChI Key

WWJFFVUVFNBJTN-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces cacaoi	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing at least hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Hydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Hexahydroxy bile acid, alcohol, or derivatives
26-hydroxysteroid
25-hydroxysteroid
Hydroxy bile acid, alcohol, or derivatives
16-hydroxysteroid
3-hydroxysteroid
6-hydroxysteroid
15-hydroxysteroid
5-hydroxysteroid
Hydroxysteroid
Fatty alcohol
Fatty acyl
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Polyol
Hydrocarbon derivative
Organooxygen compound
Primary alcohol
Organic oxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	-1.2	ALOGPS
logP	-5.6	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.61	ChemAxon
pKa (Strongest Basic)	7.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	244.87 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	111.84 m³·mol⁻¹	ChemAxon
Polarizability	46.03 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

353481

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0274375)

MOL for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D MOL for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D SDF for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D-SDF for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

PDB for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D PDB for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

SMILES for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

INCHI for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

Structure for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D Structure for NP0274375 ({[2-amino-1,4-dihydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutylidene]amino}[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)