NP-MRD: Showing NP-Card for (s)-{[(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 (NP0231542)

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Record Information

Version

1.0

Created at

2022-09-06 12:27:16 UTC

Updated at

2022-09-06 12:27:16 UTC

NP-MRD ID

NP0231542

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(s)-{[(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. Nikkomycin Z is a very strong basic compound (based on its pKa). (s)-{[(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 ansochromogenes, Streptomyces cacaoi and Streptomyces tendae. It was first documented in 1991 (PMID: 1992114). A uridine-based nucleoside-peptide antibiotic which inhibits fungal chitin biosynthesis by inhibiting chitin synthase (PMID: 19930628) (PMID: 10888330) (PMID: 12205060) (PMID: 12729648).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310211603292D          

 35 37  0  0  1  0            999 V2000
    2.6552   -7.7058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3852   -6.9263    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5751   -6.7704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0350   -7.3940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3050   -8.1736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -8.7972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0452   -8.6413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3152   -7.8618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2248   -7.2381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5853   -9.2650    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3050   -5.9908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9253   -6.3027    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7354   -6.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0055   -7.2381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -5.8349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0856   -5.9908    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6257   -5.3672    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4387   -4.5637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1450   -4.1375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.7687   -4.6776    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4477   -5.4376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5722   -4.4905    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8119   -3.7011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6154   -3.5140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1792   -4.1163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9827   -3.9292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9395   -4.9057    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1359   -5.0928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8962   -5.8822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2154   -3.3155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6786   -4.2427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3557   -6.7704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1658   -6.9263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8156   -7.3940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6552   -5.5231    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  7 10  1  0  0  0  0
  3 11  1  1  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 16 15  1  1  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 21  1  0  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 28 29  2  0  0  0  0
 19 30  1  1  0  0  0
 18 31  1  1  0  0  0
 16 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 12 35  1  6  0  0  0
M  END

     RDKit          3D

 60 62  0  0  0  0  0  0  0  0999 V2000
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    0.7867    2.1094   -1.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0249    2.5449   -1.9266 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7565    2.9793   -0.6011 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1209    0.0875   -0.7840 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1480    0.8020   -0.1721 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2318   -0.0506   -0.3680 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4259    0.3942    0.2903 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5757    0.3539    1.6087 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7676    0.8041    2.1858 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8057    1.2947    1.4216 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8831    1.7020    1.9385 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6004    1.3136    0.0822 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4532    0.8796   -0.4643 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2974    0.9122   -1.7165 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7093   -1.3644    0.1508 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3668   -2.3831   -0.5380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2317   -1.2981   -0.2557 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0435   -2.1999   -1.2858 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0885    0.6222   -0.7137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1123    1.4748   -0.2306 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0663    0.1495    0.2709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5182    1.0095    1.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4432    0.6313    2.2107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9881   -0.6350    2.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9320   -1.0470    3.1255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5341   -1.4700    1.1918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6228   -1.0721    0.2933 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3170   -0.5271   -3.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2985    1.1451   -2.5643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7072    0.5494   -3.4416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2870   -1.0802   -1.9757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1393   -2.0925   -1.5665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9441   -1.4286    1.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9469   -2.9252    0.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3112   -0.0940   -2.2134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6379    0.7348    0.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6901    3.0473   -1.0166 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3192    0.1207   -1.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3952   -0.1569   -1.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7818   -0.0254    2.2464 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8919    0.7711    3.2753 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3922    1.6873   -0.4950 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7619   -1.4743    1.2357 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3271   -2.1238   -0.5615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5905   -1.5005    0.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6902    1.2826   -1.4331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3750    2.4308   -0.2445 H   0  0  0  0  0  0  0  0  0  0  0  0
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  3  5  1  0
  5  6  2  0
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 16 17  2  0
 17 18  1  0
 18 19  2  0
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 21 22  2  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
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 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  6
  3 40  1  6
  4 41  1  0
  4 42  1  0
  7 43  1  0
  8 44  1  1
 12 46  1  6
 14 47  1  6
 23 51  1  1
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 25 53  1  1
 26 54  1  0
 16 48  1  0
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 20 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


  Mrv1652310211603292D          

 35 37  0  0  1  0            999 V2000
    2.6552   -7.7058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3852   -6.9263    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5751   -6.7704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0350   -7.3940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3050   -8.1736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -8.7972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0452   -8.6413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3152   -7.8618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2248   -7.2381    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5853   -9.2650    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3050   -5.9908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9253   -6.3027    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7354   -6.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0055   -7.2381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -5.8349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0856   -5.9908    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6257   -5.3672    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4387   -4.5637    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1450   -4.1375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.7687   -4.6776    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4477   -5.4376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5722   -4.4905    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8119   -3.7011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6154   -3.5140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1792   -4.1163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9827   -3.9292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9395   -4.9057    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1359   -5.0928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8962   -5.8822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2154   -3.3155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6786   -4.2427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3557   -6.7704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1658   -6.9263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8156   -7.3940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6552   -5.5231    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  7 10  1  0  0  0  0
  3 11  1  1  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
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 16 15  1  1  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
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 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 21  1  0  0  0  0
 20 22  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 28 29  2  0  0  0  0
 19 30  1  1  0  0  0
 18 31  1  1  0  0  0
 16 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 12 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0231542

> <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-VHDFTHOZSA-N

> <FORMULA>
C20H25N5O10

> <MOLECULAR_WEIGHT>
495.445

> <EXACT_MASS>
495.160142025

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
46.27074907662167

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanamido]-2-[(2R,3S,4R,5R)-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>
244.86999999999998

> <JCHEM_REFRACTIVITY>
111.83559999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nikkomycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-OCT-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-OCT-16         0                                  
HETATM    1  C   UNK     0       4.956 -14.384   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.452 -12.929   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.940 -12.638   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.932 -13.802   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.436 -15.257   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.428 -16.421   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.084 -16.130   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.588 -14.675   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.420 -13.511   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -1.093 -17.295   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.436 -11.183   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.461 -11.765   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.973 -12.056   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.477 -13.511   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       7.981 -10.892   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       9.493 -11.183   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.501 -10.019   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.152  -8.519   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.471  -7.723   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.635  -8.731   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.036 -10.150   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0      14.135  -8.382   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      14.582  -6.909   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      16.082  -6.559   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      17.134  -7.684   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      18.634  -7.335   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0      16.687  -9.157   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      15.187  -9.507   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      14.740 -10.980   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      11.602  -6.189   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       8.733  -7.920   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.997 -12.638   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      11.510 -12.929   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.989 -13.802   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0       4.956 -10.310   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    7                                                            
CONECT   11    3                                                            
CONECT   12    2   13   35                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   32                                                  
CONECT   17   16   18   21                                                  
CONECT   18   17   19   31                                                  
CONECT   19   18   20   30                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   17                                                       
CONECT   22   20   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   22   29                                                  
CONECT   29   28                                                            
CONECT   30   19                                                            
CONECT   31   18                                                            
CONECT   32   16   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   12                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Value	Source
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-beta-D-allo-furanuronic acid	ChEBI
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]acetic acid	ChEBI
Neopolyoxin C	ChEBI
Nikkomycin	ChEBI
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-b-D-allo-furanuronate	Generator
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-b-D-allo-furanuronic acid	Generator
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-beta-D-allo-furanuronate	Generator
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-β-D-allo-furanuronate	Generator
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-β-D-allo-furanuronic acid	Generator
(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]acetate	Generator

Chemical Formula

C₂₀H₂₅N₅O₁₀

Average Mass

495.4450 Da

Monoisotopic Mass

495.16014 Da

IUPAC Name

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

Traditional Name

nikkomycin

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-VHDFTHOZSA-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 ansochromogenes	LOTUS Database	35616633
Streptomyces cacaoi	LOTUS Database	35616633
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
N-acyl-l-alpha-amino acid
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
Tetrahydrofuran
Heteroaromatic compound
Vinylogous amide
1,3-aminoalcohol
Urea
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Carboxamide group
Amino acid
Lactam
Azacycle
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Alcohol
Organic oxide
Organopnictogen compound
Primary aliphatic amine
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Aromatic alcohol
Organonitrogen compound
Organooxygen compound
Primary amine
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nikkomycin (CHEBI:623918 )

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	46.27 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

DB12939

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

456557

PDB ID

Not Available

ChEBI ID

623918

Good Scents ID

Not Available

References

General References

Liao G, Li J, Li L, Yang H, Tian Y, Tan H: Selectively improving nikkomycin Z production by blocking the imidazolone biosynthetic pathway of nikkomycin X and uracil feeding in Streptomyces ansochromogenes. Microb Cell Fact. 2009 Nov 23;8:61. doi: 10.1186/1475-2859-8-61. [PubMed:19930628 ]
Obi K, Uda J, Iwase K, Sugimoto O, Ebisu H, Matsuda A: Novel nikkomycin analogues: inhibitors of the fungal cell wall biosynthesis enzyme chitin synthase. Bioorg Med Chem Lett. 2000 Jul 3;10(13):1451-4. doi: 10.1016/s0960-894x(00)00256-0. [PubMed:10888330 ]
Stevens DA, Calderon L, Martinez M, Clemons KV, Wilson SJ, Selitrennikoff CP: Zeamatin, clotrimazole and nikkomycin Z in therapy of a Candida vaginitis model. J Antimicrob Chemother. 2002 Sep;50(3):361-4. doi: 10.1093/jac/dkf136. [PubMed:12205060 ]
Behr JB, Gourlain T, Helimi A, Guillerm G: Design, synthesis and biological evaluation of hetaryl-nucleoside derivatives as inhibitors of chitin synthase. Bioorg Med Chem Lett. 2003 May 19;13(10):1713-6. doi: 10.1016/s0960-894x(03)00239-7. [PubMed:12729648 ]
Krainer E, Becker JM, Naider F: Synthesis and biological evaluation of dipeptidyl and tripeptidyl polyoxin and nikkomycin analogues as anticandidal prodrugs. J Med Chem. 1991 Jan;34(1):174-80. doi: 10.1021/jm00105a026. [PubMed:1992114 ]
LOTUS database [Link]

Showing NP-Card for (s)-{[(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 (NP0231542)

MOL for NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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 NP0231542 ((s)-{[(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)