NP-MRD: Showing NP-Card for Nikkomycin Lz (NP0001757)

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Record Information

Version

2.0

Created at

2020-10-21 16:13:27 UTC

Updated at

2021-07-15 16:45:11 UTC

NP-MRD ID

NP0001757

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nikkomycin Lz

Provided By

NPAtlas

Description

Nikkomycin Lz is found in Streptomyces tendae. Based on a literature review very few articles have been published on 2-{[2-amino-1,4-dihydroxy-3-methyl-4-(pyridin-2-yl)butylidene]amino}-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117443D          

 59 61  0  0  0  0            999 V2000
   -1.5799    0.3661   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8142   -0.2655   -0.1215 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5565   -1.7485    0.0365 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2667   -2.3432   -1.2513 N   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3311   -1.8874    0.8870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3824   -1.4279    2.0539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1554   -2.4985    0.4359 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9933   -2.6049    1.2958 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3183   -4.0467    1.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -4.9705    0.9599 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3961   -4.3980    2.2869 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1843   -1.9756    0.6124 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9450   -0.6131    0.3360 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2133   -0.2489   -0.1548 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3363    1.1386   -0.4335 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8910    1.5320   -1.6113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071    2.8809   -1.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5749    3.8407   -0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6733    5.0784   -1.1989 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0361    3.3786    0.1708 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9142    2.0711    0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4040    1.6530    1.5300 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2051   -0.7921    0.8267 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2833   -1.4179    0.1667 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3920   -1.8894    1.5190 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9916   -1.5057    2.7788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558    0.0297   -0.9101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1192   -0.6137   -0.2566 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2676    1.5068   -0.8623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5246    2.0023   -1.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6492    4.2014   -0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4087    3.6734   -0.4946 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2225   -3.3829   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0272   -2.1464   -1.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
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  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  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
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 18 20  1  0  0  0  0
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 14 23  1  0  0  0  0
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  2 27  1  0  0  0  0
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M  END

     RDKit          3D

 59 61  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306242117443D          

 59 61  0  0  0  0            999 V2000
   -1.5799    0.3661   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8142   -0.2655   -0.1215 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -4.2676    1.5068   -0.8623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5246    2.0023   -1.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    3.3716   -1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6492    4.2014   -0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4087    3.6734   -0.4946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2444    2.3421   -0.5442 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -0.3727   -0.8595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503    0.8267   -1.6986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    1.1620   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9224    0.1591    0.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3952   -2.2577    0.5586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2225   -3.3829   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0272   -2.1464   -1.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0722   -2.8928   -0.5269 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8434   -2.1753    2.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9400   -5.2460    2.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -2.4931   -0.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3329   -0.8435   -1.0987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2324    0.7670   -2.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4441    3.2292   -2.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832    4.0541    0.9075 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075   -0.0613    1.5219 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4791   -2.3131    0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9646   -2.8407    1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2982   -0.8170    2.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9353   -0.3206   -1.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9294   -0.5943    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3409    1.3603   -1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7037    3.7533   -1.3286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8282    5.2814   -0.7458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6020    4.3447   -0.2430 H   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  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  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  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 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
 33 34  2  0  0  0  0
 25 12  1  0  0  0  0
 34 29  1  0  0  0  0
 21 15  1  0  0  0  0
  1 35  1  0  0  0  0
  1 36  1  0  0  0  0
  1 37  1  0  0  0  0
  2 38  1  1  0  0  0
  3 39  1  1  0  0  0
  4 40  1  0  0  0  0
  4 41  1  0  0  0  0
  7 42  1  0  0  0  0
  8 43  1  1  0  0  0
 11 44  1  0  0  0  0
 12 45  1  6  0  0  0
 14 46  1  6  0  0  0
 16 47  1  0  0  0  0
 17 48  1  0  0  0  0
 20 49  1  0  0  0  0
 23 50  1  1  0  0  0
 24 51  1  0  0  0  0
 25 52  1  1  0  0  0
 26 53  1  0  0  0  0
 27 54  1  6  0  0  0
 28 55  1  0  0  0  0
 30 56  1  0  0  0  0
 31 57  1  0  0  0  0
 32 58  1  0  0  0  0
 33 59  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001757

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]([H])(N([H])C(=O)[C@]([H])(N([H])[H])[C@@]([H])(C([H])([H])[H])[C@@]([H])(O[H])C1=C([H])C([H])=C([H])C([H])=N1)[C@@]1([H])O[C@@]([H])(N2C([H])=C([H])C(=O)N([H])C2=O)[C@]([H])(O[H])[C@@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H25N5O9/c1-8(13(27)9-4-2-3-6-22-9)11(21)17(30)24-12(19(31)32)16-14(28)15(29)18(34-16)25-7-5-10(26)23-20(25)33/h2-8,11-16,18,27-29H,21H2,1H3,(H,24,30)(H,31,32)(H,23,26,33)/t8-,11-,12-,13-,14-,15-,16-,18-/m1/s1

> <INCHI_KEY>
HYBLVRJOBLCCCY-UHFFFAOYSA-N

> <FORMULA>
C20H25N5O9

> <MOLECULAR_WEIGHT>
479.446

> <EXACT_MASS>
479.165227405

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
45.56345467393812

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2R,3R,4R)-2-amino-4-hydroxy-3-methyl-4-(pyridin-2-yl)butanamido]-2-[(2R,3R,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <ALOGPS_LOGP>
-0.77

> <JCHEM_LOGP>
-5.343123830889337

> <ALOGPS_LOGS>
-2.22

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.70723406981662

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7153982055750108

> <JCHEM_PKA_STRONGEST_BASIC>
7.959766026224148

> <JCHEM_POLAR_SURFACE_AREA>
224.64

> <JCHEM_REFRACTIVITY>
109.85470000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-[(2R,3R,4R)-2-amino-4-hydroxy-3-methyl-4-(pyridin-2-yl)butanamido][(2R,3R,4R,5R)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 59 61  0  0  0  0  0  0  0  0999 V2000
   -1.5799    0.3661   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8142   -0.2655   -0.1215 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5565   -1.7485    0.0365 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2667   -2.3432   -1.2513 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3311   -1.8874    0.8870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3824   -1.4279    2.0539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1554   -2.4985    0.4359 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9933   -2.6049    1.2958 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3183   -4.0467    1.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -4.9705    0.9599 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3961   -4.3980    2.2869 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1843   -1.9756    0.6124 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9450   -0.6131    0.3360 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2133   -0.2489   -0.1548 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3363    1.1386   -0.4335 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8910    1.5320   -1.6113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071    2.8809   -1.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5749    3.8407   -0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6733    5.0784   -1.1989 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0361    3.3786    0.1708 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9142    2.0711    0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4040    1.6530    1.5300 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2051   -0.7921    0.8267 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2833   -1.4179    0.1667 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3920   -1.8894    1.5190 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9916   -1.5057    2.7788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558    0.0297   -0.9101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1192   -0.6137   -0.2566 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2676    1.5068   -0.8623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5246    2.0023   -1.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    3.3716   -1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6492    4.2014   -0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4087    3.6734   -0.4946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2444    2.3421   -0.5442 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -0.3727   -0.8595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503    0.8267   -1.6986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    1.1620   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9224    0.1591    0.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3952   -2.2577    0.5586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2225   -3.3829   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0272   -2.1464   -1.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0722   -2.8928   -0.5269 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8434   -2.1753    2.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9400   -5.2460    2.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -2.4931   -0.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3329   -0.8435   -1.0987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2324    0.7670   -2.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4441    3.2292   -2.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832    4.0541    0.9075 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075   -0.0613    1.5219 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4791   -2.3131    0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9646   -2.8407    1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2982   -0.8170    2.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9353   -0.3206   -1.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9294   -0.5943    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3409    1.3603   -1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7037    3.7533   -1.3286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8282    5.2814   -0.7458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6020    4.3447   -0.2430 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  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  2  0
 14 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  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
 33 34  2  0
 25 12  1  0
 34 29  1  0
 21 15  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  2 38  1  1
  3 39  1  1
  4 40  1  0
  4 41  1  0
  7 42  1  0
  8 43  1  1
 11 44  1  0
 12 45  1  6
 14 46  1  6
 16 47  1  0
 17 48  1  0
 20 49  1  0
 23 50  1  1
 24 51  1  0
 25 52  1  1
 26 53  1  0
 27 54  1  6
 28 55  1  0
 30 56  1  0
 31 57  1  0
 32 58  1  0
 33 59  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.580   0.366  -0.709  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.814  -0.266  -0.122  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.557  -1.749   0.037  0.00  0.00           C+0
HETATM    4  N   UNK     0      -2.267  -2.343  -1.251  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.331  -1.887   0.887  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.382  -1.428   2.054  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.155  -2.498   0.436  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.993  -2.605   1.296  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.318  -4.047   1.488  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.661  -4.971   0.960  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.396  -4.398   2.287  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.184  -1.976   0.612  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.945  -0.613   0.336  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.213  -0.249  -0.155  0.00  0.00           C+0
HETATM   15  N   UNK     0       3.336   1.139  -0.434  0.00  0.00           N+0
HETATM   16  C   UNK     0       3.891   1.532  -1.611  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.007   2.881  -1.875  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.575   3.841  -0.974  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.673   5.078  -1.199  0.00  0.00           O+0
HETATM   20  N   UNK     0       3.036   3.379   0.171  0.00  0.00           N+0
HETATM   21  C   UNK     0       2.914   2.071   0.446  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.404   1.653   1.530  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.205  -0.792   0.827  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.283  -1.418   0.167  0.00  0.00           O+0
HETATM   25  C   UNK     0       3.392  -1.889   1.519  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.992  -1.506   2.779  0.00  0.00           O+0
HETATM   27  C   UNK     0      -4.056   0.030  -0.910  0.00  0.00           C+0
HETATM   28  O   UNK     0      -5.119  -0.614  -0.257  0.00  0.00           O+0
HETATM   29  C   UNK     0      -4.268   1.507  -0.862  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.525   2.002  -1.149  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.726   3.372  -1.106  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.649   4.201  -0.774  0.00  0.00           C+0
HETATM   33  C   UNK     0      -3.409   3.673  -0.495  0.00  0.00           C+0
HETATM   34  N   UNK     0      -3.244   2.342  -0.544  0.00  0.00           N+0
HETATM   35  H   UNK     0      -0.752  -0.373  -0.860  0.00  0.00           H+0
HETATM   36  H   UNK     0      -1.750   0.827  -1.699  0.00  0.00           H+0
HETATM   37  H   UNK     0      -1.154   1.162  -0.058  0.00  0.00           H+0
HETATM   38  H   UNK     0      -2.922   0.159   0.918  0.00  0.00           H+0
HETATM   39  H   UNK     0      -3.395  -2.258   0.559  0.00  0.00           H+0
HETATM   40  H   UNK     0      -2.223  -3.383  -1.162  0.00  0.00           H+0
HETATM   41  H   UNK     0      -3.027  -2.146  -1.933  0.00  0.00           H+0
HETATM   42  H   UNK     0      -0.072  -2.893  -0.527  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.843  -2.175   2.289  0.00  0.00           H+0
HETATM   44  H   UNK     0       2.940  -5.246   2.132  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.473  -2.493  -0.305  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.333  -0.844  -1.099  0.00  0.00           H+0
HETATM   47  H   UNK     0       4.232   0.767  -2.322  0.00  0.00           H+0
HETATM   48  H   UNK     0       4.444   3.229  -2.803  0.00  0.00           H+0
HETATM   49  H   UNK     0       2.683   4.054   0.908  0.00  0.00           H+0
HETATM   50  H   UNK     0       4.607  -0.061   1.522  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.479  -2.313   0.583  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.965  -2.841   1.530  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.298  -0.817   2.732  0.00  0.00           H+0
HETATM   54  H   UNK     0      -3.935  -0.321  -1.937  0.00  0.00           H+0
HETATM   55  H   UNK     0      -4.929  -0.594   0.734  0.00  0.00           H+0
HETATM   56  H   UNK     0      -6.341   1.360  -1.401  0.00  0.00           H+0
HETATM   57  H   UNK     0      -6.704   3.753  -1.329  0.00  0.00           H+0
HETATM   58  H   UNK     0      -4.828   5.281  -0.746  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.602   4.345  -0.243  0.00  0.00           H+0
CONECT    1    2   35   36   37                                             
CONECT    2    1    3   27   38                                             
CONECT    3    2    4    5   39                                             
CONECT    4    3   40   41                                                  
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   42                                                  
CONECT    8    7    9   12   43                                             
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   44                                                       
CONECT   12    8   13   25   45                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   23   46                                             
CONECT   15   14   16   21                                                  
CONECT   16   15   17   47                                                  
CONECT   17   16   18   48                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   49                                                  
CONECT   21   20   22   15                                                  
CONECT   22   21                                                            
CONECT   23   14   24   25   50                                             
CONECT   24   23   51                                                       
CONECT   25   23   26   12   52                                             
CONECT   26   25   53                                                       
CONECT   27    2   28   29   54                                             
CONECT   28   27   55                                                       
CONECT   29   27   30   34                                                  
CONECT   30   29   31   56                                                  
CONECT   31   30   32   57                                                  
CONECT   32   31   33   58                                                  
CONECT   33   32   34   59                                                  
CONECT   34   33   29                                                       
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    2                                                            
CONECT   39    3                                                            
CONECT   40    4                                                            
CONECT   41    4                                                            
CONECT   42    7                                                            
CONECT   43    8                                                            
CONECT   44   11                                                            
CONECT   45   12                                                            
CONECT   46   14                                                            
CONECT   47   16                                                            
CONECT   48   17                                                            
CONECT   49   20                                                            
CONECT   50   23                                                            
CONECT   51   24                                                            
CONECT   52   25                                                            
CONECT   53   26                                                            
CONECT   54   27                                                            
CONECT   55   28                                                            
CONECT   56   30                                                            
CONECT   57   31                                                            
CONECT   58   32                                                            
CONECT   59   33                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  122    0
END

RDKit          3D

59 61  0  0  0  0  0  0  0  0999 V2000
   -1.5799    0.3661   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8142   -0.2655   -0.1215 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5565   -1.7485    0.0365 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2667   -2.3432   -1.2513 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3311   -1.8874    0.8870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3824   -1.4279    2.0539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1554   -2.4985    0.4359 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9933   -2.6049    1.2958 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3183   -4.0467    1.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6606   -4.9705    0.9599 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3961   -4.3980    2.2869 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1843   -1.9756    0.6124 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9450   -0.6131    0.3360 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2133   -0.2489   -0.1548 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3363    1.1386   -0.4335 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8910    1.5320   -1.6113 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0071    2.8809   -1.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5749    3.8407   -0.9743 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6733    5.0784   -1.1989 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9142    2.0711    0.4459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4040    1.6530    1.5300 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2051   -0.7921    0.8267 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2833   -1.4179    0.1667 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3920   -1.8894    1.5190 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9916   -1.5057    2.7788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0558    0.0297   -0.9101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1192   -0.6137   -0.2566 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2676    1.5068   -0.8623 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5246    2.0023   -1.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    3.3716   -1.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6492    4.2014   -0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4087    3.6734   -0.4946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2444    2.3421   -0.5442 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524   -0.3727   -0.8595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503    0.8267   -1.6986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    1.1620   -0.0579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9224    0.1591    0.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3952   -2.2577    0.5586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2225   -3.3829   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0272   -2.1464   -1.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0722   -2.8928   -0.5269 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8434   -2.1753    2.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9400   -5.2460    2.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4727   -2.4931   -0.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3329   -0.8435   -1.0987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2324    0.7670   -2.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4441    3.2292   -2.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832    4.0541    0.9075 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075   -0.0613    1.5219 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4791   -2.3131    0.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9646   -2.8407    1.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2982   -0.8170    2.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9353   -0.3206   -1.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9294   -0.5943    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3409    1.3603   -1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7037    3.7533   -1.3286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8282    5.2814   -0.7458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6020    4.3447   -0.2430 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  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  2  0
 14 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  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
 33 34  2  0
 25 12  1  0
 34 29  1  0
 21 15  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  2 38  1  1
  3 39  1  1
  4 40  1  0
  4 41  1  0
  7 42  1  0
  8 43  1  1
 11 44  1  0
 12 45  1  6
 14 46  1  6
 16 47  1  0
 17 48  1  0
 20 49  1  0
 23 50  1  1
 24 51  1  0
 25 52  1  1
 26 53  1  0
 27 54  1  6
 28 55  1  0
 30 56  1  0
 31 57  1  0
 32 58  1  0
 33 59  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-{[2-amino-1,4-dihydroxy-3-methyl-4-(pyridin-2-yl)butylidene]amino}-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetate	Generator
Nikkomycin L(Z)	MeSH

Chemical Formula

C₂₀H₂₅N₅O₉

Average Mass

479.4460 Da

Monoisotopic Mass

479.16523 Da

IUPAC Name

(2R)-2-[(2R,3R,4R)-2-amino-4-hydroxy-3-methyl-4-(pyridin-2-yl)butanamido]-2-[(2R,3R,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

Traditional Name

(R)-[(2R,3R,4R)-2-amino-4-hydroxy-3-methyl-4-(pyridin-2-yl)butanamido][(2R,3R,4R,5R)-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=CC=N1

InChI Identifier

InChI=1S/C20H25N5O9/c1-8(13(27)9-4-2-3-6-22-9)11(21)17(30)24-12(19(31)32)16-14(28)15(29)18(34-16)25-7-5-10(26)23-20(25)33/h2-8,11-16,18,27-29H,21H2,1H3,(H,24,30)(H,31,32)(H,23,26,33)

InChI Key

HYBLVRJOBLCCCY-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces tendae	NPAtlas	10470685

Species Where Detected

Species Name	Source	Reference
Streptomyces tendae Tu 901	KNApSAcK Database	22123792

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.77	ALOGPS
logP	-5.3	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	2.72	ChemAxon
pKa (Strongest Basic)	7.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	224.64 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	109.85 m³·mol⁻¹	ChemAxon
Polarizability	45.56 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

NPAtlas ID

NPA004623

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78444780

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13856319

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Nikkomycin Lz (NP0001757)

MOL for NP0001757 (Nikkomycin Lz)

3D MOL for NP0001757 (Nikkomycin Lz)

3D SDF for NP0001757 (Nikkomycin Lz)

3D-SDF for NP0001757 (Nikkomycin Lz)

PDB for NP0001757 (Nikkomycin Lz)

3D PDB for NP0001757 (Nikkomycin Lz)

SMILES for NP0001757 (Nikkomycin Lz)

INCHI for NP0001757 (Nikkomycin Lz)

Structure for NP0001757 (Nikkomycin Lz)

3D Structure for NP0001757 (Nikkomycin Lz)