NP-MRD: Showing NP-Card for Simamycin (NP0016075)

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Record Information

Version

1.0

Created at

2021-01-06 01:09:23 UTC

Updated at

2021-07-15 17:21:42 UTC

NP-MRD ID

NP0016075

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Simamycin

Provided By

NPAtlas

Description

Simamycin is found in Streptomyces sp. It was first documented in 2017 (PMID: 28096544). Based on a literature review very few articles have been published on 1-[(2R,3R,4S,5R)-5-({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117263D          

 55 56  0  0  0  0            999 V2000
    6.3191    1.4277   -0.1464 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1116    0.0051   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5540   -0.4793   -1.8338 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5345   -0.8597    0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0602   -0.4962    1.6950 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5898   -0.7289    1.8678 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7129    0.0489    0.9686 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8022   -0.1346   -0.4934 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244    0.9107    1.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9324    1.7064    0.6780 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -0.7589    0.1410    0.6891 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2008   -0.1426    0.9410 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -4.2326   -0.1550    0.1551 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -5.5754   -0.0790   -1.9119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5975    0.4696   -2.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3324    1.5071   -2.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2845    2.0518   -2.7830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0138    1.9351   -0.9019 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0147    1.3815   -0.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.6764   -2.3556    1.7582 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4854    1.8601    0.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2094    1.4513    0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5035    2.0024   -1.0605 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6476    0.3155   -2.5735 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5458   -1.0039   -1.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8474   -1.2359   -2.2436 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.6068   -1.1457    2.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3363   -1.0787   -0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1134    1.5817   -0.4077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.0491   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1501   -0.5670    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4713    0.0684    2.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5371   -0.2287    1.2332 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
  2  4  2  3  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  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
 13 14  1  0  0  0  0
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 17 18  2  0  0  0  0
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 22 16  1  0  0  0  0
  1 28  1  0  0  0  0
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 24 52  1  6  0  0  0
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 26 54  1  6  0  0  0
 27 55  1  0  0  0  0
M  END

     RDKit          3D

 55 56  0  0  0  0  0  0  0  0999 V2000
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    2.7129    0.0489    0.9686 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8022   -0.1346   -0.4934 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244    0.9107    1.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9324    1.7064    0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4178    1.4711    0.9209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7589    0.1410    0.6891 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.5754   -0.0790   -1.9119 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3324    1.5071   -2.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2845    2.0518   -2.7830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0138    1.9351   -0.9019 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306242117263D          

 55 56  0  0  0  0            999 V2000
    6.3191    1.4277   -0.1464 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1116    0.0051   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0602   -0.4962    1.6950 C   0  0  2  0  0  0  0  0  0  0  0  0
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    3.3696    0.6879   -0.9841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363   -1.0787   -0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7938   -0.2479   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8070    0.9810    2.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    2.8010    0.8644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1134    1.5817   -0.4077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.0491   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1501   -0.5670    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4713    0.0684    2.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5371   -0.2287    1.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0030   -0.8819   -2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8508    0.1225   -3.6592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5971    2.7340   -0.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3799   -1.5601   -1.2884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3166   -2.5353   -0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6393   -2.0689    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8161   -1.7118    2.5194 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
  2  4  2  3  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 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
 22 23  2  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 13  1  0  0  0  0
 22 16  1  0  0  0  0
  1 28  1  0  0  0  0
  1 29  1  0  0  0  0
  1 30  1  0  0  0  0
  3 31  1  0  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
  4 34  1  0  0  0  0
  5 35  1  0  0  0  0
  5 36  1  0  0  0  0
  6 37  1  0  0  0  0
  6 38  1  0  0  0  0
  8 39  1  0  0  0  0
  8 40  1  0  0  0  0
  8 41  1  0  0  0  0
  9 42  1  0  0  0  0
 10 43  1  0  0  0  0
 10 44  1  0  0  0  0
 12 45  1  0  0  0  0
 12 46  1  0  0  0  0
 13 47  1  1  0  0  0
 15 48  1  1  0  0  0
 17 49  1  0  0  0  0
 18 50  1  0  0  0  0
 21 51  1  0  0  0  0
 24 52  1  6  0  0  0
 25 53  1  0  0  0  0
 26 54  1  6  0  0  0
 27 55  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0016075

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OC([H])([H])C(\[H])=C(/C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=O)N([H])C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H28N2O6/c1-12(2)5-4-6-13(3)8-10-26-11-14-16(23)17(24)18(27-14)21-9-7-15(22)20-19(21)25/h5,7-9,14,16-18,23-24H,4,6,10-11H2,1-3H3,(H,20,22,25)/b13-8+/t14-,16-,17-,18-/m1/s1

> <INCHI_KEY>
AXWLJQKHNCEKHK-ZGFVZBPKSA-N

> <FORMULA>
C19H28N2O6

> <MOLECULAR_WEIGHT>
380.441

> <EXACT_MASS>
380.19473663

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
40.67405264829609

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-5-({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
0.96

> <JCHEM_LOGP>
1.2488447266666656

> <ALOGPS_LOGS>
-2.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.62463155933856

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.700745849262258

> <JCHEM_PKA_STRONGEST_BASIC>
-3.663780331809461

> <JCHEM_POLAR_SURFACE_AREA>
108.33000000000001

> <JCHEM_REFRACTIVITY>
100.2376

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.09e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-5-({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3H-pyrimidine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 55 56  0  0  0  0  0  0  0  0999 V2000
    6.3191    1.4277   -0.1464 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1116    0.0051   -0.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5540   -0.4793   -1.8338 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5345   -0.8597    0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0602   -0.4962    1.6950 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5898   -0.7289    1.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7129    0.0489    0.9686 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8022   -0.1346   -0.4934 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244    0.9107    1.5106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9324    1.7064    0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4178    1.4711    0.9209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7589    0.1410    0.6891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2008   -0.1426    0.9410 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0647    0.6025    0.1459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2326   -0.1550    0.1551 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2683    0.3598   -0.6783 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5754   -0.0790   -1.9119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5975    0.4696   -2.6665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3324    1.5071   -2.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2845    2.0518   -2.7830 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0138    1.9351   -0.9019 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0147    1.3815   -0.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7786    1.8382    0.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7216   -1.5130   -0.2436 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6062   -2.5379    0.0846 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4516   -1.6039    0.6079 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6764   -2.3556    1.7582 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4854    1.8601    0.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2094    1.4513    0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5035    2.0024   -1.0605 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6476    0.3155   -2.5735 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5458   -1.0039   -1.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8474   -1.2359   -2.2436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4107   -1.9013    0.0541 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3411    0.5407    1.9893 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6068   -1.1457    2.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3646   -0.4745    2.9423 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4131   -1.8389    1.7162 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3696    0.6879   -0.9841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363   -1.0787   -0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7938   -0.2479   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8070    0.9810    2.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    2.8010    0.8644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1134    1.5817   -0.4077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.0491   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1501   -0.5670    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4713    0.0684    2.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5371   -0.2287    1.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0030   -0.8819   -2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8508    0.1225   -3.6592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5971    2.7340   -0.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3799   -1.5601   -1.2884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3166   -2.5353   -0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6393   -2.0689    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8161   -1.7118    2.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  2  0
 15 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
 26 13  1  0
 22 16  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  3 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  0
  6 38  1  0
  8 39  1  0
  8 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  0
 10 44  1  0
 12 45  1  0
 12 46  1  0
 13 47  1  1
 15 48  1  1
 17 49  1  0
 18 50  1  0
 21 51  1  0
 24 52  1  6
 25 53  1  0
 26 54  1  6
 27 55  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       6.319   1.428  -0.146  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.112   0.005  -0.500  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.554  -0.479  -1.834  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.535  -0.860   0.355  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.060  -0.496   1.695  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590  -0.729   1.868  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.713   0.049   0.969  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.802  -0.135  -0.493  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.824   0.911   1.511  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.932   1.706   0.678  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.418   1.471   0.921  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.759   0.141   0.689  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.201  -0.143   0.941  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.065   0.603   0.146  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.233  -0.155   0.155  0.00  0.00           C+0
HETATM   16  N   UNK     0      -5.268   0.360  -0.678  0.00  0.00           N+0
HETATM   17  C   UNK     0      -5.575  -0.079  -1.912  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.598   0.470  -2.667  0.00  0.00           C+0
HETATM   19  C   UNK     0      -7.332   1.507  -2.136  0.00  0.00           C+0
HETATM   20  O   UNK     0      -8.284   2.052  -2.783  0.00  0.00           O+0
HETATM   21  N   UNK     0      -7.014   1.935  -0.902  0.00  0.00           N+0
HETATM   22  C   UNK     0      -6.015   1.381  -0.193  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.779   1.838   0.954  0.00  0.00           O+0
HETATM   24  C   UNK     0      -3.722  -1.513  -0.244  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.606  -2.538   0.085  0.00  0.00           O+0
HETATM   26  C   UNK     0      -2.452  -1.604   0.608  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.676  -2.356   1.758  0.00  0.00           O+0
HETATM   28  H   UNK     0       5.485   1.860   0.444  0.00  0.00           H+0
HETATM   29  H   UNK     0       7.209   1.451   0.546  0.00  0.00           H+0
HETATM   30  H   UNK     0       6.503   2.002  -1.061  0.00  0.00           H+0
HETATM   31  H   UNK     0       6.648   0.316  -2.574  0.00  0.00           H+0
HETATM   32  H   UNK     0       7.546  -1.004  -1.774  0.00  0.00           H+0
HETATM   33  H   UNK     0       5.847  -1.236  -2.244  0.00  0.00           H+0
HETATM   34  H   UNK     0       5.411  -1.901   0.054  0.00  0.00           H+0
HETATM   35  H   UNK     0       5.341   0.541   1.989  0.00  0.00           H+0
HETATM   36  H   UNK     0       5.607  -1.146   2.443  0.00  0.00           H+0
HETATM   37  H   UNK     0       3.365  -0.475   2.942  0.00  0.00           H+0
HETATM   38  H   UNK     0       3.413  -1.839   1.716  0.00  0.00           H+0
HETATM   39  H   UNK     0       3.370   0.688  -0.984  0.00  0.00           H+0
HETATM   40  H   UNK     0       3.336  -1.079  -0.703  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.794  -0.248  -0.964  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.807   0.981   2.581  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.078   2.801   0.864  0.00  0.00           H+0
HETATM   44  H   UNK     0       1.113   1.582  -0.408  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.557  -0.049  -0.392  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.150  -0.567   1.253  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.471   0.068   2.012  0.00  0.00           H+0
HETATM   48  H   UNK     0      -4.537  -0.229   1.233  0.00  0.00           H+0
HETATM   49  H   UNK     0      -5.003  -0.882  -2.316  0.00  0.00           H+0
HETATM   50  H   UNK     0      -6.851   0.123  -3.659  0.00  0.00           H+0
HETATM   51  H   UNK     0      -7.597   2.734  -0.522  0.00  0.00           H+0
HETATM   52  H   UNK     0      -3.380  -1.560  -1.288  0.00  0.00           H+0
HETATM   53  H   UNK     0      -5.317  -2.535  -0.605  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.639  -2.069   0.051  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.816  -1.712   2.519  0.00  0.00           H+0
CONECT    1    2   28   29   30                                             
CONECT    2    1    3    4                                                  
CONECT    3    2   31   32   33                                             
CONECT    4    2    5   34                                                  
CONECT    5    4    6   35   36                                             
CONECT    6    5    7   37   38                                             
CONECT    7    6    8    9                                                  
CONECT    8    7   39   40   41                                             
CONECT    9    7   10   42                                                  
CONECT   10    9   11   43   44                                             
CONECT   11   10   12                                                       
CONECT   12   11   13   45   46                                             
CONECT   13   12   14   26   47                                             
CONECT   14   13   15                                                       
CONECT   15   14   16   24   48                                             
CONECT   16   15   17   22                                                  
CONECT   17   16   18   49                                                  
CONECT   18   17   19   50                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   51                                                  
CONECT   22   21   23   16                                                  
CONECT   23   22                                                            
CONECT   24   15   25   26   52                                             
CONECT   25   24   53                                                       
CONECT   26   24   27   13   54                                             
CONECT   27   26   55                                                       
CONECT   28    1                                                            
CONECT   29    1                                                            
CONECT   30    1                                                            
CONECT   31    3                                                            
CONECT   32    3                                                            
CONECT   33    3                                                            
CONECT   34    4                                                            
CONECT   35    5                                                            
CONECT   36    5                                                            
CONECT   37    6                                                            
CONECT   38    6                                                            
CONECT   39    8                                                            
CONECT   40    8                                                            
CONECT   41    8                                                            
CONECT   42    9                                                            
CONECT   43   10                                                            
CONECT   44   10                                                            
CONECT   45   12                                                            
CONECT   46   12                                                            
CONECT   47   13                                                            
CONECT   48   15                                                            
CONECT   49   17                                                            
CONECT   50   18                                                            
CONECT   51   21                                                            
CONECT   52   24                                                            
CONECT   53   25                                                            
CONECT   54   26                                                            
CONECT   55   27                                                            
MASTER        0    0    0    0    0    0    0    0   55    0  112    0
END

RDKit          3D

55 56  0  0  0  0  0  0  0  0999 V2000
    6.3191    1.4277   -0.1464 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8022   -0.1346   -0.4934 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9324    1.7064    0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3324    1.5071   -2.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2845    2.0518   -2.7830 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.0147    1.3815   -0.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7786    1.8382    0.9544 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7216   -1.5130   -0.2436 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6062   -2.5379    0.0846 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4516   -1.6039    0.6079 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6764   -2.3556    1.7582 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4854    1.8601    0.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2094    1.4513    0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5035    2.0024   -1.0605 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6476    0.3155   -2.5735 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5458   -1.0039   -1.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8474   -1.2359   -2.2436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4107   -1.9013    0.0541 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3411    0.5407    1.9893 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6068   -1.1457    2.4427 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3646   -0.4745    2.9423 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4131   -1.8389    1.7162 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3696    0.6879   -0.9841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363   -1.0787   -0.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7938   -0.2479   -0.9637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8070    0.9810    2.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    2.8010    0.8644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1134    1.5817   -0.4077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.0491   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1501   -0.5670    1.2532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4713    0.0684    2.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5371   -0.2287    1.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0030   -0.8819   -2.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8508    0.1225   -3.6592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5971    2.7340   -0.5220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3799   -1.5601   -1.2884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3166   -2.5353   -0.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6393   -2.0689    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8161   -1.7118    2.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 21 22  1  0
 22 23  2  0
 15 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
 26 13  1  0
 22 16  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  3 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  0
  6 38  1  0
  8 39  1  0
  8 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  0
 10 44  1  0
 12 45  1  0
 12 46  1  0
 13 47  1  1
 15 48  1  1
 17 49  1  0
 18 50  1  0
 21 51  1  0
 24 52  1  6
 25 53  1  0
 26 54  1  6
 27 55  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₁₉H₂₈N₂O₆

Average Mass

380.4410 Da

Monoisotopic Mass

380.19474 Da

IUPAC Name

1-[(2R,3R,4S,5R)-5-({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

1-[(2R,3R,4S,5R)-5-({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3H-pyrimidine-2,4-dione

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\COC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C19H28N2O6/c1-12(2)5-4-6-13(3)8-10-26-11-14-16(23)17(24)18(27-14)21-9-7-15(22)20-19(21)25/h5,7-9,14,16-18,23-24H,4,6,10-11H2,1-3H3,(H,20,22,25)/b13-8+/t14-,16-,17-,18-/m1/s1

InChI Key

AXWLJQKHNCEKHK-ZGFVZBPKSA-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 sp.	NPAtlas	28096544

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	0.96	ALOGPS
logP	1.25	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	9.7	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.33 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	100.24 m³·mol⁻¹	ChemAxon
Polarizability	40.67 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA021620

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78438806

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

98789523

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Igarashi Y, Kyoso T, Kim Y, Oikawa T: Simamycin (5'-O-geranyluridine): a new prenylated nucleoside from Streptomyces sp. J Antibiot (Tokyo). 2017 May;70(5):607-610. doi: 10.1038/ja.2016.163. Epub 2017 Jan 18. [PubMed:28096544 ]

Showing NP-Card for Simamycin (NP0016075)

MOL for NP0016075 (Simamycin)

3D MOL for NP0016075 (Simamycin)

3D SDF for NP0016075 (Simamycin)

3D-SDF for NP0016075 (Simamycin)

PDB for NP0016075 (Simamycin)

3D PDB for NP0016075 (Simamycin)

SMILES for NP0016075 (Simamycin)

INCHI for NP0016075 (Simamycin)

Structure for NP0016075 (Simamycin)

3D Structure for NP0016075 (Simamycin)