NP-MRD: Showing NP-Card for Nomimicin (NP0010784)

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Record Information

Version

2.0

Created at

2021-01-05 20:37:44 UTC

Updated at

2021-07-15 17:07:04 UTC

NP-MRD ID

NP0010784

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nomimicin

Provided By

NPAtlas

Description

Nomimicin is found in Actinomadura sp. Nomimicin was first documented in 2012 (PMID: 22534651).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012121343D          

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M  END

     RDKit          3D

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 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 14 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  1  0
 30 31  1  6
 30 32  1  0
 32 33  2  0
 33 34  1  0
  9 35  1  0
 35 36  2  0
 33  3  1  0
 30  5  1  0
 35  5  1  0
 25 12  1  0
 25 17  1  0
  1 37  1  0
  1 38  1  0
  1 39  1  0
  2 40  1  0
  2 41  1  0
  3 42  1  6
  4 43  1  0
  4 44  1  0
 11 45  1  0
 13 46  1  0
 13 47  1  0
 13 48  1  0
 14 49  1  1
 15 50  1  0
 16 51  1  0
 17 52  1  1
 18 53  1  6
 19 54  1  0
 20 55  1  6
 21 56  1  0
 21 57  1  0
 21 58  1  0
 22 59  1  6
 23 60  1  0
 24 61  1  0
 24 62  1  0
 25 63  1  6
 26 64  1  0
 26 65  1  0
 27 66  1  0
 28 67  1  0
 29 68  1  0
 29 69  1  0
 31 70  1  0
 31 71  1  0
 31 72  1  0
 32 73  1  0
 34 74  1  0
 34 75  1  0
 34 76  1  0
M  END


  Mrv1652307012121343D          

 76 80  0  0  0  0            999 V2000
   -5.6373   -2.8518    0.8885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2617   -2.4748    0.4437 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1754   -1.3796   -0.5581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7208   -1.1578   -0.9225 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1497    0.0076   -0.1063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5735   -0.2650    1.1626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634   -0.3077    1.9731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5715   -0.4452    3.2252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -0.1719    1.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9954   -0.1367    1.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400   -0.9777    2.7168 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123    0.7221    1.1010 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1518    0.6056    2.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8753    2.1398    0.8960 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9892    2.7020    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9680    1.9982   -0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1096    0.5461   -0.1587 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7644   -0.0871   -1.3881 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1244    0.2330   -1.3008 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414   -1.5846   -1.3836 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3992   -2.2209   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1784   -1.9889   -1.3210 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0120   -3.3477   -1.4501 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6441   -1.4762    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6656    0.0149   -0.0785 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5863    2.7900    0.4672 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4828    2.7921    1.4424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7548    2.5604    1.2042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2744    2.5413   -0.1565 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7664    1.2224   -0.6709 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7583    1.3019   -2.1968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2053    1.0613   -0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8289   -0.1120   -0.2848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3129   -0.0828    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -0.0544   -0.1904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3779    0.0262   -1.4330 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1448   -2.1575    1.5443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5029   -3.7986    1.5236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3097   -3.1504    0.0472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7405   -3.3902   -0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6591   -2.2091    1.3424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6315   -1.7374   -1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1282   -2.0407   -0.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5521   -1.0334   -2.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1113   -0.7207    3.6796 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8198    1.4478    2.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6337    0.7701    3.1532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5678   -0.3903    2.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0524    2.6975    1.8944 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9567    3.7817   -0.0920 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7512    2.5166   -0.9418 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7256    0.2554    0.6831 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3925    0.3415   -2.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4142    0.1079   -0.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0407   -1.9347   -2.3594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8688   -3.1043    0.1483 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6323   -1.5653    0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3728   -2.5928   -0.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6459   -1.4708   -2.1642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7913   -3.7109   -1.9137 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3051   -1.8933    0.7877 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6218   -1.8193    0.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2704    0.3139   -1.0571 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7923    3.9198    0.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3913    2.5242   -0.5630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1869    3.0114    2.4849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4087    2.3907    2.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1368    3.2846   -0.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5751    3.0392   -0.8975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2072    2.3273   -2.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7813    1.3353   -2.6514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4994    0.6110   -2.6409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7836    1.9762   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7621    0.8131   -0.4759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8034   -0.9488   -0.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5186    0.0614    1.0936 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
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 14 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
  9 35  1  0  0  0  0
 35 36  2  0  0  0  0
 33  3  1  0  0  0  0
 30  5  1  0  0  0  0
 35  5  1  0  0  0  0
 25 12  1  0  0  0  0
 25 17  1  0  0  0  0
  1 37  1  0  0  0  0
  1 38  1  0  0  0  0
  1 39  1  0  0  0  0
  2 40  1  0  0  0  0
  2 41  1  0  0  0  0
  3 42  1  6  0  0  0
  4 43  1  0  0  0  0
  4 44  1  0  0  0  0
 11 45  1  0  0  0  0
 13 46  1  0  0  0  0
 13 47  1  0  0  0  0
 13 48  1  0  0  0  0
 14 49  1  1  0  0  0
 15 50  1  0  0  0  0
 16 51  1  0  0  0  0
 17 52  1  1  0  0  0
 18 53  1  6  0  0  0
 19 54  1  0  0  0  0
 20 55  1  6  0  0  0
 21 56  1  0  0  0  0
 21 57  1  0  0  0  0
 21 58  1  0  0  0  0
 22 59  1  6  0  0  0
 23 60  1  0  0  0  0
 24 61  1  0  0  0  0
 24 62  1  0  0  0  0
 25 63  1  6  0  0  0
 26 64  1  0  0  0  0
 26 65  1  0  0  0  0
 27 66  1  0  0  0  0
 28 67  1  0  0  0  0
 29 68  1  0  0  0  0
 29 69  1  0  0  0  0
 31 70  1  0  0  0  0
 31 71  1  0  0  0  0
 31 72  1  0  0  0  0
 32 73  1  0  0  0  0
 34 74  1  0  0  0  0
 34 75  1  0  0  0  0
 34 76  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0010784

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O\C1=C2/C(=O)O[C@@]3(C2=O)C([H])([H])[C@]([H])(C(=C([H])[C@@]3(C([H])([H])[H])C([H])([H])\C([H])=C([H])/C([H])([H])[C@]2([H])C([H])=C([H])[C@]3([H])[C@@]([H])(O[H])[C@@]([H])(C([H])([H])[H])[C@@]([H])(O[H])C([H])([H])[C@@]3([H])[C@]12C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C30H40O6/c1-6-18-15-30-26(34)23(27(35)36-30)25(33)29(5)19(9-7-8-12-28(30,4)14-16(18)2)10-11-20-21(29)13-22(31)17(3)24(20)32/h7-8,10-11,14,17-22,24,31-33H,6,9,12-13,15H2,1-5H3/b8-7-,25-23-/t17-,18+,19+,20-,21+,22-,24-,28+,29+,30+/m0/s1

> <INCHI_KEY>
AUPHDHHHJBUJQK-SBMQRCQXSA-N

> <FORMULA>
C30H40O6

> <MOLECULAR_WEIGHT>
496.644

> <EXACT_MASS>
496.282489008

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
54.54222559819067

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3R,6R,8Z,11R,14S,15R,16S,17S,19R,20R)-3-ethyl-15,17,21-trihydroxy-4,6,16,20-tetramethyl-24-oxapentacyclo[20.2.1.0^{1,6}.0^{11,20}.0^{14,19}]pentacosa-4,8,12,21-tetraene-23,25-dione

> <ALOGPS_LOGP>
3.69

> <JCHEM_LOGP>
4.230277177999999

> <ALOGPS_LOGS>
-4.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.382514215267694

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7983754352417107

> <JCHEM_PKA_STRONGEST_BASIC>
-2.857534687955334

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
141.10340000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R,6R,8Z,11R,14S,15R,16S,17S,19R,20R)-3-ethyl-15,17,21-trihydroxy-4,6,16,20-tetramethyl-24-oxapentacyclo[20.2.1.0^{1,6}.0^{11,20}.0^{14,19}]pentacosa-4,8,12,21-tetraene-23,25-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 76 80  0  0  0  0  0  0  0  0999 V2000
   -5.6373   -2.8518    0.8885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2617   -2.4748    0.4437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1754   -1.3796   -0.5581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7208   -1.1578   -0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1497    0.0076   -0.1063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5735   -0.2650    1.1626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634   -0.3077    1.9731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5715   -0.4452    3.2252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -0.1719    1.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9954   -0.1367    1.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400   -0.9777    2.7168 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123    0.7221    1.1010 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1518    0.6056    2.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8753    2.1398    0.8960 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9892    2.7020    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9680    1.9982   -0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1096    0.5461   -0.1587 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7644   -0.0871   -1.3881 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1244    0.2330   -1.3008 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414   -1.5846   -1.3836 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3992   -2.2209   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1784   -1.9889   -1.3210 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0120   -3.3477   -1.4501 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6441   -1.4762    0.0063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6656    0.0149   -0.0785 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5863    2.7900    0.4672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4828    2.7921    1.4424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7548    2.5604    1.2042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2744    2.5413   -0.1565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7664    1.2224   -0.6709 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7583    1.3019   -2.1968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2053    1.0613   -0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8289   -0.1120   -0.2848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3129   -0.0828    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -0.0544   -0.1904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3779    0.0262   -1.4330 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1448   -2.1575    1.5443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5029   -3.7986    1.5236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3097   -3.1504    0.0472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7405   -3.3902   -0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6591   -2.2091    1.3424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6315   -1.7374   -1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1282   -2.0407   -0.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5521   -1.0334   -2.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1113   -0.7207    3.6796 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8198    1.4478    2.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6337    0.7701    3.1532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5678   -0.3903    2.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0524    2.6975    1.8944 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9567    3.7817   -0.0920 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7512    2.5166   -0.9418 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7256    0.2554    0.6831 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3925    0.3415   -2.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4142    0.1079   -0.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0407   -1.9347   -2.3594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8688   -3.1043    0.1483 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6323   -1.5653    0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3728   -2.5928   -0.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6459   -1.4708   -2.1642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7913   -3.7109   -1.9137 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3051   -1.8933    0.7877 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6218   -1.8193    0.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2704    0.3139   -1.0571 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7923    3.9198    0.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3913    2.5242   -0.5630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1869    3.0114    2.4849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4087    2.3907    2.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1368    3.2846   -0.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5751    3.0392   -0.8975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2072    2.3273   -2.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7813    1.3353   -2.6514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4994    0.6110   -2.6409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7836    1.9762   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7621    0.8131   -0.4759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8034   -0.9488   -0.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5186    0.0614    1.0936 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
  4  5  1  0
  5  6  1  1
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  1
 12 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 14 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  1  0
 30 31  1  6
 30 32  1  0
 32 33  2  0
 33 34  1  0
  9 35  1  0
 35 36  2  0
 33  3  1  0
 30  5  1  0
 35  5  1  0
 25 12  1  0
 25 17  1  0
  1 37  1  0
  1 38  1  0
  1 39  1  0
  2 40  1  0
  2 41  1  0
  3 42  1  6
  4 43  1  0
  4 44  1  0
 11 45  1  0
 13 46  1  0
 13 47  1  0
 13 48  1  0
 14 49  1  1
 15 50  1  0
 16 51  1  0
 17 52  1  1
 18 53  1  6
 19 54  1  0
 20 55  1  6
 21 56  1  0
 21 57  1  0
 21 58  1  0
 22 59  1  6
 23 60  1  0
 24 61  1  0
 24 62  1  0
 25 63  1  6
 26 64  1  0
 26 65  1  0
 27 66  1  0
 28 67  1  0
 29 68  1  0
 29 69  1  0
 31 70  1  0
 31 71  1  0
 31 72  1  0
 32 73  1  0
 34 74  1  0
 34 75  1  0
 34 76  1  0
M  END

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0      -5.637  -2.852   0.889  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.262  -2.475   0.444  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.175  -1.380  -0.558  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.721  -1.158  -0.923  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.150   0.008  -0.106  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.574  -0.265   1.163  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.463  -0.308   1.973  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.571  -0.445   3.225  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.240  -0.172   1.139  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.995  -0.137   1.642  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.240  -0.978   2.717  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.012   0.722   1.101  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.152   0.606   2.160  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.875   2.140   0.896  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.989   2.702   0.102  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.968   1.998  -0.359  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.110   0.546  -0.159  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.764  -0.087  -1.388  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.124   0.233  -1.301  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.641  -1.585  -1.384  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.399  -2.221  -0.265  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.178  -1.989  -1.321  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.012  -3.348  -1.450  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.644  -1.476   0.006  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.666   0.015  -0.079  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.586   2.790   0.467  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.483   2.792   1.442  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.755   2.560   1.204  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.274   2.541  -0.157  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.766   1.222  -0.671  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.758   1.302  -2.197  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.205   1.061  -0.332  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.829  -0.112  -0.285  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.313  -0.083   0.029  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.629  -0.054  -0.190  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.378   0.026  -1.433  0.00  0.00           O+0
HETATM   37  H   UNK     0      -6.145  -2.158   1.544  0.00  0.00           H+0
HETATM   38  H   UNK     0      -5.503  -3.799   1.524  0.00  0.00           H+0
HETATM   39  H   UNK     0      -6.310  -3.150   0.047  0.00  0.00           H+0
HETATM   40  H   UNK     0      -3.740  -3.390  -0.004  0.00  0.00           H+0
HETATM   41  H   UNK     0      -3.659  -2.209   1.342  0.00  0.00           H+0
HETATM   42  H   UNK     0      -4.632  -1.737  -1.557  0.00  0.00           H+0
HETATM   43  H   UNK     0      -2.128  -2.041  -0.595  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.552  -1.033  -2.000  0.00  0.00           H+0
HETATM   45  H   UNK     0       1.111  -0.721   3.680  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.820   1.448   2.037  0.00  0.00           H+0
HETATM   47  H   UNK     0       2.634   0.770   3.153  0.00  0.00           H+0
HETATM   48  H   UNK     0       3.568  -0.390   2.209  0.00  0.00           H+0
HETATM   49  H   UNK     0       2.052   2.697   1.894  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.957   3.782  -0.092  0.00  0.00           H+0
HETATM   51  H   UNK     0       4.751   2.517  -0.942  0.00  0.00           H+0
HETATM   52  H   UNK     0       4.726   0.255   0.683  0.00  0.00           H+0
HETATM   53  H   UNK     0       4.393   0.342  -2.325  0.00  0.00           H+0
HETATM   54  H   UNK     0       6.414   0.108  -0.375  0.00  0.00           H+0
HETATM   55  H   UNK     0       5.041  -1.935  -2.359  0.00  0.00           H+0
HETATM   56  H   UNK     0       4.869  -3.104   0.148  0.00  0.00           H+0
HETATM   57  H   UNK     0       5.632  -1.565   0.579  0.00  0.00           H+0
HETATM   58  H   UNK     0       6.373  -2.593  -0.670  0.00  0.00           H+0
HETATM   59  H   UNK     0       2.646  -1.471  -2.164  0.00  0.00           H+0
HETATM   60  H   UNK     0       3.791  -3.711  -1.914  0.00  0.00           H+0
HETATM   61  H   UNK     0       3.305  -1.893   0.788  0.00  0.00           H+0
HETATM   62  H   UNK     0       1.622  -1.819   0.110  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.270   0.314  -1.057  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.792   3.920   0.346  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.391   2.524  -0.563  0.00  0.00           H+0
HETATM   66  H   UNK     0      -0.187   3.011   2.485  0.00  0.00           H+0
HETATM   67  H   UNK     0      -2.409   2.391   2.073  0.00  0.00           H+0
HETATM   68  H   UNK     0      -3.137   3.285  -0.153  0.00  0.00           H+0
HETATM   69  H   UNK     0      -1.575   3.039  -0.898  0.00  0.00           H+0
HETATM   70  H   UNK     0      -3.207   2.327  -2.401  0.00  0.00           H+0
HETATM   71  H   UNK     0      -1.781   1.335  -2.651  0.00  0.00           H+0
HETATM   72  H   UNK     0      -3.499   0.611  -2.641  0.00  0.00           H+0
HETATM   73  H   UNK     0      -4.784   1.976  -0.106  0.00  0.00           H+0
HETATM   74  H   UNK     0      -6.762   0.813  -0.476  0.00  0.00           H+0
HETATM   75  H   UNK     0      -6.803  -0.949  -0.380  0.00  0.00           H+0
HETATM   76  H   UNK     0      -6.519   0.061   1.094  0.00  0.00           H+0
CONECT    1    2   37   38   39                                             
CONECT    2    1    3   40   41                                             
CONECT    3    2    4   33   42                                             
CONECT    4    3    5   43   44                                             
CONECT    5    4    6   30   35                                             
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   35                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10   45                                                       
CONECT   12   10   13   14   25                                             
CONECT   13   12   46   47   48                                             
CONECT   14   12   15   26   49                                             
CONECT   15   14   16   50                                                  
CONECT   16   15   17   51                                                  
CONECT   17   16   18   25   52                                             
CONECT   18   17   19   20   53                                             
CONECT   19   18   54                                                       
CONECT   20   18   21   22   55                                             
CONECT   21   20   56   57   58                                             
CONECT   22   20   23   24   59                                             
CONECT   23   22   60                                                       
CONECT   24   22   25   61   62                                             
CONECT   25   24   12   17   63                                             
CONECT   26   14   27   64   65                                             
CONECT   27   26   28   66                                                  
CONECT   28   27   29   67                                                  
CONECT   29   28   30   68   69                                             
CONECT   30   29   31   32    5                                             
CONECT   31   30   70   71   72                                             
CONECT   32   30   33   73                                                  
CONECT   33   32   34    3                                                  
CONECT   34   33   74   75   76                                             
CONECT   35    9   36    5                                                  
CONECT   36   35                                                            
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    2                                                            
CONECT   41    2                                                            
CONECT   42    3                                                            
CONECT   43    4                                                            
CONECT   44    4                                                            
CONECT   45   11                                                            
CONECT   46   13                                                            
CONECT   47   13                                                            
CONECT   48   13                                                            
CONECT   49   14                                                            
CONECT   50   15                                                            
CONECT   51   16                                                            
CONECT   52   17                                                            
CONECT   53   18                                                            
CONECT   54   19                                                            
CONECT   55   20                                                            
CONECT   56   21                                                            
CONECT   57   21                                                            
CONECT   58   21                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   24                                                            
CONECT   62   24                                                            
CONECT   63   25                                                            
CONECT   64   26                                                            
CONECT   65   26                                                            
CONECT   66   27                                                            
CONECT   67   28                                                            
CONECT   68   29                                                            
CONECT   69   29                                                            
CONECT   70   31                                                            
CONECT   71   31                                                            
CONECT   72   31                                                            
CONECT   73   32                                                            
CONECT   74   34                                                            
CONECT   75   34                                                            
CONECT   76   34                                                            
MASTER        0    0    0    0    0    0    0    0   76    0  160    0
END

RDKit          3D

76 80  0  0  0  0  0  0  0  0999 V2000
   -5.6373   -2.8518    0.8885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2617   -2.4748    0.4437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1754   -1.3796   -0.5581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7208   -1.1578   -0.9225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1497    0.0076   -0.1063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5735   -0.2650    1.1626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4634   -0.3077    1.9731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5715   -0.4452    3.2252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -0.1719    1.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9954   -0.1367    1.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400   -0.9777    2.7168 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0123    0.7221    1.1010 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1518    0.6056    2.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8753    2.1398    0.8960 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9892    2.7020    0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9680    1.9982   -0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1096    0.5461   -0.1587 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7644   -0.0871   -1.3881 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1244    0.2330   -1.3008 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414   -1.5846   -1.3836 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3992   -2.2209   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1784   -1.9889   -1.3210 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0120   -3.3477   -1.4501 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6441   -1.4762    0.0063 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6656    0.0149   -0.0785 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5863    2.7900    0.4672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4828    2.7921    1.4424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7548    2.5604    1.2042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2744    2.5413   -0.1565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7664    1.2224   -0.6709 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7583    1.3019   -2.1968 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2053    1.0613   -0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8289   -0.1120   -0.2848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3129   -0.0828    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6290   -0.0544   -0.1904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3779    0.0262   -1.4330 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1448   -2.1575    1.5443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5029   -3.7986    1.5236 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7405   -3.3902   -0.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₃₀H₄₀O₆

Average Mass

496.6440 Da

Monoisotopic Mass

496.28249 Da

IUPAC Name

(1S,3R,6R,8Z,11R,14S,15R,16S,17S,19R,20R)-3-ethyl-15,17,21-trihydroxy-4,6,16,20-tetramethyl-24-oxapentacyclo[20.2.1.0^{1,6}.0^{11,20}.0^{14,19}]pentacosa-4,8,12,21-tetraene-23,25-dione

Traditional Name

(1S,3R,6R,8Z,11R,14S,15R,16S,17S,19R,20R)-3-ethyl-15,17,21-trihydroxy-4,6,16,20-tetramethyl-24-oxapentacyclo[20.2.1.0^{1,6}.0^{11,20}.0^{14,19}]pentacosa-4,8,12,21-tetraene-23,25-dione

CAS Registry Number

Not Available

SMILES

CC[C@@H]1C[C@@]23OC(=O)\C(C2=O)=C(O)\[C@]2(C)[C@H](C\C=C/C[C@]3(C)C=C1C)C=C[C@@H]1[C@@H](O)[C@@H](C)[C@@H](O)C[C@@H]21

InChI Identifier

InChI=1S/C30H40O6/c1-6-18-15-30-26(34)23(27(35)36-30)25(33)29(5)19(9-7-8-12-28(30,4)14-16(18)2)10-11-20-21(29)13-22(31)17(3)24(20)32/h7-8,10-11,14,17-22,24,31-33H,6,9,12-13,15H2,1-5H3/b8-7-,25-23-/t17-,18+,19+,20-,21+,22-,24-,28+,29+,30+/m0/s1

InChI Key

AUPHDHHHJBUJQK-SBMQRCQXSA-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
Actinomadura sp.	NPAtlas	22534651

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	3.69	ALOGPS
logP	4.23	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	3.8	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	141.1 m³·mol⁻¹	ChemAxon
Polarizability	54.54 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Igarashi Y, Iida T, Oku N, Watanabe H, Furihata K, Miyanouchi K: Nomimicin, a new spirotetronate-class polyketide from an actinomycete of the genus Actinomadura. J Antibiot (Tokyo). 2012 Jul;65(7):355-9. doi: 10.1038/ja.2012.30. Epub 2012 Apr 25. [PubMed:22534651 ]

Showing NP-Card for Nomimicin (NP0010784)

MOL for NP0010784 (Nomimicin)

3D MOL for NP0010784 (Nomimicin)

3D SDF for NP0010784 (Nomimicin)

3D-SDF for NP0010784 (Nomimicin)

PDB for NP0010784 (Nomimicin)

3D PDB for NP0010784 (Nomimicin)

SMILES for NP0010784 (Nomimicin)

INCHI for NP0010784 (Nomimicin)

Structure for NP0010784 (Nomimicin)

3D Structure for NP0010784 (Nomimicin)