NP-MRD: Showing NP-Card for Pradimicinone II (NP0022971)

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Record Information

Version

2.0

Created at

2021-01-06 08:06:45 UTC

Updated at

2021-07-15 17:40:29 UTC

NP-MRD ID

NP0022971

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pradimicinone II

Provided By

NPAtlas

Description

Pradimicinone II is found in Actinomadura, Actinomadura verrucosospora and Actinomadura verrucosospora subsp. neohibisca E-40 mutant. Pradimicinone II was first documented in 1993 (PMID: 8478259). Based on a literature review very few articles have been published on 2-({[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0³,¹².0⁴,⁹.0¹⁶,²¹]Docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105383D          

 64 68  0  0  0  0            999 V2000
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M  END

     RDKit          3D

 64 68  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306242105383D          

 64 68  0  0  0  0            999 V2000
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    3.9649   -0.3035   -1.0721 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4672   -0.3813   -1.1425 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2760   -0.0516    0.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1638    0.3720    2.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3026    0.1665    1.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6895    0.4126    3.0917 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4452   -0.7775    3.6334 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8587   -0.0028    0.0419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2271    0.2511    1.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2095   -0.2095   -1.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2120    0.4663    4.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.5634    0.3410    0.1861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0637   -0.0521   -2.9233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1111    0.5160    2.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9785    0.2853    1.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5029   -0.3282   -4.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0396    0.7218   -4.2686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5279   -0.8723   -5.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3279   -1.8909   -3.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7908   -0.9624   -4.9118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8512   -0.7080   -3.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7184   -0.6080   -2.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9527    0.5891   -0.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8496   -1.2540   -0.6251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0673    0.0318    1.0542 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7568    0.5475    3.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1630   -0.4043    4.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9801   -1.2770    2.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6853   -1.4654    4.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8286    1.4870    4.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110    0.4392    2.1129 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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
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 12 13  2  0  0  0  0
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 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 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
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 26 27  2  0  0  0  0
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 28 30  2  0  0  0  0
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 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
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 39 40  1  0  0  0  0
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  9  3  1  0  0  0  0
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 20  7  1  0  0  0  0
 41 15  1  0  0  0  0
  1 42  1  0  0  0  0
  1 43  1  0  0  0  0
  1 44  1  0  0  0  0
  4 45  1  0  0  0  0
  6 46  1  0  0  0  0
  9 47  1  0  0  0  0
 14 48  1  0  0  0  0
 18 49  1  0  0  0  0
 22 50  1  6  0  0  0
 23 51  1  0  0  0  0
 24 52  1  6  0  0  0
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 27 54  1  0  0  0  0
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 35 61  1  0  0  0  0
 35 62  1  0  0  0  0
 38 63  1  0  0  0  0
 40 64  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0022971

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]([H])(N([H])C(=O)C1=C(C([H])=C2C(=C1O[H])C1=C(C(O[H])=C3C(=O)C4=C(O[H])C([H])=C(OC([H])([H])[H])C([H])=C4C(=O)C3=C1O[H])[C@]([H])(O[H])[C@@]2([H])O[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H23NO12/c1-7-4-10-15(22(33)13(7)27(38)29-8(2)28(39)40)16-17(26(37)21(10)32)25(36)19-18(24(16)35)20(31)11-5-9(41-3)6-12(30)14(11)23(19)34/h4-6,8,21,26,30,32-33,35-37H,1-3H3,(H,29,38)(H,39,40)/t8-,21-,26-/m0/s1

> <INCHI_KEY>
SBIJXMUETDVEQB-CJERNAKNSA-N

> <FORMULA>
C28H23NO12

> <MOLECULAR_WEIGHT>
565.487

> <EXACT_MASS>
565.122025185

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
57.24509540557533

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-{[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <ALOGPS_LOGP>
1.78

> <JCHEM_LOGP>
3.841793846333333

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
7.064103542087357

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.972038897653834

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5478180899259506

> <JCHEM_POLAR_SURFACE_AREA>
231.14999999999998

> <JCHEM_REFRACTIVITY>
141.272

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.77e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-{[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 64 68  0  0  0  0  0  0  0  0999 V2000
   -7.3317    0.7247    3.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7605    0.5911    2.6590 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.4952    0.3234    0.3284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6994    0.1697   -0.8278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3372    0.0574   -2.0161 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7733    0.2690    0.6065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5526    0.4191    1.7362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3264    0.2432    0.7829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9043    0.3595    1.9460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4297    0.0887   -0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0384    0.0657   -0.1654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6131    0.1840    1.0801 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2470   -0.0798   -1.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7968   -0.2015   -2.5299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1840   -0.1792   -2.7038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6479   -0.3078   -3.9877 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9881   -0.0341   -1.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4455   -0.0069   -1.7794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9565   -0.1165   -2.9091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -0.3112   -3.8041 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7547   -1.1249   -4.7140 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3228   -0.7587   -3.6579 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1448   -0.2540   -4.6674 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9112   -0.4662   -2.3225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2932   -0.5056   -2.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9649   -0.3035   -1.0721 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4672   -0.3813   -1.1425 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2760   -0.0516    0.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9291    0.1560    1.3477 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1638    0.3720    2.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3026    0.1665    1.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6895    0.4126    3.0917 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4452   -0.7775    3.6334 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5974    1.5861    3.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9095    2.1849    2.0791 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0626    1.9683    4.3845 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8587   -0.0028    0.0419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2271    0.2511    1.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2095   -0.2095   -1.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2120    0.4663    4.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0594    1.7894    4.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.0637   -0.0521   -2.9233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1111    0.5160    2.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9785    0.2853    1.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5029   -0.3282   -4.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0396    0.7218   -4.2686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5279   -0.8723   -5.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3279   -1.8909   -3.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7908   -0.9624   -4.9118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8512   -0.7080   -3.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7184   -0.6080   -2.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9527    0.5891   -0.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8496   -1.2540   -0.6251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0673    0.0318    1.0542 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7568    0.5475    3.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1630   -0.4043    4.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9801   -1.2770    2.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6853   -1.4654    4.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8286    1.4870    4.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110    0.4392    2.1129 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
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 15 16  2  0
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 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  2  0
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 28 30  2  0
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 31 32  2  0
 31 33  1  0
 33 34  1  0
 34 35  1  0
 34 36  1  0
 36 37  2  0
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 30 39  1  0
 39 40  1  0
 39 41  2  0
  9  3  1  0
 19 12  1  0
 41 26  1  0
 20  7  1  0
 41 15  1  0
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  1 43  1  0
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  6 46  1  0
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 18 49  1  0
 22 50  1  6
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 27 54  1  0
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 33 58  1  0
 34 59  1  1
 35 60  1  0
 35 61  1  0
 35 62  1  0
 38 63  1  0
 40 64  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      -7.332   0.725   3.980  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.761   0.591   2.659  0.00  0.00           O+0
HETATM    3  C   UNK     0      -6.926   0.443   1.564  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.495   0.323   0.328  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.699   0.170  -0.828  0.00  0.00           C+0
HETATM    6  O   UNK     0      -7.337   0.057  -2.016  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.351   0.147  -0.657  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.773   0.269   0.607  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.553   0.419   1.736  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.326   0.243   0.783  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.904   0.360   1.946  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.430   0.089  -0.352  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.038   0.066  -0.165  0.00  0.00           C+0
HETATM   14  O   UNK     0      -0.613   0.184   1.080  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.247  -0.080  -1.267  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.797  -0.202  -2.530  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.184  -0.179  -2.704  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.648  -0.308  -3.988  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.988  -0.034  -1.613  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.446  -0.007  -1.779  0.00  0.00           C+0
HETATM   21  O   UNK     0      -4.957  -0.117  -2.909  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.055  -0.311  -3.804  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.755  -1.125  -4.714  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.323  -0.759  -3.658  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.145  -0.254  -4.667  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.911  -0.466  -2.322  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.293  -0.506  -2.249  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.965  -0.304  -1.072  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.467  -0.381  -1.143  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.276  -0.052   0.085  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.929   0.156   1.348  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.164   0.372   2.387  0.00  0.00           O+0
HETATM   33  N   UNK     0       5.303   0.167   1.663  0.00  0.00           N+0
HETATM   34  C   UNK     0       5.689   0.413   3.092  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.445  -0.778   3.633  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.597   1.586   3.144  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.910   2.185   2.079  0.00  0.00           O+0
HETATM   38  O   UNK     0       7.063   1.968   4.385  0.00  0.00           O+0
HETATM   39  C   UNK     0       1.859  -0.003   0.042  0.00  0.00           C+0
HETATM   40  O   UNK     0       1.227   0.251   1.180  0.00  0.00           O+0
HETATM   41  C   UNK     0       1.210  -0.210  -1.150  0.00  0.00           C+0
HETATM   42  H   UNK     0      -8.212   0.466   4.636  0.00  0.00           H+0
HETATM   43  H   UNK     0      -7.059   1.789   4.147  0.00  0.00           H+0
HETATM   44  H   UNK     0      -6.484   0.050   4.207  0.00  0.00           H+0
HETATM   45  H   UNK     0      -8.563   0.341   0.186  0.00  0.00           H+0
HETATM   46  H   UNK     0      -7.064  -0.052  -2.923  0.00  0.00           H+0
HETATM   47  H   UNK     0      -5.111   0.516   2.731  0.00  0.00           H+0
HETATM   48  H   UNK     0      -0.979   0.285   1.980  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.503  -0.328  -4.402  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.040   0.722  -4.269  0.00  0.00           H+0
HETATM   51  H   UNK     0      -0.528  -0.872  -5.649  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.328  -1.891  -3.716  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.791  -0.962  -4.912  0.00  0.00           H+0
HETATM   54  H   UNK     0       3.851  -0.708  -3.184  0.00  0.00           H+0
HETATM   55  H   UNK     0       5.718  -0.608  -2.236  0.00  0.00           H+0
HETATM   56  H   UNK     0       5.953   0.589  -0.997  0.00  0.00           H+0
HETATM   57  H   UNK     0       5.850  -1.254  -0.625  0.00  0.00           H+0
HETATM   58  H   UNK     0       6.067   0.032   1.054  0.00  0.00           H+0
HETATM   59  H   UNK     0       4.757   0.548   3.660  0.00  0.00           H+0
HETATM   60  H   UNK     0       7.163  -0.404   4.383  0.00  0.00           H+0
HETATM   61  H   UNK     0       6.980  -1.277   2.783  0.00  0.00           H+0
HETATM   62  H   UNK     0       5.685  -1.465   4.080  0.00  0.00           H+0
HETATM   63  H   UNK     0       7.829   1.487   4.819  0.00  0.00           H+0
HETATM   64  H   UNK     0       1.411   0.439   2.113  0.00  0.00           H+0
CONECT    1    2   42   43   44                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5   45                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5   46                                                       
CONECT    7    5    8   20                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    3   47                                                  
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   19                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13   48                                                       
CONECT   15   13   16   41                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17   49                                                       
CONECT   19   17   20   12                                                  
CONECT   20   19   21    7                                                  
CONECT   21   20                                                            
CONECT   22   16   23   24   50                                             
CONECT   23   22   51                                                       
CONECT   24   22   25   26   52                                             
CONECT   25   24   53                                                       
CONECT   26   24   27   41                                                  
CONECT   27   26   28   54                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28   55   56   57                                             
CONECT   30   28   31   39                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   58                                                  
CONECT   34   33   35   36   59                                             
CONECT   35   34   60   61   62                                             
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   63                                                       
CONECT   39   30   40   41                                                  
CONECT   40   39   64                                                       
CONECT   41   39   26   15                                                  
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    1                                                            
CONECT   45    4                                                            
CONECT   46    6                                                            
CONECT   47    9                                                            
CONECT   48   14                                                            
CONECT   49   18                                                            
CONECT   50   22                                                            
CONECT   51   23                                                            
CONECT   52   24                                                            
CONECT   53   25                                                            
CONECT   54   27                                                            
CONECT   55   29                                                            
CONECT   56   29                                                            
CONECT   57   29                                                            
CONECT   58   33                                                            
CONECT   59   34                                                            
CONECT   60   35                                                            
CONECT   61   35                                                            
CONECT   62   35                                                            
CONECT   63   38                                                            
CONECT   64   40                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  136    0
END

RDKit          3D

64 68  0  0  0  0  0  0  0  0999 V2000
   -7.3317    0.7247    3.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7605    0.5911    2.6590 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9264    0.4431    1.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4952    0.3234    0.3284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6994    0.1697   -0.8278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3372    0.0574   -2.0161 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3510    0.1465   -0.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7733    0.2690    0.6065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5526    0.4191    1.7362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3264    0.2432    0.7829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9043    0.3595    1.9460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4297    0.0887   -0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0384    0.0657   -0.1654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6131    0.1840    1.0801 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2470   -0.0798   -1.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7968   -0.2015   -2.5299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1840   -0.1792   -2.7038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6479   -0.3078   -3.9877 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9881   -0.0341   -1.6133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4455   -0.0069   -1.7794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9565   -0.1165   -2.9091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550   -0.3112   -3.8041 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7547   -1.1249   -4.7140 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3228   -0.7587   -3.6579 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1448   -0.2540   -4.6674 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9112   -0.4662   -2.3225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2932   -0.5056   -2.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9649   -0.3035   -1.0721 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4672   -0.3813   -1.1425 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2760   -0.0516    0.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9291    0.1560    1.3477 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1638    0.3720    2.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3026    0.1665    1.6631 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6895    0.4126    3.0917 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4452   -0.7775    3.6334 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5974    1.5861    3.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9095    2.1849    2.0791 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0626    1.9683    4.3845 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8587   -0.0028    0.0419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2271    0.2511    1.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2095   -0.2095   -1.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2120    0.4663    4.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0594    1.7894    4.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4844    0.0497    4.2066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5634    0.3410    0.1861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0637   -0.0521   -2.9233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1111    0.5160    2.7311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9785    0.2853    1.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5029   -0.3282   -4.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0396    0.7218   -4.2686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5279   -0.8723   -5.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3279   -1.8909   -3.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7908   -0.9624   -4.9118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8512   -0.7080   -3.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7184   -0.6080   -2.2365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9527    0.5891   -0.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8496   -1.2540   -0.6251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0673    0.0318    1.0542 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7568    0.5475    3.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1630   -0.4043    4.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9801   -1.2770    2.7829 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6853   -1.4654    4.0801 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8286    1.4870    4.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4110    0.4392    2.1129 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19 20  1  0
 20 21  2  0
 16 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  1  0
 28 30  2  0
 30 31  1  0
 31 32  2  0
 31 33  1  0
 33 34  1  0
 34 35  1  0
 34 36  1  0
 36 37  2  0
 36 38  1  0
 30 39  1  0
 39 40  1  0
 39 41  2  0
  9  3  1  0
 19 12  1  0
 41 26  1  0
 20  7  1  0
 41 15  1  0
  1 42  1  0
  1 43  1  0
  1 44  1  0
  4 45  1  0
  6 46  1  0
  9 47  1  0
 14 48  1  0
 18 49  1  0
 22 50  1  6
 23 51  1  0
 24 52  1  6
 25 53  1  0
 27 54  1  0
 29 55  1  0
 29 56  1  0
 29 57  1  0
 33 58  1  0
 34 59  1  1
 35 60  1  0
 35 61  1  0
 35 62  1  0
 38 63  1  0
 40 64  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
2-({[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0,.0,.0,]docosa-1(14),2,4(9),5,7,12,16(21),17,19-nonaen-6-yl](hydroxy)methylidene}amino)propanoate	Generator

Chemical Formula

C₂₈H₂₃NO₁₂

Average Mass

565.4870 Da

Monoisotopic Mass

565.12203 Da

IUPAC Name

(2S)-2-{[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

Traditional Name

(2S)-2-{[(10S,11S)-2,5,10,11,13,17-hexahydroxy-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)C3=C(O)C4=C(C(O)=C3C(=O)C2=C1)C1=C(O)C(C(=O)NC(C)C(O)=O)=C(C)C=C1[C@H](O)[C@H]4O

InChI Identifier

InChI=1S/C28H23NO12/c1-7-4-10-15(22(33)13(7)27(38)29-8(2)28(39)40)16-17(26(37)21(10)32)25(36)19-18(24(16)35)20(31)11-5-9(41-3)6-12(30)14(11)23(19)34/h4-6,8,21,26,30,32-33,35-37H,1-3H3,(H,29,38)(H,39,40)/t8?,21-,26-/m0/s1

InChI Key

SBIJXMUETDVEQB-CJERNAKNSA-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	NPAtlas	8478259
Actinomadura verrucosospora	LOTUS Database	35616633
Actinomadura verrucosospora subsp. neohibisca E-40 mutant	Bacteria	KNApSAcK

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	1.78	ALOGPS
logP	3.84	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	2.97	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	231.15 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	141.27 m³·mol⁻¹	ChemAxon
Polarizability	57.25 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA021265

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

389961

KEGG Compound ID

C06780

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441174

PDB ID

Not Available

ChEBI ID

8353

Good Scents ID

Not Available

References

General References

Furumai T, Kakinuma S, Yamamoto H, Komiyama N, Suzuki K, Saitoh K, Oki T: Biosynthesis of the pradimicin family of antibiotics. I. Generation and selection of pradimicin-nonproducing mutants. J Antibiot (Tokyo). 1993 Mar;46(3):412-9. doi: 10.7164/antibiotics.46.412. [PubMed:8478259 ]

Showing NP-Card for Pradimicinone II (NP0022971)

MOL for NP0022971 (Pradimicinone II)

3D MOL for NP0022971 (Pradimicinone II)

3D SDF for NP0022971 (Pradimicinone II)

3D-SDF for NP0022971 (Pradimicinone II)

PDB for NP0022971 (Pradimicinone II)

3D PDB for NP0022971 (Pradimicinone II)

SMILES for NP0022971 (Pradimicinone II)

INCHI for NP0022971 (Pradimicinone II)

Structure for NP0022971 (Pradimicinone II)

3D Structure for NP0022971 (Pradimicinone II)