NP-MRD: Showing NP-Card for (3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione (NP0260934)

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Record Information

Version

1.0

Created at

2022-09-08 03:14:31 UTC

Updated at

2022-09-08 03:14:32 UTC

NP-MRD ID

NP0260934

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

Description

Jadomycin A belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included. (3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione is found in Streptomyces venezuelae. It was first documented in 2012 (PMID: 23177193). Based on a literature review a significant number of articles have been published on jadomycin A (PMID: 23670961) (PMID: 32416952) (PMID: 24112541) (PMID: 23731237).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082205142D          

 31 35  0  0  1  0            999 V2000
    6.4852    2.0933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7629    1.6946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7469    0.8698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4533    0.4436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0246    0.4712    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2776    0.8212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1217    1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7138    0.2189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1124   -0.5034    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8424   -1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0323   -1.4389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7622   -2.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9521   -2.3743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3023   -2.8421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1124   -2.6861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6525   -3.3098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3825   -1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -1.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4627   -0.9711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2728   -0.8152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -0.0357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8129   -1.4389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -0.5034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1631   -1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -2.6861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0829   -2.8421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -2.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7327   -2.3743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4627   -3.1539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9226   -0.3475    0.0000 N   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
  5  3  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 11 12  1  0  0  0  0
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 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
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 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
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 28 29  1  0  0  0  0
 18 29  1  0  0  0  0
 29 30  2  0  0  0  0
 19 31  1  0  0  0  0
  9 31  1  6  0  0  0
  5 31  1  0  0  0  0
M  END

     RDKit          3D

 52 56  0  0  0  0  0  0  0  0999 V2000
    4.8588   -1.5152    0.1755 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1606   -0.2277    0.3594 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6915   -0.1918    0.2288 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0530   -1.1316    1.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1210   -0.3512   -1.1449 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3027   -1.7540   -1.6272 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2526   -2.3150   -2.2182 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1283   -2.4642   -1.2976 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1012   -1.5346   -1.5285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1454   -1.8260   -0.7818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5446   -3.1218   -0.7356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7161   -3.4515   -0.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1429   -4.8719   -0.0681 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0893   -1.1210    0.4316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9469   -0.2671    1.0460 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9240   -0.8068   -0.1905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4256    0.5635   -0.1803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2137    0.8030   -0.7292 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2994    2.1446   -0.8724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4444    2.3737   -1.3996 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5210    3.2522   -0.4005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0564    4.5310   -0.5227 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1934    4.7220   -1.1007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8515    5.5587   -0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0805    5.3585    0.5006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454    4.0539    0.6209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7475    3.0287    0.1639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2551    1.6412    0.2964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3630    1.5249    0.8105 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.4446   -1.6004   -0.7812 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6310    0.5033   -0.3677 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4262    0.2144    1.3563 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.4669   -2.1406    1.2043 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4527    0.3857   -1.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1960   -1.4932   -2.6027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9590   -3.9383   -1.1854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7707   -5.2908    0.9008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6323   -5.4391   -0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2490   -4.9718   -0.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4020   -2.7552    0.9501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8089   -0.5430    1.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5479    5.6441   -1.1979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4507    6.5643   -0.1798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6685    6.1863    0.8430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5077    3.8712    1.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
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  5 31  1  0
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  6  5  1  0
 17 10  1  0
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  1 32  1  0
  1 33  1  0
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  2 35  1  0
  2 36  1  0
  3 37  1  1
  4 38  1  0
  4 39  1  0
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 14 47  1  0
 16 48  1  0
 24 49  1  0
 25 50  1  0
 26 51  1  0
 27 52  1  0
M  END


  Mrv1652309082205142D          

 31 35  0  0  1  0            999 V2000
    6.4852    2.0933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7629    1.6946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7469    0.8698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4533    0.4436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0246    0.4712    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2776    0.8212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1217    1.6314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7138    0.2189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1124   -0.5034    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8424   -1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0323   -1.4389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7622   -2.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9521   -2.3743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3023   -2.8421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1124   -2.6861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6525   -3.3098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3825   -1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1926   -1.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4627   -0.9711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2728   -0.8152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -0.0357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8129   -1.4389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6230   -1.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -0.5034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1631   -1.9066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8931   -2.6861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0829   -2.8421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5428   -2.2184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7327   -2.3743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4627   -3.1539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  3  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
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 19 20  1  0  0  0  0
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 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
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 22 28  1  0  0  0  0
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 29 30  2  0  0  0  0
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  9 31  1  6  0  0  0
  5 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0260934

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)[C@@H]1N2[C@@H](OC1=O)C1=CC(C)=CC(O)=C1C1=C2C(=O)C2=C(O)C=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H21NO6/c1-4-11(3)19-24(30)31-23-13-8-10(2)9-15(27)16(13)18-20(25(19)23)22(29)17-12(21(18)28)6-5-7-14(17)26/h5-9,11,19,23,26-27H,4H2,1-3H3/t11?,19-,23-/m0/s1

> <INCHI_KEY>
AVMSKCRHMKXYOO-RCAPREFBSA-N

> <FORMULA>
C24H21NO6

> <MOLECULAR_WEIGHT>
419.433

> <EXACT_MASS>
419.1368874

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
43.13121077786825

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6S)-3-(butan-2-yl)-11,19-dihydroxy-9-methyl-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

> <JCHEM_LOGP>
4.8087721519999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.47214782994221

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.868682031074928

> <JCHEM_PKA_STRONGEST_BASIC>
-5.651775836360536

> <JCHEM_POLAR_SURFACE_AREA>
104.14

> <JCHEM_REFRACTIVITY>
113.59989999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      12.106   3.907   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.757   3.163   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.728   1.624   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.046   0.828   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.379   0.880   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.985   1.533   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.694   3.045   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       6.932   0.409   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.677  -0.940   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.172  -2.395   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.660  -2.686   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.156  -4.141   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.644  -4.432   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.164  -5.305   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.677  -5.014   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.685  -6.178   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.181  -3.559   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.693  -3.268   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.197  -1.813   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.709  -1.522   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.213  -0.067   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      12.717  -2.686   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.230  -2.395   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      14.734  -0.940   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      15.238  -3.559   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      14.734  -5.014   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.221  -5.305   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.213  -4.141   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.701  -4.432   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      10.197  -5.887   0.000  0.00  0.00           O+0
HETATM   31  N   UNK     0       9.189  -0.649   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   31                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   31                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17   19   29                                                  
CONECT   19   18   20   31                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   28                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   22   29                                                  
CONECT   29   28   18   30                                                  
CONECT   30   29                                                            
CONECT   31   19    9    5                                                  
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₁NO₆

Average Mass

419.4330 Da

Monoisotopic Mass

419.13689 Da

IUPAC Name

(3S,6S)-3-(butan-2-yl)-11,19-dihydroxy-9-methyl-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

Traditional Name

(3S,6S)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

CAS Registry Number

Not Available

SMILES

CCC(C)[C@@H]1N2[C@@H](OC1=O)C1=CC(C)=CC(O)=C1C1=C2C(=O)C2=C(O)C=CC=C2C1=O

InChI Identifier

InChI=1S/C24H21NO6/c1-4-11(3)19-24(30)31-23-13-8-10(2)9-15(27)16(13)18-20(25(19)23)22(29)17-12(21(18)28)6-5-7-14(17)26/h5-9,11,19,23,26-27H,4H2,1-3H3/t11?,19-,23-/m0/s1

InChI Key

AVMSKCRHMKXYOO-RCAPREFBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Benzoquinolines

Direct Parent

Phenanthridines and derivatives

Alternative Parents

Substituents

Phenanthridine
Alpha-amino acid ester
Quinoline quinone
Naphthoquinone
Naphthalene
Alpha-amino acid or derivatives
Aryl ketone
Quinone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Oxazolidinone
Vinylogous amide
Vinylogous acid
Oxazolidine
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Azacycle
Monocarboxylic acid or derivatives
Enamine
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	4.81	ChemAxon
pKa (Strongest Acidic)	7.87	ChemAxon
pKa (Strongest Basic)	-5.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	104.14 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	113.6 m³·mol⁻¹	ChemAxon
Polarizability	43.13 Å³	ChemAxon
Number of Rings	5	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78438513

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15662692

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yang X, Yu B: Total synthesis of jadomycins B, S, T, and ILEVS1080. Chemistry. 2013 Jun 24;19(26):8431-4. doi: 10.1002/chem.201301297. Epub 2013 May 13. [PubMed:23670961 ]
de Koning CB, Ngwira KJ, Rousseau AL: Biosynthesis, synthetic studies, and biological activities of the jadomycin alkaloids and related analogues. Alkaloids Chem Biol. 2020;84:125-199. doi: 10.1016/bs.alkal.2020.02.001. Epub 2020 Mar 9. [PubMed:32416952 ]
Zhang Y, Pan G, Zou Z, Fan K, Yang K, Tan H: JadR*-mediated feed-forward regulation of cofactor supply in jadomycin biosynthesis. Mol Microbiol. 2013 Nov;90(4):884-97. doi: 10.1111/mmi.12406. Epub 2013 Oct 17. [PubMed:24112541 ]
Kallio P, Patrikainen P, Belogurov GA, Mantsala P, Yang K, Niemi J, Metsa-Ketela M: Tracing the evolution of angucyclinone monooxygenases: structural determinants for C-12b hydroxylation and substrate inhibition in PgaE. Biochemistry. 2013 Jul 2;52(26):4507-16. doi: 10.1021/bi400381s. Epub 2013 Jun 17. [PubMed:23731237 ]
Fan K, Pan G, Peng X, Zheng J, Gao W, Wang J, Wang W, Li Y, Yang K: Identification of JadG as the B ring opening oxygenase catalyzing the oxidative C-C bond cleavage reaction in jadomycin biosynthesis. Chem Biol. 2012 Nov 21;19(11):1381-90. doi: 10.1016/j.chembiol.2012.09.009. [PubMed:23177193 ]
LOTUS database [Link]

Showing NP-Card for (3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione (NP0260934)

MOL for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

3D MOL for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

3D SDF for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

3D-SDF for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

PDB for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

3D PDB for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

SMILES for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

INCHI for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

Structure for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)

3D Structure for NP0260934 ((3s,6s)-11,19-dihydroxy-9-methyl-3-(sec-butyl)-5-oxa-2-azapentacyclo[11.8.0.0²,⁶.0⁷,¹².0¹⁵,²⁰]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione)