MiMeDB: Showing metabocard for Dehydroxynocardamine (MMDBc0017185)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:38:28 UTC

Update Date

2025-10-07 16:06:38 UTC

Metabolite ID

MMDBc0017185

Metabolite Identification

Common Name

Dehydroxynocardamine

Description

Dehydroxynocardamine is a member of the chemical class of metabolites known as siderophores, which are small, high-affinity iron-chelating compounds. Its chemical structure features a complex arrangement of aromatic and aliphatic moieties that facilitate its role in iron acquisition, particularly in microbial environments. Dehydroxynocardamine is involved in various biochemical pathways, including the biosynthesis of iron-binding compounds that help organisms thrive in iron-limited environments. It is often found in association with other known compounds such as nocardamine and ferrioxamine, highlighting its role in microbial metabolism and competition for iron. Studies have shown that dehydroxynocardamine is produced by certain strains of Streptomyces, indicating its significance in the ecology of soil microorganisms. The expression of dehydroxynocardamine biosynthetic gene clusters (BGCs) has been confirmed in vivo, suggesting its active role in the human microbiome as well (PMID:30578265 ). Furthermore, it has been isolated alongside other metabolites, demonstrating its presence in diverse biological samples (PMID:40160742 , PMID:38486398 , PMID:37760763 , PMID:24252813 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241518282D          

 41 41  0  0  0  0            999 V2000
    5.2191    5.3768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5154    4.6069    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1399    5.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8456    4.7186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6572    3.9154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0574    3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6301    2.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0276    1.6775    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6002    0.9719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7754    0.9891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9977    0.2489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5703   -0.4568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9678   -1.1797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7926   -1.1970    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5405   -1.8854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7156   -1.8682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9379   -2.6083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5106   -3.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9081   -4.0370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4807   -4.7427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6559   -4.7254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2286   -5.4311    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4037   -5.4139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9764   -6.1196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0063   -4.6909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4336   -3.9852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0361   -3.2623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2113   -3.2450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4635   -2.5566    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0660   -1.8337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4934   -1.1280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0959   -0.4050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5232    0.3007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1258    1.0236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5531    1.7293    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1556    2.4522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3308    2.4695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5830    3.1579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1855    3.8809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6129    4.5865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1998    5.3007    0.0000 O   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  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  2 40  1  0  0  0  0
 40 41  2  0  0  0  0
M  END


  Mrv1533004241518282D          

 41 41  0  0  0  0            999 V2000
    5.2191    5.3768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5154    4.6069    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1399    5.1460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8456    4.7186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6572    3.9154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0574    3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6301    2.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0276    1.6775    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6002    0.9719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7754    0.9891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9977    0.2489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5703   -0.4568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9678   -1.1797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7926   -1.1970    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5405   -1.8854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7156   -1.8682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9379   -2.6083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5106   -3.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9081   -4.0370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4807   -4.7427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6559   -4.7254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2286   -5.4311    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4037   -5.4139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9764   -6.1196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0063   -4.6909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4336   -3.9852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0361   -3.2623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2113   -3.2450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4635   -2.5566    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0660   -1.8337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4934   -1.1280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0959   -0.4050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5232    0.3007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1258    1.0236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5531    1.7293    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1556    2.4522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3308    2.4695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5830    3.1579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1855    3.8809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6129    4.5865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1998    5.3007    0.0000 O   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  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  2 40  1  0  0  0  0
 40 41  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017185

> <DATABASE_NAME>
MIME

> <SMILES>
ON1CCCCCNC(=O)CCC(=O)NCCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H48N6O8/c34-22-10-11-23(35)29-18-6-2-8-20-32(40)27(39)15-13-25(37)31-19-7-3-9-21-33(41)26(38)14-12-24(36)30-17-5-1-4-16-28-22/h40-41H,1-21H2,(H,28,34)(H,29,35)(H,30,36)(H,31,37)

> <INCHI_KEY>
ABHHIGWFFMCQOC-UHFFFAOYSA-N

> <FORMULA>
C27H48N6O8

> <MOLECULAR_WEIGHT>
584.715

> <EXACT_MASS>
584.35336253

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
89

> <JCHEM_AVERAGE_POLARIZABILITY>
63.63585517333745

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,12-dihydroxy-1,6,12,17,23,28-hexaazacyclotritriacontane-2,5,13,16,24,27-hexone

> <ALOGPS_LOGP>
0.69

> <JCHEM_LOGP>
-2.1503132496666657

> <ALOGPS_LOGS>
-3.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.687263751674797

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.085203817907317

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3465296772352402

> <JCHEM_POLAR_SURFACE_AREA>
197.48

> <JCHEM_REFRACTIVITY>
150.87960000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.83e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,12-dihydroxy-1,6,12,17,23,28-hexaazacyclotritriacontane-2,5,13,16,24,27-hexone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0       9.742  10.037   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0      10.295   8.600   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      11.461   9.606   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.778   8.808   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.427   7.309   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.174   5.798   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.376   4.481   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      13.118   3.131   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      12.320   1.814   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.781   1.846   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.062   0.465   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.265  -0.853   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.007  -2.202   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      14.546  -2.234   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      12.209  -3.519   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      10.669  -3.487   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      12.951  -4.869   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.153  -6.186   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.895  -7.536   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.097  -8.853   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.558  -8.821   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       9.760 -10.138   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       8.220 -10.106   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.423 -11.423   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.478  -8.756   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.276  -7.439   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.534  -6.090   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.994  -6.057   0.000  0.00  0.00           O+0
HETATM   29  N   UNK     0       8.332  -4.772   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       7.590  -3.423   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.388  -2.106   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.646  -0.756   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.443   0.561   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.701   1.911   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0       8.499   3.228   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0       7.757   4.577   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.218   4.610   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       8.555   5.895   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       7.813   7.244   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       8.611   8.562   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       7.840   9.895   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   40                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39    2   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   82    0
END

Synonyms

Value	Source
Dehydroxynocardamine	MeSH

Molecular Formula

C₂₇H₄₈N₆O₈

Average Mass

584.715

Monoisotopic Mass

584.35336253

IUPAC Name

1,12-dihydroxy-1,6,12,17,23,28-hexaazacyclotritriacontane-2,5,13,16,24,27-hexone

Traditional Name

1,12-dihydroxy-1,6,12,17,23,28-hexaazacyclotritriacontane-2,5,13,16,24,27-hexone

CAS Registry Number

Not Available

SMILES

ON1CCCCCNC(=O)CCC(=O)NCCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O

InChI Identifier

InChI=1S/C27H48N6O8/c34-22-10-11-23(35)29-18-6-2-8-20-32(40)27(39)15-13-25(37)31-19-7-3-9-21-33(41)26(38)14-12-24(36)30-17-5-1-4-16-28-22/h40-41H,1-21H2,(H,28,34)(H,29,35)(H,30,36)(H,31,37)

InChI Key

ABHHIGWFFMCQOC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolactams

Sub Class

Not Available

Direct Parent

Macrolactams

Alternative Parents

Substituents

Macrolactam
Carboxamide group
Hydroxamic acid
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.28 g/L	ALOGPS
logP	0.69	ALOGPS
logP	-2.2	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	8.09	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	197.48 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	150.88 m³·mol⁻¹	ChemAxon
Polarizability	63.64 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	313.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	125.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	439.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	448.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	280.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	137.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2202.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	706.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	297.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	317.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	255.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	147.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	193.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	65.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	550.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	153.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	302.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1473.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	967.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Dehydroxynocardamine_TMS_1	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	282.2
Gas Chromatography	Dehydroxynocardamine_TMS_2	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1967.89
Gas Chromatography	Dehydroxynocardamine_TMS_3	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	2315.8
Gas Chromatography	Dehydroxynocardamine_TMS_4	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	3484.68
Gas Chromatography	Dehydroxynocardamine_TMS_5	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	2863.98
Gas Chromatography	Dehydroxynocardamine_TMS_6	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1608.08
Gas Chromatography	Dehydroxynocardamine_TMS_7	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC1=O	standard non polar	2025-10-23	1521.9
Gas Chromatography	Dehydroxynocardamine_TMS_8	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1621.25
Gas Chromatography	Dehydroxynocardamine_TMS_9	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1826.09
Gas Chromatography	Dehydroxynocardamine_TMS_10	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	1937.03
Gas Chromatography	Dehydroxynocardamine_TMS_11	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1618.51
Gas Chromatography	Dehydroxynocardamine_TMS_12	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	2981.94
Gas Chromatography	Dehydroxynocardamine_TMS_13	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	2893.07
Gas Chromatography	Dehydroxynocardamine_TMS_14	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard non polar	2025-10-23	1416.41
Gas Chromatography	Dehydroxynocardamine_TMS_15	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard non polar	2025-10-23	728.509
Gas Chromatography	Dehydroxynocardamine_TMS_1	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC1=O	standard polar	2025-10-23	2653.02
Gas Chromatography	Dehydroxynocardamine_TMS_2	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	1595.99
Gas Chromatography	Dehydroxynocardamine_TMS_3	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	2269.08
Gas Chromatography	Dehydroxynocardamine_TMS_4	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	2370.34
Gas Chromatography	Dehydroxynocardamine_TMS_5	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)NCCCCCNC(=O)CCC1=O	standard polar	2025-10-23	2441.1
Gas Chromatography	Dehydroxynocardamine_TMS_6	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	1794.89
Gas Chromatography	Dehydroxynocardamine_TMS_7	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC1=O	standard polar	2025-10-23	1800.64
Gas Chromatography	Dehydroxynocardamine_TMS_8	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	1362.57
Gas Chromatography	Dehydroxynocardamine_TMS_9	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	1662.79
Gas Chromatography	Dehydroxynocardamine_TMS_10	C[Si](C)(C)N1CCCCCNC(=O)CCC(=O)NCCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	1484.18
Gas Chromatography	Dehydroxynocardamine_TMS_11	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	2548.51
Gas Chromatography	Dehydroxynocardamine_TMS_12	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)NCCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	1764.12
Gas Chromatography	Dehydroxynocardamine_TMS_13	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC(=O)NCCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	1121.29
Gas Chromatography	Dehydroxynocardamine_TMS_14	C[Si](C)(C)N1CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N(O)CCCCCNC(=O)CCC1=O	standard polar	2025-10-23	1105.85
Gas Chromatography	Dehydroxynocardamine_TMS_15	C[Si](C)(C)N1CCCCCN(O)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN([Si](C)(C)C)C(=O)CCC(=O)N([Si](C)(C)C)CCCCCN(O)C(=O)CCC1=O	standard polar	2025-10-23	3073.92

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	2	Human	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11606728

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

ABHHIGWFFMCQOC-UHFFFAOYSA-N

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Dehydroxynocardamine (MMDBc0017185)

MOL for #<Metabolite:0x00007fc976a32a40>

3D MOL for #<Metabolite:0x00007fc976a32a40>

3D SDF for #<Metabolite:0x00007fc976a32a40>

3D-SDF for #<Metabolite:0x00007fc976a32a40>

PDB for #<Metabolite:0x00007fc976a32a40>

3D PDB for #<Metabolite:0x00007fc976a32a40>

SMILES for #<Metabolite:0x00007fc976a32a40>

INCHI for #<Metabolite:0x00007fc976a32a40>

Structure for #<Metabolite:0x00007fc976a32a40>

3D Structure for #<Metabolite:0x00007fc976a32a40>