MiMeDB: Showing metabocard for Safracin A (MMDBc0020429)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:28:11 UTC

Update Date

2025-10-07 16:07:06 UTC

Metabolite ID

MMDBc0020429

Metabolite Identification

Common Name

Safracin A

Description

Safracin A is a member of the saframycin family of antibiotics, characterized by its unique chemical structure that contributes to its biological activity. The saframycin class is known for its complex bicyclic core, which is essential for its antibacterial properties. In terms of chemical pathways, safracin A is involved in the inhibition of bacterial DNA synthesis, thereby affecting the replication and transcription processes essential for bacterial growth. This mechanism is similar to that of other antibiotics within the same family, including safracin B, which is a hydroxylated derivative of safracin A (PMID:4019320 ). Notably, while safracin A exhibits therapeutic potential, it has been observed that the toxic and effective doses of safracin B are significantly lower than those of safracin A (PMID:4019320 ). Additionally, safracin B has been reported to enhance the life span of tumor-bearing mice more effectively than safracin A (PMID:4019320 ), indicating differences in their biological efficacy and safety profiles. Overall, safracin A represents an important compound within the saframycin antibiotic family, contributing to ongoing research in antimicrobial therapy.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152112282D          

 43 47  0  0  1  0            999 V2000
    9.3793    2.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0600    1.4546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8638    7.3722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2514    3.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3928    1.2190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0401    2.4554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1351    3.3506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0891    4.1377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8134    2.2203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1503    4.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5759    4.3224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5543    2.6401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.0435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0849    6.5774    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.3101    3.3428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3707    4.5434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0145    2.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3912    2.8092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3713    3.8100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.9044    2.6245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    3.2212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1096    2.4035    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4367    1.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3236    1.9140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9946    3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1486    1.9218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4168    2.8383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5070    5.9885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8837    6.3714    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7281    5.1937    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9727    3.5061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1702    3.6040    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6578    1.0426    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9179    1.1956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7736    4.2220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7082    6.1945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5678    1.2112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179    3.0443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2860    6.7834    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4707    5.3623    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5778    2.9468    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.0160    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0096    1.5845    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 12  1  1  0  0  0  0
 12  7  2  0  0  0  0
 13  2  1  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 15  8  1  0  0  0  0
 16  8  1  0  0  0  0
 16 11  1  0  0  0  0
 17  9  1  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  6  0  0  0
 20 15  2  0  0  0  0
 21 17  2  0  0  0  0
 21 19  1  0  0  0  0
 22 18  1  0  0  0  0
 22 20  1  0  0  0  0
 23 13  1  0  0  0  0
 23 17  1  0  0  0  0
 24 20  1  0  0  0  0
 25 21  1  0  0  0  0
 26 12  1  0  0  0  0
 26 24  2  0  0  0  0
 27 13  2  0  0  0  0
 27 25  1  0  0  0  0
 28 14  1  0  0  0  0
 14 29  1  1  0  0  0
 30 10  1  4  0  0  0
 30 28  2  0  0  0  0
 31  4  1  0  0  0  0
 31 16  1  0  0  0  0
 31 22  1  0  0  0  0
 32 11  1  0  0  0  0
 32 18  1  0  0  0  0
 32 19  1  0  0  0  0
 33 23  2  0  0  0  0
 34 24  1  0  0  0  0
 35 25  2  0  0  0  0
 36 28  1  0  0  0  0
 37  5  1  0  0  0  0
 37 26  1  0  0  0  0
 38  6  1  0  0  0  0
 38 27  1  0  0  0  0
 14 39  1  1  0  0  0
 16 40  1  6  0  0  0
 18 41  1  1  0  0  0
 19 42  1  1  0  0  0
 22 43  1  6  0  0  0
M  END


  Mrv1652305152112282D          

 43 47  0  0  1  0            999 V2000
    9.3793    2.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0600    1.4546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8638    7.3722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2514    3.1056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3928    1.2190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0401    2.4554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1351    3.3506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0891    4.1377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8134    2.2203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1503    4.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5759    4.3224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5543    2.6401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.0435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0849    6.5774    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.3101    3.3428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3707    4.5434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0145    2.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3912    2.8092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3713    3.8100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.9044    2.6245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    3.2212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1096    2.4035    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4367    1.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3236    1.9140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9946    3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1486    1.9218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4168    2.8383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5070    5.9885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8837    6.3714    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7281    5.1937    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9727    3.5061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1702    3.6040    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6578    1.0426    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9179    1.1956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7736    4.2220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7082    6.1945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5678    1.2112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179    3.0443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2860    6.7834    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4707    5.3623    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5778    2.9468    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.0160    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0096    1.5845    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 12  1  1  0  0  0  0
 12  7  2  0  0  0  0
 13  2  1  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 15  8  1  0  0  0  0
 16  8  1  0  0  0  0
 16 11  1  0  0  0  0
 17  9  1  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  6  0  0  0
 20 15  2  0  0  0  0
 21 17  2  0  0  0  0
 21 19  1  0  0  0  0
 22 18  1  0  0  0  0
 22 20  1  0  0  0  0
 23 13  1  0  0  0  0
 23 17  1  0  0  0  0
 24 20  1  0  0  0  0
 25 21  1  0  0  0  0
 26 12  1  0  0  0  0
 26 24  2  0  0  0  0
 27 13  2  0  0  0  0
 27 25  1  0  0  0  0
 28 14  1  0  0  0  0
 14 29  1  1  0  0  0
 30 10  1  4  0  0  0
 30 28  2  0  0  0  0
 31  4  1  0  0  0  0
 31 16  1  0  0  0  0
 31 22  1  0  0  0  0
 32 11  1  0  0  0  0
 32 18  1  0  0  0  0
 32 19  1  0  0  0  0
 33 23  2  0  0  0  0
 34 24  1  0  0  0  0
 35 25  2  0  0  0  0
 36 28  1  0  0  0  0
 37  5  1  0  0  0  0
 37 26  1  0  0  0  0
 38  6  1  0  0  0  0
 38 27  1  0  0  0  0
 14 39  1  1  0  0  0
 16 40  1  6  0  0  0
 18 41  1  1  0  0  0
 19 42  1  1  0  0  0
 22 43  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020429

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(N)C(O)=NC[C@]1([H])N2C[C@@]3([H])CC4=C(C(O)=C(OC)C(C)=C4)[C@]([H])(N3C)[C@]2([H])CC2=C1C(=O)C(OC)=C(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C28H36N4O6/c1-12-7-15-8-16-11-32-18(22(31(16)4)20(15)24(34)26(12)37-5)9-17-21(19(32)10-30-28(36)14(3)29)25(35)27(38-6)13(2)23(17)33/h7,14,16,18-19,22,34H,8-11,29H2,1-6H3,(H,30,36)/t14-,16+,18-,19-,22+/m0/s1

> <INCHI_KEY>
AZDDAJXLYMVMAW-BVFBRMCBSA-N

> <FORMULA>
C28H36N4O6

> <MOLECULAR_WEIGHT>
524.618

> <EXACT_MASS>
524.263484895

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
56.70086077673262

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-N-{[(1S,2S,10R,13R)-19-hydroxy-7,18-dimethoxy-6,17,21-trimethyl-5,8-dioxo-11,21-diazapentacyclo[11.7.1.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-4(9),6,15(20),16,18-pentaen-10-yl]methyl}propanimidic acid

> <ALOGPS_LOGP>
1.36

> <JCHEM_LOGP>
-0.171238049186227

> <ALOGPS_LOGS>
-3.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
9.568996441373118

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7620417182976462

> <JCHEM_PKA_STRONGEST_BASIC>
8.9495311988572

> <JCHEM_POLAR_SURFACE_AREA>
137.92

> <JCHEM_REFRACTIVITY>
144.49590000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.71e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-N-{[(1S,2S,10R,13R)-19-hydroxy-7,18-dimethoxy-6,17,21-trimethyl-5,8-dioxo-11,21-diazapentacyclo[11.7.1.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-4(9),6,15(20),16,18-pentaen-10-yl]methyl}propanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      17.508   4.943   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.845   2.715   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.079  13.761   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.803   5.797   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.533   2.276   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.942   4.583   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.186   6.255   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.233   7.724   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.985   4.145   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.747   8.596   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.408   8.068   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.968   4.928   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.924   3.814   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.492  12.278   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.646   6.240   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.892   8.481   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.494   4.529   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.064   5.244   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.160   7.112   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.888   4.899   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.081   6.013   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.405   4.486   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.415   3.430   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.671   3.573   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.590   6.397   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      15.211   3.587   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.511   5.298   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.413  11.179   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      10.983  11.893   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       8.826   9.695   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      11.149   6.545   0.000  0.00  0.00           N+0
HETATM   32  N   UNK     0       9.651   6.728   0.000  0.00  0.00           N+0
HETATM   33  O   UNK     0       6.828   1.946   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      12.913   2.232   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       5.177   7.881   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       6.922  11.563   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      15.993   2.261   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       3.020   5.683   0.000  0.00  0.00           O+0
HETATM   39  H   UNK     0       8.001  12.662   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0      12.079  10.010   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       8.545   5.501   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       6.669   7.497   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0      11.218   2.958   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4   31                                                            
CONECT    5   37                                                            
CONECT    6   38                                                            
CONECT    7   12   15                                                       
CONECT    8   15   16                                                       
CONECT    9   17   18                                                       
CONECT   10   19   30                                                       
CONECT   11   16   32                                                       
CONECT   12    1    7   26                                                  
CONECT   13    2   23   27                                                  
CONECT   14    3   28   29   39                                             
CONECT   15    7    8   20                                                  
CONECT   16    8   11   31   40                                             
CONECT   17    9   21   23                                                  
CONECT   18    9   22   32   41                                             
CONECT   19   10   21   32   42                                             
CONECT   20   15   22   24                                                  
CONECT   21   17   19   25                                                  
CONECT   22   18   20   31   43                                             
CONECT   23   13   17   33                                                  
CONECT   24   20   26   34                                                  
CONECT   25   21   27   35                                                  
CONECT   26   12   24   37                                                  
CONECT   27   13   25   38                                                  
CONECT   28   14   30   36                                                  
CONECT   29   14                                                            
CONECT   30   10   28                                                       
CONECT   31    4   16   22                                                  
CONECT   32   11   18   19                                                  
CONECT   33   23                                                            
CONECT   34   24                                                            
CONECT   35   25                                                            
CONECT   36   28                                                            
CONECT   37    5   26                                                       
CONECT   38    6   27                                                       
CONECT   39   14                                                            
CONECT   40   16                                                            
CONECT   41   18                                                            
CONECT   42   19                                                            
CONECT   43   22                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   94    0
END

Synonyms

Not Available

Molecular Formula

C₂₈H₃₆N₄O₆

Average Mass

524.618

Monoisotopic Mass

524.263484895

IUPAC Name

(2S)-2-amino-N-{[(1S,2S,10R,13R)-19-hydroxy-7,18-dimethoxy-6,17,21-trimethyl-5,8-dioxo-11,21-diazapentacyclo[11.7.1.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-4(9),6,15(20),16,18-pentaen-10-yl]methyl}propanimidic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(N)C(O)=NC[C@]1([H])N2C[C@@]3([H])CC4=C(C(O)=C(OC)C(C)=C4)[C@]([H])(N3C)[C@]2([H])CC2=C1C(=O)C(OC)=C(C)C2=O

InChI Identifier

InChI=1S/C28H36N4O6/c1-12-7-15-8-16-11-32-18(22(31(16)4)20(15)24(34)26(12)37-5)9-17-21(19(32)10-30-28(36)14(3)29)25(35)27(38-6)13(2)23(17)33/h7,14,16,18-19,22,34H,8-11,29H2,1-6H3,(H,30,36)/t14-,16+,18-,19-,22+/m0/s1

InChI Key

AZDDAJXLYMVMAW-BVFBRMCBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acid amides

Alternative Parents

Substituents

Alpha-amino acid amide
Isoquinoline quinone
Benzazocine
Alanine or derivatives
Isoquinolone
Tetrahydroisoquinoline
Anisole
1-hydroxy-4-unsubstituted benzenoid
N-methylpiperazine
Alkyl aryl ether
Aralkylamine
N-alkylpiperazine
Piperazine
1,4-diazinane
Benzenoid
Vinylogous ester
Tertiary aliphatic amine
Carboxamide group
Tertiary amine
Ketone
Secondary carboxylic acid amide
Azacycle
Ether
Organoheterocyclic compound
Primary amine
Organic oxygen compound
Amine
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.27 g/L	ALOGPS
logP	1.36	ALOGPS
logP	-0.17	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	1.76	ChemAxon
pKa (Strongest Basic)	8.95	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	137.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	144.5 m³·mol⁻¹	ChemAxon
Polarizability	56.7 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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	270.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	133.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	403.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	353.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	300.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	159.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1630.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	256.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	315.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	232.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	192.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	144.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	141.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	133.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	256.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	74.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	299.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1481.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	854.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Safracin A_TMS_1	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2486.28
Gas Chromatography	Safracin A_TMS_2	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	1468.33
Gas Chromatography	Safracin A_TMS_3	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	1708.17
Gas Chromatography	Safracin A_TMS_4	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	1060.2
Gas Chromatography	Safracin A_TMS_5	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	956.609
Gas Chromatography	Safracin A_TMS_6	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2001.03
Gas Chromatography	Safracin A_TMS_7	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2126.12
Gas Chromatography	Safracin A_TMS_8	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2661.01
Gas Chromatography	Safracin A_TMS_9	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2107.81
Gas Chromatography	Safracin A_TMS_10	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2010.22
Gas Chromatography	Safracin A_TMS_11	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard non polar	2025-10-23	2158.47
Gas Chromatography	Safracin A_TMS_1	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	2317.54
Gas Chromatography	Safracin A_TMS_2	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	3147.63
Gas Chromatography	Safracin A_TMS_3	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	2554.85
Gas Chromatography	Safracin A_TMS_4	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	1108.46
Gas Chromatography	Safracin A_TMS_5	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	3860.36
Gas Chromatography	Safracin A_TMS_6	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	2481.02
Gas Chromatography	Safracin A_TMS_7	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	524.418
Gas Chromatography	Safracin A_TMS_8	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	288.874
Gas Chromatography	Safracin A_TMS_9	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	1166.82
Gas Chromatography	Safracin A_TMS_10	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	2466.32
Gas Chromatography	Safracin A_TMS_11	COC1=C(C)C(=O)C2=C(C1=O)[C@H](CN=C(O[Si](C)(C)C)[C@H](C)N([Si](C)(C)C)[Si](C)(C)C)N1C[C@H]3CC4=CC(C)=C(OC)C(O[Si](C)(C)C)=C4[C@@H]([C@@H]1C2)N3C	standard polar	2025-10-23	1499.0

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	Proteobacteria	1	Human ; Human subgingival plaque	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

C00018534

Chemspider ID

140880

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

160293

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

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 Safracin A (MMDBc0020429)

MOL for #<Metabolite:0x00007f9aa07d7110>

3D MOL for #<Metabolite:0x00007f9aa07d7110>

3D SDF for #<Metabolite:0x00007f9aa07d7110>

3D-SDF for #<Metabolite:0x00007f9aa07d7110>

PDB for #<Metabolite:0x00007f9aa07d7110>

3D PDB for #<Metabolite:0x00007f9aa07d7110>

SMILES for #<Metabolite:0x00007f9aa07d7110>

INCHI for #<Metabolite:0x00007f9aa07d7110>

Structure for #<Metabolite:0x00007f9aa07d7110>

3D Structure for #<Metabolite:0x00007f9aa07d7110>