MiMeDB: Showing metabocard for Pederin (MMDBc0020399)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:25:26 UTC

Update Date

2025-10-07 16:07:05 UTC

Metabolite ID

MMDBc0020399

Metabolite Identification

Common Name

Pederin

Description

Pederin is a polyketide metabolite known for its potent biological activity. Chemically, it is characterized by a complex structure that includes a unique bicyclic core and various functional groups, which contribute to its ability to inhibit protein synthesis in eukaryotic cells by binding to ribosomes (PMID:37963163 ). Pederin and its derivatives have been investigated for their cytotoxic effects, showing significantly greater potency against cancer cell lines compared to non-cancerous cells (PMID:38986017 ). Additionally, pederin-type compounds, including diaphorin, have been shown to promote gene expression, indicating their potential utility in pest management and industrial applications (PMID:38411238 ). The biosynthesis of pederin-family polyketides involves a diverse array of microorganisms, particularly those associated with insect niches, which are known to produce various biologically active compounds (PMID:37909860 ). Recent studies have also explored the dynamics of pederin-producing bacteria within the developmental stages of the beetle Paederus fuscipes, further elucidating the ecological roles of these metabolites (PMID:37771128 ). Overall, pederin exemplifies the intricate relationship between chemistry and biology, with significant implications for therapeutic and agricultural applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152112252D          

 43 44  0  0  1  0            999 V2000
   -6.7283   -3.9930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3533   -3.7065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4139   -4.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1792   -2.9253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1186   -2.9253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3621   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -5.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -7.2697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6014   -6.9507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -4.7947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9765   -5.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7910   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2586   -4.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0711   -4.4817    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.6014   -5.1137    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5055   -3.9697    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6489   -5.2072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3633   -3.9697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9344   -3.9697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.7923   -6.4447    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.0778   -6.0322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6489   -6.0322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6489   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5068   -6.0322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3633   -6.4447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0778   -3.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7923   -7.2697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0778   -5.2072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0765   -3.9697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -4.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -6.4447    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7889   -6.8075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -4.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3192   -5.8890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5408   -3.8498    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8836   -4.3385    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -3.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -3.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -4.3822    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7923   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 14  1  2  0  0  0  0
 14 12  1  0  0  0  0
 15  2  1  6  0  0  0
 15 14  1  0  0  0  0
 16  3  1  6  0  0  0
 16 15  1  0  0  0  0
 17 10  1  0  0  0  0
 17 13  1  0  0  0  0
 18 11  1  0  0  0  0
 19 11  1  0  0  0  0
 20 10  1  1  0  0  0
 22 21  1  0  0  0  0
 18 23  1  6  0  0  0
 24  4  1  0  0  0  0
 24  5  1  0  0  0  0
 24 19  1  0  0  0  0
 24 20  1  0  0  0  0
 25 12  1  0  0  0  0
 25 21  1  6  0  0  0
 26 22  2  0  0  0  0
 23 26  1  6  0  0  0
 19 27  1  1  0  0  0
 21 28  1  6  0  0  0
 22 29  1  4  0  0  0
 30  6  1  0  0  0  0
 30 13  1  0  0  0  0
 31  7  1  0  0  0  0
 17 31  1  6  0  0  0
 32  8  1  0  0  0  0
 32 23  1  0  0  0  0
 33  9  1  0  0  0  0
 25 33  1  1  0  0  0
 34 18  1  0  0  0  0
 34 20  1  0  0  0  0
 35 16  1  0  0  0  0
 35 25  1  0  0  0  0
 15 36  1  1  0  0  0
 16 37  1  1  0  0  0
 17 38  1  6  0  0  0
 18 39  1  1  0  0  0
 19 40  1  6  0  0  0
 20 41  1  6  0  0  0
 21 42  1  6  0  0  0
 23 43  1  1  0  0  0
M  END


  Mrv1652305152112252D          

 43 44  0  0  1  0            999 V2000
   -6.7283   -3.9930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3533   -3.7065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4139   -4.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1792   -2.9253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1186   -2.9253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3621   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -5.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -7.2697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6014   -6.9507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -4.7947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9765   -5.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7910   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2586   -4.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0711   -4.4817    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.6014   -5.1137    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5055   -3.9697    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6489   -5.2072    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3633   -3.9697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9344   -3.9697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.7923   -6.4447    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.0778   -6.0322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6489   -6.0322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6489   -3.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5068   -6.0322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3633   -6.4447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0778   -3.5572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7923   -7.2697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0778   -5.2072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0765   -3.9697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -4.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -6.4447    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7889   -6.8075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -4.7947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3192   -5.8890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5408   -3.8498    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8836   -4.3385    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -3.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -3.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2199   -4.3822    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7923   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3633   -5.6197    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 14  1  2  0  0  0  0
 14 12  1  0  0  0  0
 15  2  1  6  0  0  0
 15 14  1  0  0  0  0
 16  3  1  6  0  0  0
 16 15  1  0  0  0  0
 17 10  1  0  0  0  0
 17 13  1  0  0  0  0
 18 11  1  0  0  0  0
 19 11  1  0  0  0  0
 20 10  1  1  0  0  0
 22 21  1  0  0  0  0
 18 23  1  6  0  0  0
 24  4  1  0  0  0  0
 24  5  1  0  0  0  0
 24 19  1  0  0  0  0
 24 20  1  0  0  0  0
 25 12  1  0  0  0  0
 25 21  1  6  0  0  0
 26 22  2  0  0  0  0
 23 26  1  6  0  0  0
 19 27  1  1  0  0  0
 21 28  1  6  0  0  0
 22 29  1  4  0  0  0
 30  6  1  0  0  0  0
 30 13  1  0  0  0  0
 31  7  1  0  0  0  0
 17 31  1  6  0  0  0
 32  8  1  0  0  0  0
 32 23  1  0  0  0  0
 33  9  1  0  0  0  0
 25 33  1  1  0  0  0
 34 18  1  0  0  0  0
 34 20  1  0  0  0  0
 35 16  1  0  0  0  0
 35 25  1  0  0  0  0
 15 36  1  1  0  0  0
 16 37  1  1  0  0  0
 17 38  1  6  0  0  0
 18 39  1  1  0  0  0
 19 40  1  6  0  0  0
 20 41  1  6  0  0  0
 21 42  1  6  0  0  0
 23 43  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020399

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](COC)(C[C@@]1([H])O[C@@]([H])(C[C@@]([H])(O)C1(C)C)[C@]([H])(OC)N=C(O)[C@@]([H])(O)[C@]1(CC(=C)[C@@]([H])(C)[C@@]([H])(C)O1)OC)OC

> <INCHI_IDENTIFIER>
InChI=1S/C25H45NO9/c1-14-12-25(33-9,35-16(3)15(14)2)21(28)22(29)26-23(32-8)18-11-19(27)24(4,5)20(34-18)10-17(31-7)13-30-6/h15-21,23,27-28H,1,10-13H2,2-9H3,(H,26,29)/t15-,16-,17+,18+,19-,20-,21-,23+,25-/m1/s1

> <INCHI_KEY>
ZNEZZONMADKYTB-VRCUBXEUSA-N

> <FORMULA>
C25H45NO9

> <MOLECULAR_WEIGHT>
503.633

> <EXACT_MASS>
503.309432033

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
54.05316867613746

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-N-[(S)-[(2S,4R,6R)-6-[(2S)-2,3-dimethoxypropyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]ethanimidic acid

> <ALOGPS_LOGP>
1.58

> <JCHEM_LOGP>
1.8834916529999979

> <ALOGPS_LOGS>
-3.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.49925547997832

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8661958190183103

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2853174620763208

> <JCHEM_POLAR_SURFACE_AREA>
128.43000000000004

> <JCHEM_REFRACTIVITY>
129.00409999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.51e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pederine

> <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     -12.560  -7.454   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -15.593  -6.919   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -17.573  -9.278   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.668  -5.460   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.688  -5.460   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.676  -6.640   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.011  -9.720   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -7.344 -13.570   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -16.056 -12.975   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.011  -6.640   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -10.012  -8.950   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -13.023 -10.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.343  -6.640   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -13.549  -8.633   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -15.066  -8.366   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -16.056  -9.546   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.677  -7.410   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -8.678  -9.720   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -10.012  -7.410   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.344  -7.410   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -12.679 -12.030   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -11.345 -11.260   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.678 -11.260   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -8.678  -6.640   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -14.013 -11.260   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0     -10.012 -12.030   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0     -11.345  -6.640   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0     -12.679 -13.570   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0     -11.345  -9.720   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -2.010  -7.410   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -4.677  -8.950   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -7.344 -12.030   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0     -14.539 -12.707   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -7.344  -8.950   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0     -15.529 -10.993   0.000  0.00  0.00           O+0
HETATM   36  H   UNK     0     -14.076  -7.186   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0     -16.583  -8.099   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      -4.677  -5.870   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      -7.344 -10.490   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0     -10.012  -5.870   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -6.011  -8.180   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0     -12.679 -10.490   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0     -10.012 -10.490   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2   15                                                            
CONECT    3   16                                                            
CONECT    4   24                                                            
CONECT    5   24                                                            
CONECT    6   30                                                            
CONECT    7   31                                                            
CONECT    8   32                                                            
CONECT    9   33                                                            
CONECT   10   17   20                                                       
CONECT   11   18   19                                                       
CONECT   12   14   25                                                       
CONECT   13   17   30                                                       
CONECT   14    1   12   15                                                  
CONECT   15    2   14   16   36                                             
CONECT   16    3   15   35   37                                             
CONECT   17   10   13   31   38                                             
CONECT   18   11   23   34   39                                             
CONECT   19   11   24   27   40                                             
CONECT   20   10   24   34   41                                             
CONECT   21   22   25   28   42                                             
CONECT   22   21   26   29                                                  
CONECT   23   18   26   32   43                                             
CONECT   24    4    5   19   20                                             
CONECT   25   12   21   33   35                                             
CONECT   26   22   23                                                       
CONECT   27   19                                                            
CONECT   28   21                                                            
CONECT   29   22                                                            
CONECT   30    6   13                                                       
CONECT   31    7   17                                                       
CONECT   32    8   23                                                       
CONECT   33    9   25                                                       
CONECT   34   18   20                                                       
CONECT   35   16   25                                                       
CONECT   36   15                                                            
CONECT   37   16                                                            
CONECT   38   17                                                            
CONECT   39   18                                                            
CONECT   40   19                                                            
CONECT   41   20                                                            
CONECT   42   21                                                            
CONECT   43   23                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   88    0
END

Synonyms

Value	Source
(+)-Pederin	ChEBI
(+)-Pederine	ChEBI
Paederine	ChEBI
Pederine	ChEBI
N-((6-(2,3-Dimethoxypropyl)tetrahydro-4-hydroxy-5,5-dimethyl-2H-pyran-2-yl)methoxymethyl)tetrahydro-alpha-hydroxy-2-methoxy-5,6-dimethyl-4-methylene-2H-pyran-2-acetamide	MeSH

Molecular Formula

C₂₅H₄₅NO₉

Average Mass

503.633

Monoisotopic Mass

503.309432033

IUPAC Name

(2R)-N-[(S)-[(2S,4R,6R)-6-[(2S)-2,3-dimethoxypropyl]-4-hydroxy-5,5-dimethyloxan-2-yl](methoxy)methyl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]ethanimidic acid

Traditional Name

pederine

CAS Registry Number

Not Available

SMILES

[H][C@@](COC)(C[C@@]1([H])O[C@@]([H])(C[C@@]([H])(O)C1(C)C)[C@]([H])(OC)N=C(O)[C@@]([H])(O)[C@]1(CC(=C)[C@@]([H])(C)[C@@]([H])(C)O1)OC)OC

InChI Identifier

InChI=1S/C25H45NO9/c1-14-12-25(33-9,35-16(3)15(14)2)21(28)22(29)26-23(32-8)18-11-19(27)24(4,5)20(34-18)10-17(31-7)13-30-6/h15-21,23,27-28H,1,10-13H2,2-9H3,(H,26,29)/t15-,16-,17+,18+,19-,20-,21-,23+,25-/m1/s1

InChI Key

ZNEZZONMADKYTB-VRCUBXEUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ketals. These are acetals derived from ketones by replacement of the oxo group by two hydrocarbyloxy groups R2C(OR)2 ( R not Hydrogen ). This term, once abandoned, has been reinstated as a subclass of acetals.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Ethers

Direct Parent

Ketals

Alternative Parents

Substituents

Ketal
Oxane
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid derivative
Dialkyl ether
Organoheterocyclic compound
Oxacycle
Organopnictogen compound
Organonitrogen compound
Alcohol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

secondary alcohol (CHEBI:78591 )
diol (CHEBI:78591 )
polyketide (CHEBI:78591 )
carboxamide (CHEBI:78591 )
cyclic ketal (CHEBI:78591 )
oxanes (CHEBI:78591 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.25 g/L	ALOGPS
logP	1.58	ALOGPS
logP	1.88	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	2.87	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	128.43 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	129 m³·mol⁻¹	ChemAxon
Polarizability	54.05 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum

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	22.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	41.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	626.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	757.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	745.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	162.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	3407.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	100.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	417.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	481.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	120.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	144.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	183.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	8.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	214.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	117.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	429.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	2015.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1113.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Pederin_TMS_1	C=C1C[C@](OC)([C@H](O)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	2048.58
Gas Chromatography	Pederin_TMS_2	C=C1C[C@](OC)([C@H](O)C(=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	1921.71
Gas Chromatography	Pederin_TMS_3	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	1812.63
Gas Chromatography	Pederin_TMS_4	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	2314.69
Gas Chromatography	Pederin_TMS_5	C=C1C[C@](OC)([C@H](O)C(=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	3000.5
Gas Chromatography	Pederin_TMS_6	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	3066.19
Gas Chromatography	Pederin_TMS_7	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard non polar	2025-10-23	2480.57
Gas Chromatography	Pederin_TMS_1	C=C1C[C@](OC)([C@H](O)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	2390.13
Gas Chromatography	Pederin_TMS_2	C=C1C[C@](OC)([C@H](O)C(=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	1721.9
Gas Chromatography	Pederin_TMS_3	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	1577.21
Gas Chromatography	Pederin_TMS_4	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(O)=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	2223.44
Gas Chromatography	Pederin_TMS_5	C=C1C[C@](OC)([C@H](O)C(=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	1877.73
Gas Chromatography	Pederin_TMS_6	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(=N[C@@H](OC)[C@@H]2C[C@@H](O)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	2725.17
Gas Chromatography	Pederin_TMS_7	C=C1C[C@](OC)([C@H](O[Si](C)(C)C)C(=N[C@@H](OC)[C@@H]2C[C@@H](O[Si](C)(C)C)C(C)(C)[C@@H](C[C@@H](COC)OC)O2)O[Si](C)(C)C)O[C@H](C)[C@@H]1C	standard polar	2025-10-23	1615.31

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 sputum; Human subgingival plaque; Human feces	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

C00040484

Chemspider ID

4529295

KEGG Compound ID

C15760

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pederin

METLIN ID

Not Available

PubChem Compound

5381287

PDB ID

Not Available

ChEBI ID

78591

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 Pederin (MMDBc0020399)

MOL for #<Metabolite:0x00007f9ac2ee21b8>

3D MOL for #<Metabolite:0x00007f9ac2ee21b8>

3D SDF for #<Metabolite:0x00007f9ac2ee21b8>

3D-SDF for #<Metabolite:0x00007f9ac2ee21b8>

PDB for #<Metabolite:0x00007f9ac2ee21b8>

3D PDB for #<Metabolite:0x00007f9ac2ee21b8>

SMILES for #<Metabolite:0x00007f9ac2ee21b8>

INCHI for #<Metabolite:0x00007f9ac2ee21b8>

Structure for #<Metabolite:0x00007f9ac2ee21b8>

3D Structure for #<Metabolite:0x00007f9ac2ee21b8>