MiMeDB: Showing metabocard for 1â€²,2â€²-epoxy-3â€²,4â€²-didehydro-penicillide (MMDBc0019429)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:30:04 UTC

Update Date

2025-10-07 16:06:58 UTC

Metabolite ID

MMDBc0019429

Metabolite Identification

Common Name

1â€²,2â€²-epoxy-3â€²,4â€²-didehydro-penicillide

Description

1â€²,2â€²-epoxy-3â€²,4â€²-didehydro-penicillide is a member of the penicillin class of antibiotics. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its properties and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152111302D          

 29 32  0  0  1  0            999 V2000
    7.5802    0.2896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2600    0.8365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6400   -1.0825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6055    0.3343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6584   -1.9524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8404   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6801   -0.5356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4936   -1.9524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8138    0.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7623    0.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1779   -1.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4981   -0.6433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9741   -1.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3116   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3382   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6539   -0.6433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4465   -0.5802    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8138   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4719   -0.5356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7920   -1.0825    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3382    0.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6273   -2.8222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9216    0.7022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7876    0.2266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760    0.4346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -1.7212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5542   -1.3982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7920   -0.0780    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6843   -1.9004    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
 10  1  2  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  7  2  0  0  0  0
 11  8  1  0  0  0  0
 12  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13  5  1  0  0  0  0
 14  8  2  0  0  0  0
 15  6  1  0  0  0  0
 16 15  2  0  0  0  0
 17 10  1  1  0  0  0
 18 12  2  0  0  0  0
 18 14  1  0  0  0  0
 19 13  2  0  0  0  0
 19 16  1  0  0  0  0
 20 13  1  6  0  0  0
 20 17  1  0  0  0  0
 21 16  1  0  0  0  0
 22 14  1  0  0  0  0
 23 21  2  0  0  0  0
 24  4  1  0  0  0  0
 24 19  1  0  0  0  0
 25  9  1  0  0  0  0
 25 21  1  0  0  0  0
 26 15  1  0  0  0  0
 26 18  1  0  0  0  0
 27 17  1  0  0  0  0
 27 20  1  0  0  0  0
 17 28  1  6  0  0  0
 20 29  1  1  0  0  0
M  END


  Mrv1652305152111302D          

 29 32  0  0  1  0            999 V2000
    7.5802    0.2896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2600    0.8365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6400   -1.0825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6055    0.3343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6584   -1.9524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8404   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6801   -0.5356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4936   -1.9524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8138    0.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7623    0.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1779   -1.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4981   -0.6433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9741   -1.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3116   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3382   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6539   -0.6433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4465   -0.5802    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8138   -1.4055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4719   -0.5356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7920   -1.0825    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3382    0.1189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6273   -2.8222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9216    0.7022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7876    0.2266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760    0.4346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5760   -1.7212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5542   -1.3982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7920   -0.0780    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6843   -1.9004    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
 10  1  2  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  7  2  0  0  0  0
 11  8  1  0  0  0  0
 12  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13  5  1  0  0  0  0
 14  8  2  0  0  0  0
 15  6  1  0  0  0  0
 16 15  2  0  0  0  0
 17 10  1  1  0  0  0
 18 12  2  0  0  0  0
 18 14  1  0  0  0  0
 19 13  2  0  0  0  0
 19 16  1  0  0  0  0
 20 13  1  6  0  0  0
 20 17  1  0  0  0  0
 21 16  1  0  0  0  0
 22 14  1  0  0  0  0
 23 21  2  0  0  0  0
 24  4  1  0  0  0  0
 24 19  1  0  0  0  0
 25  9  1  0  0  0  0
 25 21  1  0  0  0  0
 26 15  1  0  0  0  0
 26 18  1  0  0  0  0
 27 17  1  0  0  0  0
 27 20  1  0  0  0  0
 17 28  1  6  0  0  0
 20 29  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019429

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O[C@]1([H])C1=C(OC)C2=C(OC3=C(COC2=O)C=C(C)C=C3O)C=C1)C(C)=C

> <INCHI_IDENTIFIER>
InChI=1S/C21H20O6/c1-10(2)17-20(27-17)13-5-6-15-16(19(13)24-4)21(23)25-9-12-7-11(3)8-14(22)18(12)26-15/h5-8,17,20,22H,1,9H2,2-4H3/t17-,20-/m1/s1

> <INCHI_KEY>
BLJNAQWNZHOUNA-YLJYHZDGSA-N

> <FORMULA>
C21H20O6

> <MOLECULAR_WEIGHT>
368.385

> <EXACT_MASS>
368.125988364

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
38.474045958227606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
16-hydroxy-7-methoxy-14-methyl-6-[(2R,3R)-3-(prop-1-en-2-yl)oxiran-2-yl]-2,10-dioxatricyclo[10.4.0.0^{3,8}]hexadeca-1(12),3(8),4,6,13,15-hexaen-9-one

> <ALOGPS_LOGP>
2.92

> <JCHEM_LOGP>
3.878819094333333

> <ALOGPS_LOGS>
-4.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.221896152627721

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.395529938835605

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6380904537065413

> <JCHEM_POLAR_SURFACE_AREA>
77.52000000000001

> <JCHEM_REFRACTIVITY>
98.74719999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.15e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
16-hydroxy-7-methoxy-14-methyl-6-[(2R,3R)-3-(prop-1-en-2-yl)oxiran-2-yl]-2,10-dioxatricyclo[10.4.0.0^{3,8}]hexadeca-1(12),3(8),4,6,13,15-hexaen-9-one

> <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      14.150   0.541   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.685   1.561   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.195  -2.021   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.464   0.624   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.696  -3.644   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.169  -3.845   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.270  -1.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.921  -3.644   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.386   0.222   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.623   0.340   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.332  -2.222   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.796  -1.201   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.285  -2.222   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.448  -3.845   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.231  -2.624   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.821  -1.201   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.034  -1.083   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.386  -2.624   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.347  -1.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.812  -2.021   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.231   0.222   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       3.038  -5.268   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.320   1.311   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.937   0.423   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.809   0.811   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.809  -3.213   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.235  -2.610   0.000  0.00  0.00           O+0
HETATM   28  H   UNK     0      10.812  -0.146   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0      10.611  -3.547   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   24                                                            
CONECT    5    6   13                                                       
CONECT    6    5   15                                                       
CONECT    7   11   12                                                       
CONECT    8   11   14                                                       
CONECT    9   12   25                                                       
CONECT   10    1    2   17                                                  
CONECT   11    3    7    8                                                  
CONECT   12    7    9   18                                                  
CONECT   13    5   19   20                                                  
CONECT   14    8   18   22                                                  
CONECT   15    6   16   26                                                  
CONECT   16   15   19   21                                                  
CONECT   17   10   20   27   28                                             
CONECT   18   12   14   26                                                  
CONECT   19   13   16   24                                                  
CONECT   20   13   17   27   29                                             
CONECT   21   16   23   25                                                  
CONECT   22   14                                                            
CONECT   23   21                                                            
CONECT   24    4   19                                                       
CONECT   25    9   21                                                       
CONECT   26   15   18                                                       
CONECT   27   17   20                                                       
CONECT   28   17                                                            
CONECT   29   20                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

Synonyms

Not Available

Molecular Formula

C₂₁H₂₀O₆

Average Mass

368.385

Monoisotopic Mass

368.125988364

IUPAC Name

16-hydroxy-7-methoxy-14-methyl-6-[(2R,3R)-3-(prop-1-en-2-yl)oxiran-2-yl]-2,10-dioxatricyclo[10.4.0.0^{3,8}]hexadeca-1(12),3(8),4,6,13,15-hexaen-9-one

Traditional Name

16-hydroxy-7-methoxy-14-methyl-6-[(2R,3R)-3-(prop-1-en-2-yl)oxiran-2-yl]-2,10-dioxatricyclo[10.4.0.0^{3,8}]hexadeca-1(12),3(8),4,6,13,15-hexaen-9-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O[C@]1([H])C1=C(OC)C2=C(OC3=C(COC2=O)C=C(C)C=C3O)C=C1)C(C)=C

InChI Identifier

InChI=1S/C21H20O6/c1-10(2)17-20(27-17)13-5-6-15-16(19(13)24-4)21(23)25-9-12-7-11(3)8-14(22)18(12)26-15/h5-8,17,20,22H,1,9H2,2-4H3/t17-,20-/m1/s1

InChI Key

BLJNAQWNZHOUNA-YLJYHZDGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diarylethers. These are organic compounds containing the dialkyl ether functional group, with the formula ROR', where R and R' are aryl groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Ethers

Direct Parent

Diarylethers

Alternative Parents

Substituents

Diaryl ether
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Benzenoid
Carboxylic acid ester
Lactone
Oxirane
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
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	0.022 g/L	ALOGPS
logP	2.92	ALOGPS
logP	3.88	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	8.4	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	77.52 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	98.75 m³·mol⁻¹	ChemAxon
Polarizability	38.47 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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
Eukaryota/Fungi	Ascomycota	1	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

Not Available

Chemspider ID

78438593

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588489

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 1â€²,2â€²-epoxy-3â€²,4â€²-didehydro-penicillide (MMDBc0019429)

MOL for #<Metabolite:0x00007f8dc8022800>

3D MOL for #<Metabolite:0x00007f8dc8022800>

3D SDF for #<Metabolite:0x00007f8dc8022800>

3D-SDF for #<Metabolite:0x00007f8dc8022800>

PDB for #<Metabolite:0x00007f8dc8022800>

3D PDB for #<Metabolite:0x00007f8dc8022800>

SMILES for #<Metabolite:0x00007f8dc8022800>

INCHI for #<Metabolite:0x00007f8dc8022800>

Structure for #<Metabolite:0x00007f8dc8022800>

3D Structure for #<Metabolite:0x00007f8dc8022800>