MiMeDB: Showing metabocard for Nordeoxyverrucosidin (MMDBc0028005)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 17:37:59 UTC

Update Date

2022-08-31 06:53:22 UTC

Metabolite ID

MMDBc0028005

Metabolite Identification

Common Name

Nordeoxyverrucosidin

Description

Nordeoxyverrucosidin belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Based on a literature review very few articles have been published on Nordeoxyverrucosidin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152119382D          

 33 35  0  0  1  0            999 V2000
    2.9570   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -2.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4975    1.3909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9070   -1.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224    1.1050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2438   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -2.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5294   -5.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9570   -1.1411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -3.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9570   -1.9661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -4.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -4.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425    0.6062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5294   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -6.0911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579   -0.4737    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2425   -0.7286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4579    0.3513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8149   -6.9161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2438   -4.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -5.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7275   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -1.9661    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -3.2036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -0.7286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6592    1.1896    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224   -1.2274    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 13  1  1  0  0  0  0
 13  9  2  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  1  0  0  0  0
 14 12  2  0  0  0  0
 15  3  1  0  0  0  0
 15 10  2  0  0  0  0
 16  4  1  0  0  0  0
 17  5  1  1  0  0  0
 18 11  2  0  0  0  0
 18 16  1  0  0  0  0
 19 11  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  2  0  0  0  0
 22  6  1  6  0  0  0
 22 12  1  1  0  0  0
 22 21  1  0  0  0  0
 23  7  1  1  0  0  0
 23 17  1  0  0  0  0
 23 21  1  0  0  0  0
 24 19  2  0  0  0  0
 25  8  1  0  0  0  0
 25 18  1  0  0  0  0
 26 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27 17  1  0  0  0  0
 27 22  1  0  0  0  0
 28 21  1  0  0  0  0
 28 23  1  0  0  0  0
 29  9  1  0  0  0  0
 30 10  1  0  0  0  0
 31 12  1  0  0  0  0
 17 32  1  6  0  0  0
 21 33  1  1  0  0  0
M  END


  Mrv1652305152119382D          

 33 35  0  0  1  0            999 V2000
    2.9570   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425   -2.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4975    1.3909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9070   -1.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224    1.1050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2438   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -2.3786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -3.6161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5294   -5.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9570   -1.1411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -3.2036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9570   -1.9661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -4.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -4.4411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2425    0.6062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5294   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8149   -6.0911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -4.8536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579   -0.4737    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2425   -0.7286    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4579    0.3513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8149   -6.9161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2438   -4.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -5.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7275   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7434   -0.0612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3859   -1.9661    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004   -3.2036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -0.7286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6592    1.1896    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1224   -1.2274    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 13  1  1  0  0  0  0
 13  9  2  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  1  0  0  0  0
 14 12  2  0  0  0  0
 15  3  1  0  0  0  0
 15 10  2  0  0  0  0
 16  4  1  0  0  0  0
 17  5  1  1  0  0  0
 18 11  2  0  0  0  0
 18 16  1  0  0  0  0
 19 11  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  2  0  0  0  0
 22  6  1  6  0  0  0
 22 12  1  1  0  0  0
 22 21  1  0  0  0  0
 23  7  1  1  0  0  0
 23 17  1  0  0  0  0
 23 21  1  0  0  0  0
 24 19  2  0  0  0  0
 25  8  1  0  0  0  0
 25 18  1  0  0  0  0
 26 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27 17  1  0  0  0  0
 27 22  1  0  0  0  0
 28 21  1  0  0  0  0
 28 23  1  0  0  0  0
 29  9  1  0  0  0  0
 30 10  1  0  0  0  0
 31 12  1  0  0  0  0
 17 32  1  6  0  0  0
 21 33  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0028005

> <DATABASE_NAME>
MIME

> <SMILES>
[H]/C(=C(/C)\C(\[H])=C(/C)C1=C(C)C(OC)=CC(=O)O1)/C(/C)=C(\[H])[C@]1(C)O[C@]([H])(C)[C@@]2(C)O[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H30O5/c1-13(10-15(3)20-16(4)18(25-8)11-19(24)26-20)9-14(2)12-22(6)21-23(7,28-21)17(5)27-22/h9-12,17,21H,1-8H3/b13-9+,14-12+,15-10+/t17-,21+,22+,23-/m1/s1

> <INCHI_KEY>
LRRJYOPCACBLEA-MHWPPRIHSA-N

> <FORMULA>
C23H30O5

> <MOLECULAR_WEIGHT>
386.488

> <EXACT_MASS>
386.209324066

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
43.21723616664864

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-[(2E,4E,6E)-4,6-dimethyl-7-[(1S,2S,4R,5R)-2,4,5-trimethyl-3,6-dioxabicyclo[3.1.0]hexan-2-yl]hepta-2,4,6-trien-2-yl]-4-methoxy-5-methyl-2H-pyran-2-one

> <ALOGPS_LOGP>
4.88

> <JCHEM_LOGP>
3.580221859

> <ALOGPS_LOGS>
-4.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9040336984374497

> <JCHEM_POLAR_SURFACE_AREA>
57.290000000000006

> <JCHEM_REFRACTIVITY>
112.74810000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.67e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[(2E,4E,6E)-4,6-dimethyl-7-[(1S,2S,4R,5R)-2,4,5-trimethyl-3,6-dioxabicyclo[3.1.0]hexan-2-yl]hepta-2,4,6-trien-2-yl]-4-methoxy-5-methylpyran-2-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       5.520  -6.750   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.186  -4.440   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.853  -9.060   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.854  -6.750   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.662   2.596   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.560  -2.767   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.095   2.063   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.522  -6.750   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.853  -4.440   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.187  -6.750   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.188 -10.600   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.520  -2.130   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.853  -5.980   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.520  -3.670   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.187  -8.290   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.854  -8.290   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.186   1.132   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.188  -9.060   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.854 -11.370   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.521  -9.060   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.721  -0.884   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.186  -1.360   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.721   0.656   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.854 -12.910   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      13.522  -8.290   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       9.521 -10.600   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       5.091  -0.114   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.388  -0.114   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0       8.187  -3.670   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       9.521  -5.980   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       6.853  -1.360   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       3.097   2.221   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       2.095  -2.291   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4   16                                                            
CONECT    5   17                                                            
CONECT    6   22                                                            
CONECT    7   23                                                            
CONECT    8   25                                                            
CONECT    9   13   14   29                                                  
CONECT   10   13   15   30                                                  
CONECT   11   18   19                                                       
CONECT   12   14   22   31                                                  
CONECT   13    1    9   10                                                  
CONECT   14    2    9   12                                                  
CONECT   15    3   10   20                                                  
CONECT   16    4   18   20                                                  
CONECT   17    5   23   27   32                                             
CONECT   18   11   16   25                                                  
CONECT   19   11   24   26                                                  
CONECT   20   15   16   26                                                  
CONECT   21   22   23   28   33                                             
CONECT   22    6   12   21   27                                             
CONECT   23    7   17   21   28                                             
CONECT   24   19                                                            
CONECT   25    8   18                                                       
CONECT   26   19   20                                                       
CONECT   27   17   22                                                       
CONECT   28   21   23                                                       
CONECT   29    9                                                            
CONECT   30   10                                                            
CONECT   31   12                                                            
CONECT   32   17                                                            
CONECT   33   21                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

Synonyms

Not Available

Molecular Formula

C₂₃H₃₀O₅

Average Mass

386.488

Monoisotopic Mass

386.209324066

IUPAC Name

6-[(2E,4E,6E)-4,6-dimethyl-7-[(1S,2S,4R,5R)-2,4,5-trimethyl-3,6-dioxabicyclo[3.1.0]hexan-2-yl]hepta-2,4,6-trien-2-yl]-4-methoxy-5-methyl-2H-pyran-2-one

Traditional Name

6-[(2E,4E,6E)-4,6-dimethyl-7-[(1S,2S,4R,5R)-2,4,5-trimethyl-3,6-dioxabicyclo[3.1.0]hexan-2-yl]hepta-2,4,6-trien-2-yl]-4-methoxy-5-methylpyran-2-one

CAS Registry Number

Not Available

SMILES

[H]/C(=C(/C)\C(\[H])=C(/C)C1=C(C)C(OC)=CC(=O)O1)/C(/C)=C(\[H])[C@]1(C)O[C@]([H])(C)[C@@]2(C)O[C@@]12[H]

InChI Identifier

InChI=1S/C23H30O5/c1-13(10-15(3)20-16(4)18(25-8)11-19(24)26-20)9-14(2)12-22(6)21-23(7,28-21)17(5)27-22/h9-12,17,21H,1-8H3/b13-9+,14-12+,15-10+/t17-,21+,22+,23-/m1/s1

InChI Key

LRRJYOPCACBLEA-MHWPPRIHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Aromatic monoterpenoid
Bicyclic monoterpenoid
Monoterpenoid
Alkyl aryl ether
Pyranone
Para-dioxane
Pyran
Heteroaromatic compound
Vinylogous ester
Oxolane
Lactone
Oxacycle
Dialkyl ether
Oxirane
Ether
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Organic oxygen 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	0.0077 g/L	ALOGPS
logP	4.88	ALOGPS
logP	3.58	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	57.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	112.75 m³·mol⁻¹	ChemAxon
Polarizability	43.22 Å³	ChemAxon
Number of Rings	3	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

Metabolic Reactions

Not Available

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

Source Type	Source Sub-type	Species	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

71048688

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

100899241

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Nordeoxyverrucosidin (MMDBc0028005)

MOL for #<Metabolite:0x00007f46e4f0b590>

3D MOL for #<Metabolite:0x00007f46e4f0b590>

3D SDF for #<Metabolite:0x00007f46e4f0b590>

3D-SDF for #<Metabolite:0x00007f46e4f0b590>

PDB for #<Metabolite:0x00007f46e4f0b590>

3D PDB for #<Metabolite:0x00007f46e4f0b590>

SMILES for #<Metabolite:0x00007f46e4f0b590>

INCHI for #<Metabolite:0x00007f46e4f0b590>

Structure for #<Metabolite:0x00007f46e4f0b590>

3D Structure for #<Metabolite:0x00007f46e4f0b590>