MiMeDB: Showing metabocard for Phomaligadione B (MMDBc0017939)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:13:58 UTC

Update Date

2022-08-31 06:43:15 UTC

Metabolite ID

MMDBc0017939

Metabolite Identification

Common Name

Phomaligadione B

Description

Phomaligadione B belongs to the class of organic compounds known as m-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 3-position, respectively. Based on a literature review a significant number of articles have been published on Phomaligadione B.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110132D          

 20 20  0  0  1  0            999 V2000
   -0.1501    2.7880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788    3.6130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6737    5.7955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8953    3.4697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1111    5.3657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5643    2.3755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0505    4.1017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788    2.7880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9559    5.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7683    4.8770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5202    3.4697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4256    4.3882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9933    2.3755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7077    3.6130    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8024    2.6945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6131    4.5315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9933    1.5505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2986    5.5090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7077    2.7880    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5643    3.2005    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  8  2  1  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  7  1  0  0  0  0
 10  9  2  0  0  0  0
 11  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13  8  1  0  0  0  0
 14  4  1  6  0  0  0
 14 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15 11  2  0  0  0  0
 16 12  2  0  0  0  0
 17 13  2  0  0  0  0
 18  5  1  0  0  0  0
 18 10  1  0  0  0  0
 19 13  1  0  0  0  0
 14 19  1  1  0  0  0
 20  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017939

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C14H20O5/c1-6-8(2)13(17)19-14(4)11(15)7-10(18-5)9(3)12(14)16/h8H,6-7H2,1-5H3/t8?,14-/m1/s1

> <INCHI_KEY>
NYKNLDBQDASCRB-NVDIHYKVSA-N

> <FORMULA>
C14H20O5

> <MOLECULAR_WEIGHT>
268.309

> <EXACT_MASS>
268.131073744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.92752425473723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R)-4-methoxy-1,3-dimethyl-2,6-dioxocyclohex-3-en-1-yl 2-methylbutanoate

> <ALOGPS_LOGP>
1.78

> <JCHEM_LOGP>
2.503088998666666

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.02909467397492

> <JCHEM_PKA_STRONGEST_BASIC>
-4.791774901897683

> <JCHEM_POLAR_SURFACE_AREA>
69.67

> <JCHEM_REFRACTIVITY>
70.0399

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.18e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R)-4-methoxy-1,3-dimethyl-2,6-dioxocyclohex-3-en-1-yl 2-methylbutanoate

> <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      -0.280   5.204   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.387   6.744   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.991  10.818   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.538   6.477   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.541  10.016   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.053   4.434   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.561   7.657   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.387   5.204   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.518   9.371   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.034   9.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.571   6.477   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.528   8.191   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.721   4.434   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.054   6.744   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.098   5.030   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.011   8.459   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.721   2.894   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       8.024  10.283   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.054   5.204   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       1.053   5.974   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    8                                                            
CONECT    3    9                                                            
CONECT    4   14                                                            
CONECT    5   18                                                            
CONECT    6    1    8                                                       
CONECT    7   10   11                                                       
CONECT    8    2    6   13   20                                             
CONECT    9    3   10   12                                                  
CONECT   10    7    9   18                                                  
CONECT   11    7   14   15                                                  
CONECT   12    9   14   16                                                  
CONECT   13    8   17   19                                                  
CONECT   14    4   11   12   19                                             
CONECT   15   11                                                            
CONECT   16   12                                                            
CONECT   17   13                                                            
CONECT   18    5   10                                                       
CONECT   19   13   14                                                       
CONECT   20    8                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

Synonyms

Not Available

Molecular Formula

C₁₄H₂₀O₅

Average Mass

268.309

Monoisotopic Mass

268.131073744

IUPAC Name

(1R)-4-methoxy-1,3-dimethyl-2,6-dioxocyclohex-3-en-1-yl 2-methylbutanoate

Traditional Name

(1R)-4-methoxy-1,3-dimethyl-2,6-dioxocyclohex-3-en-1-yl 2-methylbutanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C14H20O5/c1-6-8(2)13(17)19-14(4)11(15)7-10(18-5)9(3)12(14)16/h8H,6-7H2,1-5H3/t8?,14-/m1/s1

InChI Key

NYKNLDBQDASCRB-NVDIHYKVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as m-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 3-position, respectively.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

M-benzoquinones

Alternative Parents

Substituents

M-benzoquinone
Cyclohexenone
Alpha-acyloxy ketone
Fatty acid ester
Fatty acyl
Vinylogous ester
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.92 g/L	ALOGPS
logP	1.78	ALOGPS
logP	2.5	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	11.03	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	69.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	70.04 m³·mol⁻¹	ChemAxon
Polarizability	27.93 Å³	ChemAxon
Number of Rings	1	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

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

78439828

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588059

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 Phomaligadione B (MMDBc0017939)

MOL for #<Metabolite:0x00005645c8e0f240>

3D MOL for #<Metabolite:0x00005645c8e0f240>

3D SDF for #<Metabolite:0x00005645c8e0f240>

3D-SDF for #<Metabolite:0x00005645c8e0f240>

PDB for #<Metabolite:0x00005645c8e0f240>

3D PDB for #<Metabolite:0x00005645c8e0f240>

SMILES for #<Metabolite:0x00005645c8e0f240>

INCHI for #<Metabolite:0x00005645c8e0f240>

Structure for #<Metabolite:0x00005645c8e0f240>

3D Structure for #<Metabolite:0x00005645c8e0f240>