MiMeDB: Showing metabocard for Pseudapene C (MMDBc0025500)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 15:15:20 UTC

Update Date

2022-08-31 06:50:39 UTC

MiMeDB ID

MMDBc0025500

Metabolite Identification

Common Name

Pseudapene C

Description

Pseudapene C belongs to the class of organic compounds known as acyloins. These are organic compounds containing an alpha hydroxy ketone. Acyloins are formally derived from reductive coupling of carboxylic acyl groups. Based on a literature review a significant number of articles have been published on Pseudapene C.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152117152D          

 20 21  0  0  1  0            999 V2000
   -2.3517    2.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142    2.7196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8129   -0.4634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483   -0.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428    0.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    1.6561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142    1.2907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    1.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5267    2.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.3212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2892    1.2907    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7733    0.5762    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1233    0.5762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.5762    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7733    1.4012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1233    2.0051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2892   -0.1383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6442    2.2160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7017    0.5762    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6442   -0.2387    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  7  2  0  0  0  0
 10  3  2  0  0  0  0
 10  5  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14  4  1  6  0  0  0
 14  8  1  0  0  0  0
 14 12  1  0  0  0  0
 14 13  1  1  0  0  0
 15  6  1  0  0  0  0
 15  8  1  0  0  0  0
 15 12  1  0  0  0  0
 11 16  1  6  0  0  0
 17 13  2  0  0  0  0
 15 18  1  6  0  0  0
 11 19  1  6  0  0  0
 12 20  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0025500

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(C=C(C)C)C(=O)[C@@]1(C)C[C@@]2(O)CCC(=C)[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O3/c1-9(2)7-11(16)13(17)14(4)8-15(18)6-5-10(3)12(14)15/h7,11-12,16,18H,3,5-6,8H2,1-2,4H3/t11-,12+,14+,15+/m1/s1

> <INCHI_KEY>
SRCGDEZWCNEOKY-DHMWGJHJSA-N

> <FORMULA>
C15H22O3

> <MOLECULAR_WEIGHT>
250.338

> <EXACT_MASS>
250.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.530447983559572

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-2-hydroxy-1-[(1S,5S,6S)-1-hydroxy-6-methyl-4-methylidenebicyclo[3.2.0]heptan-6-yl]-4-methylpent-3-en-1-one

> <ALOGPS_LOGP>
1.02

> <JCHEM_LOGP>
1.899614074666667

> <ALOGPS_LOGS>
-2.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.576712193951238

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.755973066615486

> <JCHEM_PKA_STRONGEST_BASIC>
-3.001931770735162

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
71.0889

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-hydroxy-1-[(1S,5S,6S)-1-hydroxy-6-methyl-4-methylidenebicyclo[3.2.0]heptan-6-yl]-4-methylpent-3-en-1-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      -4.390   3.743   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.080   5.077   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.251  -0.865   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.770  -0.464   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.680   1.846   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.775   3.091   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.080   2.409   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.770   2.616   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.850   3.743   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.775   0.600   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.540   2.409   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.310   1.076   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.230   1.076   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.770   1.076   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.310   2.616   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.230   3.743   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.540  -0.258   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.069   4.137   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0      -1.310   1.076   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.069  -0.446   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   14                                                            
CONECT    5    6   10                                                       
CONECT    6    5   15                                                       
CONECT    7    9   11                                                       
CONECT    8   14   15                                                       
CONECT    9    1    2    7                                                  
CONECT   10    3    5   12                                                  
CONECT   11    7   13   16   19                                             
CONECT   12   10   14   15   20                                             
CONECT   13   11   14   17                                                  
CONECT   14    4    8   12   13                                             
CONECT   15    6    8   12   18                                             
CONECT   16   11                                                            
CONECT   17   13                                                            
CONECT   18   15                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₃

Average Molecular Weight

250.338

Monoisotopic Molecular Weight

250.156894568

IUPAC Name

(2R)-2-hydroxy-1-[(1S,5S,6S)-1-hydroxy-6-methyl-4-methylidenebicyclo[3.2.0]heptan-6-yl]-4-methylpent-3-en-1-one

Traditional Name

(2R)-2-hydroxy-1-[(1S,5S,6S)-1-hydroxy-6-methyl-4-methylidenebicyclo[3.2.0]heptan-6-yl]-4-methylpent-3-en-1-one

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(C=C(C)C)C(=O)[C@@]1(C)C[C@@]2(O)CCC(=C)[C@@]12[H]

InChI Identifier

InChI=1S/C15H22O3/c1-9(2)7-11(16)13(17)14(4)8-15(18)6-5-10(3)12(14)15/h7,11-12,16,18H,3,5-6,8H2,1-2,4H3/t11-,12+,14+,15+/m1/s1

InChI Key

SRCGDEZWCNEOKY-DHMWGJHJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acyloins. These are organic compounds containing an alpha hydroxy ketone. Acyloins are formally derived from reductive coupling of carboxylic acyl groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Acyloins

Alternative Parents

Substituents

Acyloin
Tertiary alcohol
Cyclic alcohol
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Cyclobutanol
Organic oxide
Hydrocarbon derivative
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.25 g/L	ALOGPS
logP	1.02	ALOGPS
logP	1.9	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	12.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	71.09 m³·mol⁻¹	ChemAxon
Polarizability	27.53 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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_1_3) - 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)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum

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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Fungi	Ascomycota	1	Human Feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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

77089222

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146682121

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 Pseudapene C (MMDBc0025500)

MOL for #<Metabolite:0x00007f09201b0460>

3D MOL for #<Metabolite:0x00007f09201b0460>

3D SDF for #<Metabolite:0x00007f09201b0460>

3D-SDF for #<Metabolite:0x00007f09201b0460>

PDB for #<Metabolite:0x00007f09201b0460>

3D PDB for #<Metabolite:0x00007f09201b0460>

SMILES for #<Metabolite:0x00007f09201b0460>

INCHI for #<Metabolite:0x00007f09201b0460>

Structure for #<Metabolite:0x00007f09201b0460>

3D Structure for #<Metabolite:0x00007f09201b0460>