MiMeDB: Showing metabocard for Psoracorylifol D (MMDBc0006664)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:08:00 UTC

Update Date

2025-10-07 16:05:12 UTC

Metabolite ID

MMDBc0006664

Metabolite Identification

Common Name

Psoracorylifol D

Description

Psoracorylifol D is a flavonoid, a class of compounds known for their diverse biological activities and potential health benefits. This metabolite has been identified in the context of traditional herbal medicine, particularly from the plant species Psoralea corylifolia, which is recognized for its therapeutic properties. The chemical structure of Psoracorylifol D contributes to its role in various biological processes, including antioxidant and anti-inflammatory activities. Research has highlighted its presence alongside other significant compounds such as p-hydroxybenzaldehyde, psoralen, and isobavachalone, indicating its potential synergistic effects when combined with these metabolites (PMID:23302649 ). The exploration of Psoracorylifol D within the broader spectrum of flavonoids underscores its importance in phytochemistry and its relevance in the development of natural products for medicinal use. Further studies may elucidate its specific mechanisms of action and therapeutic applications, reinforcing the significance of this compound in both traditional and modern pharmacology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102082D          

 23 25  0  0  1  0            999 V2000
    2.9683   -1.3847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3597    0.1267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3597    1.0655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0582   -0.3308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2538   -0.9722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6204    0.2904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0004   -0.9970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3637   -0.0675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7437   -1.3550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2538    1.3394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6118    0.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0612   -0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4254   -0.8902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4495    1.5230    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8045    0.1836    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4495   -0.3308    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6812    0.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2538   -0.1472    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1687   -1.2482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8045    1.0086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2659    2.3273    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7121   -0.6362    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7001   -1.1168    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  8  6  1  0  0  0  0
  9  7  2  0  0  0  0
 11 10  1  0  0  0  0
 12  6  2  0  0  0  0
 12  7  1  0  0  0  0
 13  8  2  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 12  1  1  0  0  0
 16 15  1  0  0  0  0
 17  2  1  0  0  0  0
 17  3  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18  4  1  6  0  0  0
 18  5  1  1  0  0  0
 18 11  1  0  0  0  0
 18 16  1  0  0  0  0
 19 13  1  0  0  0  0
 20 14  1  0  0  0  0
 20 15  1  0  0  0  0
 14 21  1  1  0  0  0
 15 22  1  6  0  0  0
 16 23  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0006664

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CC[C@@](C)(C=C)[C@]([H])([C@]([H])(O1)C1=CC=C(O)C=C1)C2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C18H24O2/c1-5-18(4)11-10-14-17(2,3)16(18)15(20-14)12-6-8-13(19)9-7-12/h5-9,14-16,19H,1,10-11H2,2-4H3/t14-,15-,16-,18-/m1/s1

> <INCHI_KEY>
KYAKMCAFTRNVKQ-YFHUEUNASA-N

> <FORMULA>
C18H24O2

> <MOLECULAR_WEIGHT>
272.388

> <EXACT_MASS>
272.177630013

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
31.166556549782577

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-[(1S,2S,5R,7S)-2-ethenyl-2,8,8-trimethyl-6-oxabicyclo[3.2.1]octan-7-yl]phenol

> <ALOGPS_LOGP>
4.51

> <JCHEM_LOGP>
4.321986682

> <ALOGPS_LOGS>
-4.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.472189365508243

> <JCHEM_PKA_STRONGEST_BASIC>
-4.204079712972608

> <JCHEM_POLAR_SURFACE_AREA>
29.46

> <JCHEM_REFRACTIVITY>
80.9679

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.73e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(1S,2S,5R,7S)-2-ethenyl-2,8,8-trimethyl-6-oxabicyclo[3.2.1]octan-7-yl]phenol

> <JCHEM_VEBER_RULE>
1

$$$$

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       5.541  -2.585   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.405   0.237   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.405   1.989   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.709  -0.617   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.207  -1.815   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.158   0.542   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.001  -1.861   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.546  -0.126   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.388  -2.529   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.207   2.500   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.875   1.113   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.114  -0.325   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.661  -1.662   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.706   2.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.502   0.343   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.706  -0.617   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.138   1.113   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.207  -0.275   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -4.048  -2.330   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.502   1.883   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       2.363   4.344   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.329  -1.188   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       3.173  -2.085   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2   17                                                            
CONECT    3   17                                                            
CONECT    4   18                                                            
CONECT    5    1   18                                                       
CONECT    6    8   12                                                       
CONECT    7    9   12                                                       
CONECT    8    6   13                                                       
CONECT    9    7   13                                                       
CONECT   10   11   14                                                       
CONECT   11   10   18                                                       
CONECT   12    6    7   15                                                  
CONECT   13    8    9   19                                                  
CONECT   14   10   17   20   21                                             
CONECT   15   12   16   20   22                                             
CONECT   16   15   17   18   23                                             
CONECT   17    2    3   14   16                                             
CONECT   18    4    5   11   16                                             
CONECT   19   13                                                            
CONECT   20   14   15                                                       
CONECT   21   14                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₂₄O₂

Average Mass

272.388

Monoisotopic Mass

272.177630013

IUPAC Name

4-[(1S,2S,5R,7S)-2-ethenyl-2,8,8-trimethyl-6-oxabicyclo[3.2.1]octan-7-yl]phenol

Traditional Name

4-[(1S,2S,5R,7S)-2-ethenyl-2,8,8-trimethyl-6-oxabicyclo[3.2.1]octan-7-yl]phenol

CAS Registry Number

Not Available

SMILES

[H][C@]12CC[C@@](C)(C=C)[C@]([H])([C@]([H])(O1)C1=CC=C(O)C=C1)C2(C)C

InChI Identifier

InChI=1S/C18H24O2/c1-5-18(4)11-10-14-17(2,3)16(18)15(20-14)12-6-8-13(19)9-7-12/h5-9,14-16,19H,1,10-11H2,2-4H3/t14-,15-,16-,18-/m1/s1

InChI Key

KYAKMCAFTRNVKQ-YFHUEUNASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxepanes

Sub Class

Not Available

Direct Parent

Oxepanes

Alternative Parents

Substituents

1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxepane
Benzenoid
Monocyclic benzene moiety
Oxolane
Oxacycle
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
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	0.0037 g/L	ALOGPS
logP	4.51	ALOGPS
logP	4.32	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	9.47	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	29.46 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	80.97 m³·mol⁻¹	ChemAxon
Polarizability	31.17 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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 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

C00048834

Chemspider ID

9797939

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11623191

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Psoracorylifol D (MMDBc0006664)

MOL for #<Metabolite:0x00007f2adc2a1cb0>

3D MOL for #<Metabolite:0x00007f2adc2a1cb0>

3D SDF for #<Metabolite:0x00007f2adc2a1cb0>

3D-SDF for #<Metabolite:0x00007f2adc2a1cb0>

PDB for #<Metabolite:0x00007f2adc2a1cb0>

3D PDB for #<Metabolite:0x00007f2adc2a1cb0>

SMILES for #<Metabolite:0x00007f2adc2a1cb0>

INCHI for #<Metabolite:0x00007f2adc2a1cb0>

Structure for #<Metabolite:0x00007f2adc2a1cb0>

3D Structure for #<Metabolite:0x00007f2adc2a1cb0>