MiMeDB: Showing metabocard for R-Dihydrodaidzein (MMDBc0057127)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-10-25 16:47:17 UTC

Update Date

2025-10-07 16:09:50 UTC

Metabolite ID

MMDBc0057127

Metabolite Identification

Common Name

R-Dihydrodaidzein

Description

R-Dihydrodaidzein is a flavonoid, specifically a metabolite derived from the isoflavonoid daidzein. Its chemical structure features a 3-phenylchromen-4-one backbone, characterized by the presence of hydroxyl groups that contribute to its biological activity. The compound is produced through the reduction of daidzein, and it is known to be synthesized in a highly stereo-selective manner alongside R-dihydrogenistein from daidzein and genistein (PMID:29699942 ). In terms of biochemical pathways, R-dihydrodaidzein participates in various metabolic processes, including those related to estrogenic activity, as it can interact with estrogen receptors. This interaction may influence signaling pathways involved in cell proliferation and differentiation. Additionally, R-dihydrodaidzein may undergo further metabolic transformations in the body, contributing to the overall pharmacokinetics of isoflavones and their potential effects on health.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310252218472D          

 19 21  0  0  1  0            999 V2000
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 11  1  0  0  0  0
  9 12  1  0  0  0  0
  2 13  1  6  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 16 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057127

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=CC=C(C=C1)[C@@H]1COC2=C(C=CC(O)=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O4/c16-10-3-1-9(2-4-10)13-8-19-14-7-11(17)5-6-12(14)15(13)18/h1-7,13,16-17H,8H2/t13-/m0/s1

> <INCHI_KEY>
JHYXBPPMXZIHKG-ZDUSSCGKSA-N

> <FORMULA>
C15H12O4

> <MOLECULAR_WEIGHT>
256.257

> <EXACT_MASS>
256.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.216038026676756

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-7-hydroxy-3-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.77

> <JCHEM_LOGP>
2.3812234356666666

> <ALOGPS_LOGS>
-3.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.50108139864841

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.775319135720283

> <JCHEM_PKA_STRONGEST_BASIC>
-4.906004166215412

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
69.6956

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-7-hydroxy-3-(4-hydroxyphenyl)-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-OCT-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-OCT-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3   13                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   11                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    1                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10    5                                                       
CONECT   12    9                                                            
CONECT   13    2   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₁₂O₄

Average Mass

256.257

Monoisotopic Mass

256.073558866

IUPAC Name

(3R)-7-hydroxy-3-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(3R)-7-hydroxy-3-(4-hydroxyphenyl)-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

OC1=CC=C(C=C1)[C@@H]1COC2=C(C=CC(O)=C2)C1=O

InChI Identifier

InChI=1S/C15H12O4/c16-10-3-1-9(2-4-10)13-8-19-14-7-11(17)5-6-12(14)15(13)18/h1-7,13,16-17H,8H2/t13-/m0/s1

InChI Key

JHYXBPPMXZIHKG-ZDUSSCGKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoflavanones. These are polycyclic compounds containing an isoflavan skeleton which bears a ketone at position C4.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Isoflavans

Direct Parent

Isoflavanones

Alternative Parents

Substituents

Hydroxyisoflavonoid
Isoflavanone
Isoflavanol
Chromone
1-benzopyran
Benzopyran
Chromane
Aryl alkyl ketone
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Ketone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.14 g/L	ALOGPS
logP	2.77	ALOGPS
logP	2.38	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	7.78	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.7 m³·mol⁻¹	ChemAxon
Polarizability	26.22 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

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

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
MMDBr0025997	Daidzein	R-Dihydrodaidzein	Daidzein reductase	Reduction	PMID: 31527435	31527435
MMDBr0025999	R-Dihydrodaidzein	S-Dihydrodaidzein	Dihydrodaidzein racemase	Racemization	PMID: 31527435	31527435

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

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

9754505

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11579739

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Mayo B, Vazquez L, Florez AB: Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects. Nutrients. 2019 Sep 16;11(9). pii: nu11092231. doi: 10.3390/nu11092231. [PubMed:31527435 ]

Showing metabocard for R-Dihydrodaidzein (MMDBc0057127)

MOL for #<Metabolite:0x00007fd3e9d907a0>

3D MOL for #<Metabolite:0x00007fd3e9d907a0>

3D SDF for #<Metabolite:0x00007fd3e9d907a0>

3D-SDF for #<Metabolite:0x00007fd3e9d907a0>

PDB for #<Metabolite:0x00007fd3e9d907a0>

3D PDB for #<Metabolite:0x00007fd3e9d907a0>

SMILES for #<Metabolite:0x00007fd3e9d907a0>

INCHI for #<Metabolite:0x00007fd3e9d907a0>

Structure for #<Metabolite:0x00007fd3e9d907a0>

3D Structure for #<Metabolite:0x00007fd3e9d907a0>