MiMeDB: Showing metabocard for R-Dihydrogenistein (MMDBc0057128)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-10-25 16:47:23 UTC

Update Date

2025-10-07 16:09:51 UTC

Metabolite ID

MMDBc0057128

Metabolite Identification

Common Name

R-Dihydrogenistein

Description

R-Dihydrogenistein is a flavonoid, a class of compounds characterized by a three-ring structure that contributes to various biological activities. This metabolite is produced through the biotransformation of daidzein and genistein, demonstrating a high degree of stereoselectivity in its formation (PMID:29699942 ). The chemical structure of R-Dihydrogenistein features a hydroxylated flavan backbone, which is critical for its interaction with biological pathways. Specifically, it may be involved in the modulation of estrogenic activity and the inhibition of certain enzymes, contributing to its potential roles in various physiological processes. The pathways it participates in include those related to hormone regulation and antioxidant defense mechanisms, highlighting its relevance in both chemistry and biology. Understanding the synthesis and function of R-Dihydrogenistein can provide insights into its potential applications in health and disease management.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310252218472D          

 20 22  0  0  1  0            999 V2000
   -2.1434   -2.8875    0.0000 O   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
   -1.4289   -1.6500    0.0000 C   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
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    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
    2.8579   -2.4750    0.0000 O   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
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  8  5  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
  8 19  1  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057128

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=CC=C(C=C1)[C@@H]1COC2=CC(O)=CC(O)=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)11-7-20-13-6-10(17)5-12(18)14(13)15(11)19/h1-6,11,16-18H,7H2/t11-/m0/s1

> <INCHI_KEY>
UQGVUYNHDKMLSE-NSHDSACASA-N

> <FORMULA>
C15H12O5

> <MOLECULAR_WEIGHT>
272.256

> <EXACT_MASS>
272.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
27.03824762650917

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-5,7-dihydroxy-3-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.45

> <JCHEM_LOGP>
2.7276581139999996

> <ALOGPS_LOGS>
-3.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.200102025348171

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.841124533247802

> <JCHEM_PKA_STRONGEST_BASIC>
-4.916250210706317

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
71.67649999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.28e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-5,7-dihydroxy-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  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
CONECT    8    5    9   19                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   11   19                                                  
CONECT   19   18    8   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₁₂O₅

Average Mass

272.256

Monoisotopic Mass

272.068473486

IUPAC Name

(3R)-5,7-dihydroxy-3-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(3R)-5,7-dihydroxy-3-(4-hydroxyphenyl)-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

OC1=CC=C(C=C1)[C@@H]1COC2=CC(O)=CC(O)=C2C1=O

InChI Identifier

InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)11-7-20-13-6-10(17)5-12(18)14(13)15(11)19/h1-6,11,16-18H,7H2/t11-/m0/s1

InChI Key

UQGVUYNHDKMLSE-NSHDSACASA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.23 g/L	ALOGPS
logP	2.45	ALOGPS
logP	2.73	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	7.84	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	86.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	71.68 m³·mol⁻¹	ChemAxon
Polarizability	27.04 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

Not Available

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
MMDBr0025998	Genistein	R-Dihydrogenistein	Daidzein reductase	Reduction	PMID: 31527435	31527435
MMDBr0026000	R-Dihydrogenistein	S-Dihydrogenistein	Unknown Protein	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

34985339

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

76968882

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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-Dihydrogenistein (MMDBc0057128)

MOL for #<Metabolite:0x00007f8dd04002d0>

3D MOL for #<Metabolite:0x00007f8dd04002d0>

3D SDF for #<Metabolite:0x00007f8dd04002d0>

3D-SDF for #<Metabolite:0x00007f8dd04002d0>

PDB for #<Metabolite:0x00007f8dd04002d0>

3D PDB for #<Metabolite:0x00007f8dd04002d0>

SMILES for #<Metabolite:0x00007f8dd04002d0>

INCHI for #<Metabolite:0x00007f8dd04002d0>

Structure for #<Metabolite:0x00007f8dd04002d0>

3D Structure for #<Metabolite:0x00007f8dd04002d0>