MiMeDB: Showing metabocard for (+)-geodin (MMDBc0054735)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:22:08 UTC

Update Date

2022-08-12 20:09:04 UTC

MiMeDB ID

MMDBc0054735

Metabolite Identification

Common Name

(+)-geodin

Description

(+)-Geodin, also known as estin(1-) or geodin(1-), belongs to the class of organic compounds known as benzofurans. These are organic compounds containing a benzene ring fused to a furan. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Based on a literature review a significant number of articles have been published on (+)-Geodin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221222D          

 26 28  0  0  1  0            999 V2000
    6.3569    2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    0.7018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    4.9886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    3.5596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6425    2.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2940    2.8452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    3.5596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6425    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    3.6702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    2.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4289    3.5126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    4.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    2.8452    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3569    3.6702    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    1.1952    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.4690    2.8452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    4.4952    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.4289    4.3376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6114    4.7590    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    1.4162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    4.9886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4289    2.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
 13 10  2  0  0  0  0
 13 11  1  0  0  0  0
 14 10  1  0  0  0  0
 14 12  2  0  0  0  0
 15 10  1  0  0  0  0
 16  8  1  0  0  0  0
 17  8  1  0  0  0  0
 17  9  1  0  0  0  0
 17 15  1  0  0  0  0
 18 11  1  0  0  0  0
 19 12  1  0  0  0  0
 20  7  2  0  0  0  0
 21 13  1  0  0  0  0
 22 15  2  0  0  0  0
 23 16  2  0  0  0  0
 24  2  1  0  0  0  0
 24  9  1  0  0  0  0
 25  3  1  0  0  0  0
 25 16  1  0  0  0  0
 26 14  1  0  0  0  0
 17 26  1  1  0  0  0
M  CHG  1  21  -1
M  END


  Mrv1652306172221222D          

 26 28  0  0  1  0            999 V2000
    6.3569    2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    0.7018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    4.9886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    3.5596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6425    2.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2940    2.8452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    3.5596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6425    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    2.0202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    3.6702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    2.4327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4289    3.5126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    4.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    2.8452    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3569    3.6702    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    1.1952    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.4690    2.8452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9280    4.4952    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.4289    4.3376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6114    4.7590    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9440    1.4162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5315    4.9886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4289    2.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
 13 10  2  0  0  0  0
 13 11  1  0  0  0  0
 14 10  1  0  0  0  0
 14 12  2  0  0  0  0
 15 10  1  0  0  0  0
 16  8  1  0  0  0  0
 17  8  1  0  0  0  0
 17  9  1  0  0  0  0
 17 15  1  0  0  0  0
 18 11  1  0  0  0  0
 19 12  1  0  0  0  0
 20  7  2  0  0  0  0
 21 13  1  0  0  0  0
 22 15  2  0  0  0  0
 23 16  2  0  0  0  0
 24  2  1  0  0  0  0
 24  9  1  0  0  0  0
 25  3  1  0  0  0  0
 25 16  1  0  0  0  0
 26 14  1  0  0  0  0
 17 26  1  1  0  0  0
M  CHG  1  21  -1
M  END
> <DATABASE_ID>
MMDBc0054735

> <DATABASE_NAME>
MIME

> <SMILES>
COC(=O)C1=CC(=O)C=C(OC)[C@]11OC2=C(Cl)C(C)=C(Cl)C([O-])=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H12Cl2O7/c1-6-11(18)13(21)10-14(12(6)19)26-17(15(10)22)8(16(23)25-3)4-7(20)5-9(17)24-2/h4-5,21H,1-3H3/p-1/t17-/m1/s1

> <INCHI_KEY>
LUBKKVGXMXTXOZ-QGZVFWFLSA-M

> <FORMULA>
C17H11Cl2O7

> <MOLECULAR_WEIGHT>
398.17

> <EXACT_MASS>
396.9887317

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
35.859596453192445

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-5,7-dichloro-6'-methoxy-2'-(methoxycarbonyl)-6-methyl-3,4'-dioxo-3H-spiro[1-benzofuran-2,1'-cyclohexane]-2',5'-dien-4-olate

> <JCHEM_LOGP>
3.5544201170000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.691697211323398

> <JCHEM_PKA_STRONGEST_BASIC>
-4.652852774961251

> <JCHEM_POLAR_SURFACE_AREA>
101.96000000000001

> <JCHEM_REFRACTIVITY>
104.53269999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-5,7-dichloro-6'-methoxy-2'-(methoxycarbonyl)-6-methyl-3,4'-dioxospiro[1-benzofuran-2,1'-cyclohexane]-2',5'-dien-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      11.866   3.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.725   1.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.185   9.312   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.185   6.645   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.185   3.977   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.533   4.541   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.415   5.311   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.725   6.645   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.725   3.977   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.865   6.081   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.533   6.081   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.199   3.771   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.199   6.851   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.865   4.541   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.401   6.557   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.495   7.978   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.495   5.311   0.000  0.00  0.00           C+0
HETATM   18 Cl   UNK     0      11.866   6.851   0.000  0.00  0.00          Cl+0
HETATM   19 Cl   UNK     0       9.199   2.231   0.000  0.00  0.00          Cl+0
HETATM   20  O   UNK     0       0.875   5.311   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       9.199   8.391   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0       6.401   8.097   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.741   8.884   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.495   2.644   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.725   9.312   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       6.401   4.065   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2   24                                                            
CONECT    3   25                                                            
CONECT    4    7    8                                                       
CONECT    5    7    9                                                       
CONECT    6    1   11   12                                                  
CONECT    7    4    5   20                                                  
CONECT    8    4   16   17                                                  
CONECT    9    5   17   24                                                  
CONECT   10   13   14   15                                                  
CONECT   11    6   13   18                                                  
CONECT   12    6   14   19                                                  
CONECT   13   10   11   21                                                  
CONECT   14   10   12   26                                                  
CONECT   15   10   17   22                                                  
CONECT   16    8   23   25                                                  
CONECT   17    8    9   15   26                                             
CONECT   18   11                                                            
CONECT   19   12                                                            
CONECT   20    7                                                            
CONECT   21   13                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24    2    9                                                       
CONECT   25    3   16                                                       
CONECT   26   14   17                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

Synonyms

Value	Source
Estin(1-)	ChEBI
Geodin(1-)	ChEBI

Chemical Formula

C₁₇H₁₁Cl₂O₇

Average Molecular Weight

398.17

Monoisotopic Molecular Weight

396.9887317

IUPAC Name

(2R)-5,7-dichloro-6'-methoxy-2'-(methoxycarbonyl)-6-methyl-3,4'-dioxo-3H-spiro[1-benzofuran-2,1'-cyclohexane]-2',5'-dien-4-olate

Traditional Name

(2R)-5,7-dichloro-6'-methoxy-2'-(methoxycarbonyl)-6-methyl-3,4'-dioxospiro[1-benzofuran-2,1'-cyclohexane]-2',5'-dien-4-olate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CC(=O)C=C(OC)[C@]11OC2=C(Cl)C(C)=C(Cl)C([O-])=C2C1=O

InChI Identifier

InChI=1S/C17H12Cl2O7/c1-6-11(18)13(21)10-14(12(6)19)26-17(15(10)22)8(16(23)25-3)4-7(20)5-9(17)24-2/h4-5,21H,1-3H3/p-1/t17-/m1/s1

InChI Key

LUBKKVGXMXTXOZ-QGZVFWFLSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzofurans. These are organic compounds containing a benzene ring fused to a furan. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzofurans

Sub Class

Not Available

Direct Parent

Benzofurans

Alternative Parents

Substituents

Coumaran
Benzofuran
Aryl alkyl ketone
Aryl ketone
Phenoxide
Alkyl aryl ether
Benzenoid
Aryl halide
Aryl chloride
Vinylogous ester
Vinylogous acid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Cyclic ketone
Ketone
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organochloride
Organohalogen compound
Carbonyl group
Organic anion
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
logP	3.55	ChemAxon
pKa (Strongest Acidic)	6.69	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	101.96 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	104.53 m³·mol⁻¹	ChemAxon
Polarizability	35.86 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

Spectrum Type	Description	Deposition Date
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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146672111

PDB ID

Not Available

ChEBI ID

150868

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (+)-geodin (MMDBc0054735)

MOL for #<Metabolite:0x000055b769f42f88>

3D MOL for #<Metabolite:0x000055b769f42f88>

3D SDF for #<Metabolite:0x000055b769f42f88>

3D-SDF for #<Metabolite:0x000055b769f42f88>

PDB for #<Metabolite:0x000055b769f42f88>

3D PDB for #<Metabolite:0x000055b769f42f88>

SMILES for #<Metabolite:0x000055b769f42f88>

INCHI for #<Metabolite:0x000055b769f42f88>

Structure for #<Metabolite:0x000055b769f42f88>

3D Structure for #<Metabolite:0x000055b769f42f88>