MiMeDB: Showing metabocard for GEODIN (MMDBc0017663)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:58:56 UTC

Update Date

2022-08-31 06:42:45 UTC

Metabolite ID

MMDBc0017663

Metabolite Identification

Common Name

GEODIN

Description

Geodin, also known as estin, 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. Geodin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004191514262D          

 26 28  0  0  0  0            999 V2000
    3.4556    3.4613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6631    2.6628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0335    2.0426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2102    2.5321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1110    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3485    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1821    0.3049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1110   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0885   -1.2017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5188   -1.9603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136   -0.2549    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3242   -1.1500    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7976   -0.3310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7478    1.2573    0.0000 Cl  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
    0.2919    2.0219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3386    1.9115    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
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  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
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END


  Mrv1533004191514262D          

 26 28  0  0  0  0            999 V2000
    3.4556    3.4613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6631    2.6628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0335    2.0426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2102    2.5321    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1110    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3485    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1821    0.3049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1110   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0885   -1.2017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5188   -1.9603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136   -0.2549    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3242   -1.1500    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7976   -0.3310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7478    1.2573    0.0000 Cl  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
    0.2919    2.0219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3386    1.9115    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
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  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
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017663

> <DATABASE_NAME>
MIME

> <SMILES>
COC(=O)C1=CC(=O)C=C(OC)C11OC2=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

> <INCHI_KEY>
LUBKKVGXMXTXOZ-UHFFFAOYSA-N

> <FORMULA>
C17H12Cl2O7

> <MOLECULAR_WEIGHT>
399.18

> <EXACT_MASS>
397.9960081

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
36.2105781002236

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 5,7-dichloro-4-hydroxy-2'-methoxy-6-methyl-3,4'-dioxo-3H-spiro[1-benzofuran-2,1'-cyclohexane]-2',5'-diene-6'-carboxylate

> <ALOGPS_LOGP>
3.41

> <JCHEM_LOGP>
3.5544201170000003

> <ALOGPS_LOGS>
-4.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.691697211323403

> <JCHEM_PKA_STRONGEST_BASIC>
-4.652852774961251

> <JCHEM_POLAR_SURFACE_AREA>
99.13000000000002

> <JCHEM_REFRACTIVITY>
93.98239999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 5,7-dichloro-4-hydroxy-2'-methoxy-6-methyl-3,4'-dioxospiro[1-benzofuran-2,1'-cyclohexane]-2',5'-diene-6'-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       6.450   6.461   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.838   4.971   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.662   3.813   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.126   4.727   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.807   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.347   2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.117   0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       9.673   0.569   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.347  -0.564   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.807  -0.564   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.765  -2.243   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.568  -3.659   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.037   0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.132  -0.476   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17 Cl   UNK     0       0.605  -2.147   0.000  0.00  0.00          Cl+0
HETATM   18  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.489  -0.618   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0      -1.396   2.347   0.000  0.00  0.00          Cl+0
HETATM   22  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.545   3.774   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.132   2.016   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       4.365   3.568   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10    5   14   25                                             
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15   25                                                  
CONECT   25   24   13   26                                                  
CONECT   26   25                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

Synonyms

Value	Source
Estin	MeSH
Methyl 5,7-dichloro-4-hydroxy-6'-methoxy-6-methyl-3,4'-dioxo-3H-spiro[1-benzofuran-2,1'-cyclohexane]-2',5'-diene-2'-carboxylic acid	Generator

Molecular Formula

C₁₇H₁₂Cl₂O₇

Average Mass

399.18

Monoisotopic Mass

397.9960081

IUPAC Name

methyl 5,7-dichloro-4-hydroxy-2'-methoxy-6-methyl-3,4'-dioxo-3H-spiro[1-benzofuran-2,1'-cyclohexane]-2',5'-diene-6'-carboxylate

Traditional Name

methyl 5,7-dichloro-4-hydroxy-2'-methoxy-6-methyl-3,4'-dioxospiro[1-benzofuran-2,1'-cyclohexane]-2',5'-diene-6'-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CC(=O)C=C(OC)C11OC2=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

InChI Key

LUBKKVGXMXTXOZ-UHFFFAOYSA-N

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 ketone
Aryl alkyl ketone
Alkyl aryl ether
Aryl chloride
Aryl halide
Benzenoid
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous ester
Vinylogous acid
Ketone
Carboxylic acid ester
Cyclic ketone
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Oxacycle
Organic oxygen compound
Organooxygen compound
Organochloride
Organohalogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
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	0.011 g/L	ALOGPS
logP	3.41	ALOGPS
logP	3.55	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	6.69	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	99.13 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	93.98 m³·mol⁻¹	ChemAxon
Polarizability	36.21 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	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 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)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View 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

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

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
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

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

216465

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 GEODIN (MMDBc0017663)

MOL for #<Metabolite:0x00007fecce730880>

3D MOL for #<Metabolite:0x00007fecce730880>

3D SDF for #<Metabolite:0x00007fecce730880>

3D-SDF for #<Metabolite:0x00007fecce730880>

PDB for #<Metabolite:0x00007fecce730880>

3D PDB for #<Metabolite:0x00007fecce730880>

SMILES for #<Metabolite:0x00007fecce730880>

INCHI for #<Metabolite:0x00007fecce730880>

Structure for #<Metabolite:0x00007fecce730880>

3D Structure for #<Metabolite:0x00007fecce730880>