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Showing metabocard for Didymic acid (HMDB0341152)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 19:22:31 UTC
Update Date2022-09-22 18:35:03 UTC
HMDB IDHMDB0341152
Secondary Accession NumbersNone
Metabolite Identification
Common NameDidymic acid
DescriptionDidymic acid, also known as didymate, belongs to the class of organic compounds known as dibenzofurans. Dibenzofurans are compounds containing a dibenzofuran moiety, which consists of two benzene rings fused to a central furan ring. Based on a literature review very few articles have been published on Didymic acid.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341152 (Didymic acid)


  Mrv1652309092222002D          

 27 29  0  0  0  0            999 V2000
    2.4393   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4393   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1538   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8682   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2972   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2972   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827   -0.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827    0.0931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8682   -1.1444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116   -0.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116    0.0931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7261   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7261   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1832   -3.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0036   -3.2751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3392   -2.5214    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3392   -4.0288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8543   -4.6962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1898   -5.4499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0103   -5.5361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0338   -4.6100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6982   -3.8563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8778   -3.7701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3928   -4.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -4.3513    0.0000 C   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 14 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  2  0  0  0  0
 16 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341152 (Didymic acid)

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3D SDF for HMDB0341152 (Didymic acid)

  Mrv1652309092222002D          

 27 29  0  0  0  0            999 V2000
    2.4393   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4393   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1538   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8682   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2972   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2972   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827   -0.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5827    0.0931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8682   -1.1444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116   -0.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116    0.0931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7261   -1.1444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7261   -1.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0116   -2.3819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1832   -3.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0036   -3.2751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3392   -2.5214    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3392   -4.0288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8543   -4.6962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1898   -5.4499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0103   -5.5361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0338   -4.6100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6982   -3.8563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8778   -3.7701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3928   -4.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -4.3513    0.0000 C   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 14 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  2  0  0  0  0
 16 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341152

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC1=C(C(O)=O)C(O)=CC2=C1C1=C(O2)C=C(OC)C=C1CCC

> <INCHI_IDENTIFIER>
InChI=1S/C22H26O5/c1-4-6-7-9-15-20(22(24)25)16(23)12-18-21(15)19-13(8-5-2)10-14(26-3)11-17(19)27-18/h10-12,23H,4-9H2,1-3H3,(H,24,25)

> <INCHI_KEY>
IDZVZCQOFFSQMO-UHFFFAOYSA-N

> <FORMULA>
C22H26O5

> <MOLECULAR_WEIGHT>
370.445

> <EXACT_MASS>
370.178023937

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
41.47903206218622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxy-11-methoxy-3-pentyl-13-propyl-8-oxatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,5,10,12-hexaene-4-carboxylic acid

> <JCHEM_LOGP>
6.691848186333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.676209526924609

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1402756964999186

> <JCHEM_PKA_STRONGEST_BASIC>
-2.842890941415185

> <JCHEM_POLAR_SURFACE_AREA>
79.9

> <JCHEM_REFRACTIVITY>
104.61549999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-11-methoxy-3-pentyl-13-propyl-8-oxatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,5,10,12-hexaene-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341152 (Didymic acid)
Download
PDB for HMDB0341152 (Didymic acid)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       4.553  -2.136   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.553  -3.676   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.887  -4.446   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.221  -3.676   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.554  -4.446   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.888  -3.676   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.888  -2.136   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.554  -1.366   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.554   0.174   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.221  -2.136   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      11.222  -1.366   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      11.222   0.174   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      12.555  -2.136   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.555  -3.676   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.222  -4.446   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.542  -5.953   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.073  -6.113   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.700  -4.707   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      13.700  -7.520   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.795  -8.766   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.421 -10.173   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      14.953 -10.334   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.263  -8.605   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.637  -7.198   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.105  -7.037   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.200  -8.283   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.668  -8.122   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14    6   16                                                  
CONECT   16   15   17   24                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17   14                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24                                                       
CONECT   24   23   16   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

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3D PDB for HMDB0341152 (Didymic acid)
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SMILES for HMDB0341152 (Didymic acid)
CCCCCC1=C(C(O)=O)C(O)=CC2=C1C1=C(O2)C=C(OC)C=C1CCC
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INCHI for HMDB0341152 (Didymic acid)
InChI=1S/C22H26O5/c1-4-6-7-9-15-20(22(24)25)16(23)12-18-21(15)19-13(8-5-2)10-14(26-3)11-17(19)27-18/h10-12,23H,4-9H2,1-3H3,(H,24,25)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
DidymateGenerator
Chemical FormulaC22H26O5
Average Molecular Weight370.445
Monoisotopic Molecular Weight370.178023937
IUPAC Name5-hydroxy-11-methoxy-3-pentyl-13-propyl-8-oxatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,5,10,12-hexaene-4-carboxylic acid
Traditional Name5-hydroxy-11-methoxy-3-pentyl-13-propyl-8-oxatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,5,10,12-hexaene-4-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCC1=C(C(O)=O)C(O)=CC2=C1C1=C(O2)C=C(OC)C=C1CCC
InChI Identifier
InChI=1S/C22H26O5/c1-4-6-7-9-15-20(22(24)25)16(23)12-18-21(15)19-13(8-5-2)10-14(26-3)11-17(19)27-18/h10-12,23H,4-9H2,1-3H3,(H,24,25)
InChI KeyIDZVZCQOFFSQMO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dibenzofurans. Dibenzofurans are compounds containing a dibenzofuran moiety, which consists of two benzene rings fused to a central furan ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassBenzofurans  
Sub ClassDibenzofurans  
Direct ParentDibenzofurans  
Alternative Parents
Substituents
  • Dibenzofuran
    • 

  • Hydroxybenzoic acid
    • 

  • Salicylic acid or derivatives
    • 

  • Anisole
    • 

  • Phenol ether
    • 

  • Phenol
    • 

  • Alkyl aryl ether
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Benzenoid
    • 

  • Vinylogous acid
    • 

  • Furan
    • 

  • Heteroaromatic compound
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP6.69ChemAxon
pKa (Strongest Acidic)3.14ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area79.9 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity104.62 m³·mol⁻¹ChemAxon
Polarizability41.48 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal  details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00030127  
Chemspider ID57568397  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15558736  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Neto FC, Raftery D: Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. Anal Chem. 2021 Sep 7;93(35):12001-12010. doi: 10.1021/acs.analchem.1c02041. Epub 2021 Aug 26. [PubMed:34436864  ]