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Showing metabocard for 2-Indolecarboxylic acid (HMDB0002285)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:46 UTC
Update Date2023-02-21 17:16:19 UTC
HMDB IDHMDB0002285
Secondary Accession Numbers
  • HMDB02285
Metabolite Identification
Common Name2-Indolecarboxylic acid
Description2-Indolecarboxylic acid is a strong inhibitor of lipid peroxidation, similar to melatonin and some structurally related indole compounds. Lipid peroxidation with tert-butyl hydroperoxide is a source of free radicals (PMID 12236544 ). 2-Indolecarboxylic acid is a phenolic components known to exist in Korean ginseng (Koryo Insam Hakhoechi (1996), 20(3), 284-290) and brown rice (Han'guk Nonghwa Hakhoechi (1995), 38(5), 478-83).
Structure
Data?1676999779
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002285 (2-Indolecarboxylic acid)

4-Hydroxy-L-glutamate.mol
  Mrv0541 02231219282D          

 12 13  0  0  0  0            999 V2000
    0.2456    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2456   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2535   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9680   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9680    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2535    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5555    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680   -0.7145    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  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
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4  9  2  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0002285 (2-Indolecarboxylic acid)

HMDB0002285
     RDKit          3D
2-Indolecarboxylic acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    3.5632    1.6703   -0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0847    0.5173   -0.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9247   -0.5752   -0.1991 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514    0.2886   -0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9988   -0.9218   -0.2272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3584   -0.6668   -0.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4684   -1.4995   -0.2653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7014   -0.8870   -0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8602    0.4618   -0.1709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7486    1.2755   -0.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958    0.7005   -0.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7241    1.2610   -0.1175 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9867   -1.2149   -0.9862 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4436   -1.9281   -0.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3715   -2.5697   -0.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5890   -1.5343   -0.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8458    0.9417   -0.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8586    2.3735   -0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    2.3070   -0.0637 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12  4  1  0
 11  6  1  0
  3 13  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 12 19  1  0
M  END
Download

3D SDF for HMDB0002285 (2-Indolecarboxylic acid)

4-Hydroxy-L-glutamate.mol
  Mrv0541 02231219282D          

 12 13  0  0  0  0            999 V2000
    0.2456    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2456   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2535   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9680   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9680    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2535    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5555    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9680   -0.7145    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  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
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  4  9  2  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002285

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CC2=C(N1)C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C9H7NO2/c11-9(12)8-5-6-3-1-2-4-7(6)10-8/h1-5,10H,(H,11,12)

> <INCHI_KEY>
HCUARRIEZVDMPT-UHFFFAOYSA-N

> <FORMULA>
C9H7NO2

> <MOLECULAR_WEIGHT>
161.1574

> <EXACT_MASS>
161.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
16.172480278919686

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indole-2-carboxylic acid

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
1.6495918406666665

> <ALOGPS_LOGS>
-1.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.566380710465612

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5999552060906654

> <JCHEM_POLAR_SURFACE_AREA>
53.09

> <JCHEM_REFRACTIVITY>
44.2782

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.78e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indole-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0002285 (2-Indolecarboxylic acid)

HMDB0002285
     RDKit          3D
2-Indolecarboxylic acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    3.5632    1.6703   -0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0847    0.5173   -0.1467 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9247   -0.5752   -0.1991 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514    0.2886   -0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9988   -0.9218   -0.2272 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3584   -0.6668   -0.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4684   -1.4995   -0.2653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7014   -0.8870   -0.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8602    0.4618   -0.1709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7486    1.2755   -0.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4958    0.7005   -0.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7241    1.2610   -0.1175 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9867   -1.2149   -0.9862 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4436   -1.9281   -0.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3715   -2.5697   -0.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5890   -1.5343   -0.2747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8458    0.9417   -0.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8586    2.3735   -0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    2.3070   -0.0637 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12  4  1  0
 11  6  1  0
  3 13  1  0
  5 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 12 19  1  0
M  END
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PDB for HMDB0002285 (2-Indolecarboxylic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4-Hydroxy-L-glutamate.mol                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0       0.458   1.246   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.364   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.458  -1.246   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.006  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.340  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.674  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.674   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.340   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.006   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.904   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.674   1.334   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.674  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    1    4                                                  
CONECT   10   11   12    2                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0002285 (2-Indolecarboxylic acid)

COMPND    HMDB0002285
HETATM    1  O1  UNL     1       3.563   1.670  -0.087  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.085   0.517  -0.147  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.925  -0.575  -0.199  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.651   0.289  -0.163  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.999  -0.922  -0.227  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.358  -0.667  -0.219  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.468  -1.499  -0.265  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.701  -0.887  -0.239  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.860   0.462  -0.171  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.749   1.275  -0.126  1.00  0.00           C  
HETATM   11  C9  UNL     1      -0.496   0.700  -0.150  1.00  0.00           C  
HETATM   12  N1  UNL     1       0.724   1.261  -0.117  1.00  0.00           N  
HETATM   13  H1  UNL     1       3.987  -1.215  -0.986  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.444  -1.928  -0.277  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.372  -2.570  -0.319  1.00  0.00           H  
HETATM   16  H4  UNL     1      -3.589  -1.534  -0.275  1.00  0.00           H  
HETATM   17  H5  UNL     1      -3.846   0.942  -0.150  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.859   2.374  -0.070  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.921   2.307  -0.064  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   12
CONECT    5    6   14
CONECT    6    7    7   11
CONECT    7    8   15
CONECT    8    9    9   16
CONECT    9   10   17
CONECT   10   11   11   18
CONECT   11   12
CONECT   12   19
END
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SMILES for HMDB0002285 (2-Indolecarboxylic acid)

OC(=O)C1=CC2=C(N1)C=CC=C2
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INCHI for HMDB0002285 (2-Indolecarboxylic acid)

InChI=1S/C9H7NO2/c11-9(12)8-5-6-3-1-2-4-7(6)10-8/h1-5,10H,(H,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-IndolecarboxylateGenerator
indol-2-Carboxylic acidChEMBL, HMDB
indol-2-CarboxylateGenerator, HMDB
1H-Indole-2-carboxylateHMDB, Generator
1H-Indole-2-carboxylic acidHMDB
2-CarboxyindoleHMDB
Indole-2-carboxylateHMDB
Indole-2-carboxylic acidHMDB, MeSH
Chemical FormulaC9H7NO2
Average Molecular Weight161.1574
Monoisotopic Molecular Weight161.047678473
IUPAC Name1H-indole-2-carboxylic acid
Traditional Nameindole-2-carboxylic acid
CAS Registry Number1477-50-5
SMILES
OC(=O)C1=CC2=C(N1)C=CC=C2
InChI Identifier
InChI=1S/C9H7NO2/c11-9(12)8-5-6-3-1-2-4-7(6)10-8/h1-5,10H,(H,11,12)
InChI KeyHCUARRIEZVDMPT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolecarboxylic acids and derivatives. Indolecarboxylic acids and derivatives are compounds containing a carboxylic acid group (or a derivative thereof) linked to an indole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndolecarboxylic acids and derivatives
Direct ParentIndolecarboxylic acids and derivatives
Alternative Parents
Substituents
  • Indolecarboxylic acid derivative
  • Indole
  • Pyrrole-2-carboxylic acid
  • Pyrrole-2-carboxylic acid or derivatives
  • Substituted pyrrole
  • Benzenoid
  • Pyrrole
  • Heteroaromatic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility719.9 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.31HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified6.228 +/- 5.119 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022948
KNApSAcK IDNot Available
Chemspider ID65731
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6593
PubChem Compound72899
PDB IDNot Available
ChEBI ID130363
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1251471
References
Synthesis ReferenceFeng, Liu-xing; Ding, Shao-min; Song, Hua-fu. Synthesis process of indole-2-carboxylic acid. Huaxue Yu Nianhe (2003), (4), 196-197.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Seal AN, Pratley JE, Haig T, An M: Identification and quantitation of compounds in a series of allelopathic and non-allelopathic rice root exudates. J Chem Ecol. 2004 Aug;30(8):1647-62. [PubMed:15537165 ]
  2. Eaton RW, Chapman PJ: Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J Bacteriol. 1995 Dec;177(23):6983-8. [PubMed:7592495 ]
  3. Cross PE, Dickinson RP, Parry MJ, Randall MJ: Selective thromboxane synthetase inhibitors. 3. 1H-imidazol-1-yl-substituted benzo[b]furan-, benzo[b]thiophene-, and indole-2- and -3-carboxylic acids. J Med Chem. 1986 Sep;29(9):1637-43. [PubMed:3746813 ]
  4. Kawa K: Distribution and functional properties of 5-HT3 receptors in the rat hippocampal dentate gyrus: a patch-clamp study. J Neurophysiol. 1994 May;71(5):1935-47. [PubMed:7520482 ]
  5. Stetinova V, Smetanova L, Grossmann V, Anzenbacher P: In vitro and in vivo assessment of the antioxidant activity of melatonin and related indole derivatives. Gen Physiol Biophys. 2002 Jun;21(2):153-62. [PubMed:12236544 ]
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