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Showing metabocard for Indole-3-carboxylic acid (HMDB0003320)

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enzymes (2) Show 2 proteins
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-05-22 15:12:50 UTC
Update Date2023-02-21 17:16:36 UTC
HMDB IDHMDB0003320
Secondary Accession Numbers
  • HMDB03320
Metabolite Identification
Common NameIndole-3-carboxylic acid
DescriptionIndole-3-carboxylic acid, also known as 3-carboxyindole or 3-indolecarboxylate, 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. Naphthylmethylindoles: Any compound containing a 1H-indol-3-yl-(1-naphthyl)methane structure with substitution at the nitrogen atom of the indole ring by an alkyl, haloalkyl, alkenyl, cycloalkylmethyl, cycloalkylethyl, 1-(N-methyl-2-piperidinyl)methyl, or 2-(4-morpholinyl)ethyl group whether or not further substituted in the indole ring to any extent and whether or not substituted in the naphthyl ring to any extent. One example given is JWH-250. Outside of the human body, indole-3-carboxylic acid has been detected, but not quantified in several different foods, such as brassicas, broccoli, pulses, common beets, and barley. This could make indole-3-carboxylic acid a potential biomarker for the consumption of these foods. Notice the pentyl group substituted onto the nitrogen atom of the indole ring. Note that this definition encompasses only those compounds that have OH groups attached to both the phenyl and the cyclohexyl rings, and so does not include compounds such as O-1871 which lacks the cyclohexyl OH group, or compounds such as JWH-337 or JWH-344 which lack the phenolic OH group.
Structure
Data?1676999796
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003320 (Indole-3-carboxylic acid)


  Mrv1652305271900162D          

 12 13  0  0  0  0            999 V2000
   26.4963  -17.4113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1381  -16.9674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.4328  -19.6935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.6890  -17.5814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6522  -19.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.4328  -18.3656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6522  -18.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9143  -19.0296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9376  -19.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9376  -18.2046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2231  -19.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2231  -18.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  7 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
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3D MOL for HMDB0003320 (Indole-3-carboxylic acid)

HMDB0003320
     RDKit          3D
Indole-3-carboxylic acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.0963   -2.0904    0.9508 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3562   -0.9342    0.5469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6852   -0.5492    0.4948 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3239    0.0066    0.1356 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4836    1.3028   -0.3260 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2746    1.8284   -0.5977 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6982    0.9397   -0.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0739    0.9796   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7807   -0.1451   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1545   -1.2896    0.3770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -1.3084    0.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0398   -0.2023    0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0862   -0.4887   -0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4674    1.7659   -0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0836    2.7847   -0.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5136    1.8929   -0.8063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8497   -0.1350   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7236   -2.1710    0.6604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2384   -2.1868    0.8310 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12  4  1  0
 12  7  1  0
  3 13  1  0
  5 14  1  0
  6 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
M  END
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3D SDF for HMDB0003320 (Indole-3-carboxylic acid)


  Mrv1652305271900162D          

 12 13  0  0  0  0            999 V2000
   26.4963  -17.4113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1381  -16.9674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.4328  -19.6935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.6890  -17.5814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6522  -19.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.4328  -18.3656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6522  -18.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9143  -19.0296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9376  -19.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9376  -18.2046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2231  -19.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2231  -18.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  7 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003320

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CNC2=CC=CC=C12

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

> <INCHI_KEY>
KMAKOBLIOCQGJP-UHFFFAOYSA-N

> <FORMULA>
C9H7NO2

> <MOLECULAR_WEIGHT>
161.1574

> <EXACT_MASS>
161.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.956151131125452

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indole-3-carboxylic acid

> <ALOGPS_LOGP>
1.79

> <JCHEM_LOGP>
1.729590717

> <ALOGPS_LOGS>
-1.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.853175363146892

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5201821132292035

> <JCHEM_POLAR_SURFACE_AREA>
53.089999999999996

> <JCHEM_REFRACTIVITY>
44.4007

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indole - 3 carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0003320 (Indole-3-carboxylic acid)

HMDB0003320
     RDKit          3D
Indole-3-carboxylic acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.0963   -2.0904    0.9508 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3562   -0.9342    0.5469 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6852   -0.5492    0.4948 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3239    0.0066    0.1356 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4836    1.3028   -0.3260 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2746    1.8284   -0.5977 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6982    0.9397   -0.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0739    0.9796   -0.4444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7807   -0.1451   -0.0815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1545   -1.2896    0.3770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -1.3084    0.4748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0398   -0.2023    0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0862   -0.4887   -0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4674    1.7659   -0.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0836    2.7847   -0.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5136    1.8929   -0.8063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8497   -0.1350   -0.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7236   -2.1710    0.6604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2384   -2.1868    0.8310 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  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12  4  1  0
 12  7  1  0
  3 13  1  0
  5 14  1  0
  6 15  1  0
  8 16  1  0
  9 17  1  0
 10 18  1  0
 11 19  1  0
M  END
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PDB for HMDB0003320 (Indole-3-carboxylic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      49.460 -32.501   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      46.924 -31.672   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      47.475 -36.761   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      47.953 -32.819   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      46.017 -36.292   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      47.475 -34.282   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      46.017 -34.752   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      48.373 -35.522   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      44.684 -37.062   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      44.684 -33.982   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      43.350 -36.292   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      43.350 -34.752   0.000  0.00  0.00           C+0
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    5    8                                                       
CONECT    4    1    2    6                                                  
CONECT    5    3    7    9                                                  
CONECT    6    4    7    8                                                  
CONECT    7    5    6   10                                                  
CONECT    8    3    6                                                       
CONECT    9    5   11                                                       
CONECT   10    7   12                                                       
CONECT   11    9   12                                                       
CONECT   12   10   11                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for HMDB0003320 (Indole-3-carboxylic acid)

COMPND    HMDB0003320
HETATM    1  O1  UNL     1       2.096  -2.090   0.951  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.356  -0.934   0.547  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.685  -0.549   0.495  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.324   0.007   0.136  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.484   1.303  -0.326  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.275   1.828  -0.598  1.00  0.00           N  
HETATM    7  C4  UNL     1      -0.698   0.940  -0.339  1.00  0.00           C  
HETATM    8  C5  UNL     1      -2.074   0.980  -0.444  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.781  -0.145  -0.082  1.00  0.00           C  
HETATM   10  C7  UNL     1      -2.155  -1.290   0.377  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.785  -1.308   0.475  1.00  0.00           C  
HETATM   12  C9  UNL     1      -0.040  -0.202   0.121  1.00  0.00           C  
HETATM   13  H1  UNL     1       4.086  -0.489  -0.454  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.467   1.766  -0.429  1.00  0.00           H  
HETATM   15  H3  UNL     1       0.084   2.785  -0.959  1.00  0.00           H  
HETATM   16  H4  UNL     1      -2.514   1.893  -0.806  1.00  0.00           H  
HETATM   17  H5  UNL     1      -3.850  -0.135  -0.156  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.724  -2.171   0.660  1.00  0.00           H  
HETATM   19  H7  UNL     1      -0.238  -2.187   0.831  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   15
CONECT    7    8    8   12
CONECT    8    9   16
CONECT    9   10   10   17
CONECT   10   11   18
CONECT   11   12   12   19
END
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SMILES for HMDB0003320 (Indole-3-carboxylic acid)

OC(=O)C1=CNC2=CC=CC=C12
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INCHI for HMDB0003320 (Indole-3-carboxylic acid)

InChI=1S/C9H7NO2/c11-9(12)7-5-10-8-4-2-1-3-6(7)8/h1-5,10H,(H,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Indole-3-carboxylateGenerator
3-CarboxyindoleHMDB
1H-Indole-3-carboxylateHMDB
1H-Indole-3-carboxylic acidHMDB
3-Indole carboxylic acidHMDB
3-IndolecarboxylateHMDB
3-Indolecarboxylic acidHMDB
3-IndoleformateHMDB
3-Indoleformic acidHMDB
3-IndolylcarboxylateHMDB
3-Indolylcarboxylic acidHMDB
Indole - 3 carboxylateHMDB
Indole - 3 carboxylic acidHMDB
Indole-3-carboxylicacidHMDB
Indole-3-carboxylic acidKEGG
Indole-b-carboxylateGenerator
Indole-b-carboxylic acidGenerator
Indole-beta-carboxylateGenerator
Indole-β-carboxylateGenerator
Indole-β-carboxylic acidGenerator
Chemical FormulaC9H7NO2
Average Molecular Weight161.1574
Monoisotopic Molecular Weight161.047678473
IUPAC Name1H-indole-3-carboxylic acid
Traditional Nameindole - 3 carboxylic acid
CAS Registry Number771-50-6
SMILES
OC(=O)C1=CNC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H7NO2/c11-9(12)7-5-10-8-4-2-1-3-6(7)8/h1-5,10H,(H,11,12)
InChI KeyKMAKOBLIOCQGJP-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-3-carboxylic acid
  • Pyrrole-3-carboxylic acid or derivatives
  • Substituted pyrrole
  • Benzenoid
  • Pyrrole
  • Heteroaromatic compound
  • Vinylogous amide
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Carboxylic acid
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point206.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP1.99HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg124.50130932474
[M+H]+MetCCS_train_pos132.36730932474
[M-H]-Not Available124.501http://allccs.zhulab.cn/database/detail?ID=AllCCS00000356
[M+H]+Not Available132.357http://allccs.zhulab.cn/database/detail?ID=AllCCS00000356
Predicted Molecular Properties
PropertyValueSource
Water Solubility2.42 g/LALOGPS
logP1.79ALOGPS
logP1.73ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area53.09 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity44.4 m³·mol⁻¹ChemAxon
Polarizability15.96 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+134.00331661259
DarkChem[M-H]-130.19731661259
DeepCCS[M-2H]-166.1130932474
DeepCCS[M+Na]+141.64830932474
AllCCS[M+H]+133.632859911
AllCCS[M+H-H2O]+129.032859911
AllCCS[M+NH4]+137.932859911
AllCCS[M+Na]+139.132859911
AllCCS[M-H]-131.132859911
AllCCS[M+Na-2H]-131.732859911
AllCCS[M+HCOO]-132.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.4.92 minutes32390414
Predicted by Siyang on May 30, 202211.0201 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.86 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1619.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid383.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid123.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid234.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid251.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid395.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid431.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)162.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid836.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid357.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1122.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid330.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid343.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate464.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA294.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water133.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Indole-3-carboxylic acidOC(=O)C1=CNC2=CC=CC=C123069.2Standard polar33892256
Indole-3-carboxylic acidOC(=O)C1=CNC2=CC=CC=C121744.4Standard non polar33892256
Indole-3-carboxylic acidOC(=O)C1=CNC2=CC=CC=C121933.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Indole-3-carboxylic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)C1=C[NH]C2=CC=CC=C121877.1Semi standard non polar33892256
Indole-3-carboxylic acid,1TMS,isomer #2C[Si](C)(C)N1C=C(C(=O)O)C2=CC=CC=C211904.4Semi standard non polar33892256
Indole-3-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C2=CC=CC=C121990.2Semi standard non polar33892256
Indole-3-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C2=CC=CC=C121938.8Standard non polar33892256
Indole-3-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C2=CC=CC=C121989.5Standard polar33892256
Indole-3-carboxylic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=C[NH]C2=CC=CC=C122137.4Semi standard non polar33892256
Indole-3-carboxylic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1C=C(C(=O)O)C2=CC=CC=C212163.3Semi standard non polar33892256
Indole-3-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C122367.6Semi standard non polar33892256
Indole-3-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C122305.1Standard non polar33892256
Indole-3-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C122261.0Standard polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Metastatic melanoma		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Metastatic melanoma
  1. Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY: Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia. 2017 Oct;19(10):848-855. doi: 10.1016/j.neo.2017.08.004. Epub 2017 Sep 15. [PubMed:28923537 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000935
KNApSAcK IDC00000113
Chemspider ID63063
KEGG Compound IDC19837
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkStructural scheduling of synthetic cannabinoids
METLIN ID3795
PubChem Compound69867
PDB IDNot Available
ChEBI ID24809
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Liebich HM, Forst C: Basic profiles of organic acids in urine. J Chromatogr. 1990 Jan 26;525(1):1-14. [PubMed:2338430 ]
  2. HARTMANN F, FREIBERG E, RUGE W: [Indolepatterns in the urine of liver patients]. Klin Wochenschr. 1962 Jul 15;40:721-9. [PubMed:13905029 ]
  3. Byrd DJ, Kochen W, Idzko D, Knorr E: The analysis of indolic tryptophan metabolites in human urine. Thin-layer chromatography and in situ quantitation. J Chromatogr. 1974 Jul 17;94(0):85-106. [PubMed:4844607 ]

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Indole-3-carboxylic acid → 3,4,5-trihydroxy-6-(1H-indole-3-carbonyloxy)oxane-2-carboxylic aciddetails
Enzyme Details
2. Glycine N-acyltransferase
General function:
Involved in glycine N-acyltransferase activity
Specific function:
Mitochondrial acyltransferase which transfers an acyl group to the N-terminus of glycine and glutamine, although much less efficiently. Can conjugate numerous substrates to form a variety of N-acylglycines, with a preference for benzoyl-CoA over phenylacetyl-CoA as acyl donors. Thereby detoxify xenobiotics, such as benzoic acid or salicylic acid, and endogenous organic acids, such as isovaleric acid.
Gene Name:
GLYAT
Uniprot ID:
Q6IB77
Molecular weight:
18506.33
Reactions
Indole-3-carboxylic acid → 2-{[hydroxy(1H-indol-3-yl)methylidene]amino}acetic aciddetails