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Showing metabocard for indole-3-glycol aldehyde (HMDB0304393)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 09:26:37 UTC
Update Date2021-09-24 09:26:37 UTC
HMDB IDHMDB0304393
Secondary Accession NumbersNone
Metabolite Identification
Common Nameindole-3-glycol aldehyde
DescriptionIndole-3-glycol aldehyde, also known as 2-hydroxy-2-(1h-indol-3-yl)acetaldehyde, is a member of the class of compounds known as 3-alkylindoles. 3-alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. Indole-3-glycol aldehyde is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). Indole-3-glycol aldehyde can be found in a number of food items such as tree fern, jostaberry, pitanga, and pine nut, which makes indole-3-glycol aldehyde a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304393 (indole-3-glycol aldehyde)

  Mrv1533005141521452D          

 13 14  0  0  0  0            999 V2000
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    0.9256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358    1.3672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809    2.1518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  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
  3  8  2  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
M  END
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3D MOL for HMDB0304393 (indole-3-glycol aldehyde)

HMDB0304393
     RDKit          3D
indole-3-glycol aldehyde
 22 23  0  0  0  0  0  0  0  0999 V2000
   -4.2024    0.3591    0.2241 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1816    0.0253   -0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0468   -0.6560    0.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3556   -0.8325    1.7141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8620    0.2431    0.2736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7891    1.6034    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4742    2.0226    0.2971 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2809    0.9718   -0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197    0.8688   -0.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1507   -0.3543   -0.6458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3137   -1.4586   -0.6587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731   -1.3503   -0.3668 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4345   -0.1275   -0.0530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0320    0.2081   -1.4003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8409   -1.6080   -0.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6212   -1.7437    1.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6445    2.2057    0.7605 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8391    2.9986    0.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2426    1.7395   -0.3158 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2239   -0.4620   -0.8830 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7267   -2.4469   -0.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.2060   -0.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  5  1  0
 13  8  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
M  END
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3D SDF for HMDB0304393 (indole-3-glycol aldehyde)

  Mrv1533005141521452D          

 13 14  0  0  0  0            999 V2000
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    0.9256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358    1.3672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809    2.1518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  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
  3  8  2  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304393

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(C=O)C1=CNC2=C1C=CC=C2

> <INCHI_IDENTIFIER>
InChI=1S/C10H9NO2/c12-6-10(13)8-5-11-9-4-2-1-3-7(8)9/h1-6,10-11,13H

> <INCHI_KEY>
XKZDNWMDLGQXML-UHFFFAOYSA-N

> <FORMULA>
C10H9NO2

> <MOLECULAR_WEIGHT>
175.187

> <EXACT_MASS>
175.063328534

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
17.767255477138743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-2-(1H-indol-3-yl)acetaldehyde

> <ALOGPS_LOGP>
1.27

> <JCHEM_LOGP>
0.8359813853333334

> <ALOGPS_LOGS>
-1.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.126096754961353

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.95869601886633

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6873470831082757

> <JCHEM_POLAR_SURFACE_AREA>
53.089999999999996

> <JCHEM_REFRACTIVITY>
48.8649

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.98e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-indoleglycolaldehyde

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304393 (indole-3-glycol aldehyde)

HMDB0304393
     RDKit          3D
indole-3-glycol aldehyde
 22 23  0  0  0  0  0  0  0  0999 V2000
   -4.2024    0.3591    0.2241 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1816    0.0253   -0.3331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0468   -0.6560    0.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3556   -0.8325    1.7141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8620    0.2431    0.2736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7891    1.6034    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4742    2.0226    0.2971 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2809    0.9718   -0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6197    0.8688   -0.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1507   -0.3543   -0.6458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3137   -1.4586   -0.6587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731   -1.3503   -0.3668 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4345   -0.1275   -0.0530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0320    0.2081   -1.4003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8409   -1.6080   -0.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6212   -1.7437    1.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6445    2.2057    0.7605 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8391    2.9986    0.3851 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2426    1.7395   -0.3158 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2239   -0.4620   -0.8830 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7267   -2.4469   -0.9078 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2971   -2.2060   -0.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13  5  1  0
 13  8  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  6 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
M  END
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PDB for HMDB0304393 (indole-3-glycol aldehyde)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.143   1.728   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.680   2.552   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.204   4.017   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3   10                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8    1                                                       
CONECT   10    2   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END
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3D PDB for HMDB0304393 (indole-3-glycol aldehyde)

COMPND    HMDB0304393
HETATM    1  O1  UNL     1      -4.202   0.359   0.224  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.182   0.025  -0.333  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.047  -0.656   0.366  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.356  -0.832   1.714  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.862   0.243   0.274  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.789   1.603   0.485  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.474   2.023   0.297  1.00  0.00           N  
HETATM    8  C5  UNL     1       1.281   0.972  -0.043  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.620   0.869  -0.334  1.00  0.00           C  
HETATM   10  C7  UNL     1       3.151  -0.354  -0.646  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.314  -1.459  -0.659  1.00  0.00           C  
HETATM   12  C9  UNL     1       0.973  -1.350  -0.367  1.00  0.00           C  
HETATM   13  C10 UNL     1       0.434  -0.128  -0.053  1.00  0.00           C  
HETATM   14  H1  UNL     1      -3.032   0.208  -1.400  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.841  -1.608  -0.119  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.621  -1.744   1.925  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.645   2.206   0.760  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.839   2.999   0.385  1.00  0.00           H  
HETATM   19  H6  UNL     1       3.243   1.740  -0.316  1.00  0.00           H  
HETATM   20  H7  UNL     1       4.224  -0.462  -0.883  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.727  -2.447  -0.908  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.297  -2.206  -0.371  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   14
CONECT    3    4    5   15
CONECT    4   16
CONECT    5    6    6   13
CONECT    6    7   17
CONECT    7    8   18
CONECT    8    9    9   13
CONECT    9   10   19
CONECT   10   11   11   20
CONECT   11   12   21
CONECT   12   13   13   22
END
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SMILES for HMDB0304393 (indole-3-glycol aldehyde)

OC(C=O)C1=CNC2=C1C=CC=C2
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INCHI for HMDB0304393 (indole-3-glycol aldehyde)

InChI=1S/C10H9NO2/c12-6-10(13)8-5-11-9-4-2-1-3-7(8)9/h1-6,10-11,13H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-IndolylglycolaldehydeChEBI
3-IndoleglycolaldehydeKEGG
Chemical FormulaC10H9NO2
Average Molecular Weight175.187
Monoisotopic Molecular Weight175.063328534
IUPAC Name2-hydroxy-2-(1H-indol-3-yl)acetaldehyde
Traditional Name3-indoleglycolaldehyde
CAS Registry NumberNot Available
SMILES
OC(C=O)C1=CNC2=C1C=CC=C2
InChI Identifier
InChI=1S/C10H9NO2/c12-6-10(13)8-5-11-9-4-2-1-3-7(8)9/h1-6,10-11,13H
InChI KeyXKZDNWMDLGQXML-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndoles
Direct Parent3-alkylindoles
Alternative Parents
Substituents
  • 3-alkylindole
  • Substituted pyrrole
  • Benzenoid
  • Pyrrole
  • Heteroaromatic compound
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Azacycle
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aldehyde
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot 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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030940
KNApSAcK IDNot Available
Chemspider ID388979
KEGG Compound IDC03230
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439951
PDB IDNot Available
ChEBI ID15976
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 ReferencesNot Available