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Showing metabocard for 5-Hydroxyindole (HMDB0059805)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-03-04 20:35:15 UTC
Update Date2023-02-21 17:29:25 UTC
HMDB IDHMDB0059805
Secondary Accession Numbers
  • HMDB59805
Metabolite Identification
Common Name5-Hydroxyindole
Description5-Hydroxyindole, also known as indol-5-ol, belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group. 5-Hydroxyindole is an extremely weak basic (essentially neutral) compound (based on its pKa). These are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.
Structure
Data?1677000565
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059805 (5-Hydroxyindole)

  Mrv1652304272018442D          

 10 11  0  0  0  0            999 V2000
   -1.0093   -1.7715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1809   -0.9645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3884   -1.4744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247   -2.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0532   -2.8334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  4  2  0  0  0  0
  3  6  1  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0059805 (5-Hydroxyindole)

HMDB0059805
     RDKit          3D
5-Hydroxyindole
 17 18  0  0  0  0  0  0  0  0999 V2000
    3.1688   -1.0212   -0.1761 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9014   -0.4409   -0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7137    0.9079   -0.3932 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4676    1.4995   -0.3805 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6618    0.7330   -0.1249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9711    1.0436   -0.0532 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6384   -0.0931    0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7464   -1.1328    0.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -0.6198    0.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7779   -1.1982    0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6993   -1.0628    0.6831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5905    1.5113   -0.5932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3336    2.5680   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4054    1.9785   -0.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7107   -0.2380    0.3594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9308   -2.1779    0.5464 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8939   -2.2572    0.2811 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  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  2  1  0
  9  5  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
 10 17  1  0
M  END
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3D SDF for HMDB0059805 (5-Hydroxyindole)

  Mrv1652304272018442D          

 10 11  0  0  0  0            999 V2000
   -1.0093   -1.7715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1809   -0.9645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3884   -1.4744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2247   -2.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0532   -2.8334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  4  2  0  0  0  0
  3  6  1  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059805

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=CC2=C(NC=C2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO/c10-7-1-2-8-6(5-7)3-4-9-8/h1-5,9-10H

> <INCHI_KEY>
LMIQERWZRIFWNZ-UHFFFAOYSA-N

> <FORMULA>
C8H7NO

> <MOLECULAR_WEIGHT>
133.1473

> <EXACT_MASS>
133.052763851

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.801860314432467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indol-5-ol

> <ALOGPS_LOGP>
1.53

> <JCHEM_LOGP>
1.768442487333333

> <ALOGPS_LOGS>
-1.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.622731498087642

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.572356139390685

> <JCHEM_PKA_STRONGEST_BASIC>
-5.507064086661161

> <JCHEM_POLAR_SURFACE_AREA>
36.019999999999996

> <JCHEM_REFRACTIVITY>
39.12539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.20e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxyindol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0059805 (5-Hydroxyindole)

HMDB0059805
     RDKit          3D
5-Hydroxyindole
 17 18  0  0  0  0  0  0  0  0999 V2000
    3.1688   -1.0212   -0.1761 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9014   -0.4409   -0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7137    0.9079   -0.3932 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4676    1.4995   -0.3805 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6618    0.7330   -0.1249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9711    1.0436   -0.0532 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6384   -0.0931    0.2259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7464   -1.1328    0.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -0.6198    0.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7779   -1.1982    0.0942 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6993   -1.0628    0.6831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5905    1.5113   -0.5932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3336    2.5680   -0.5674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4054    1.9785   -0.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7107   -0.2380    0.3594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9308   -2.1779    0.5464 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8939   -2.2572    0.2811 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  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  2  1  0
  9  5  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
 10 17  1  0
M  END
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PDB for HMDB0059805 (5-Hydroxyindole)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0      -1.884  -3.307   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.204  -1.800   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.310   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.405   1.246   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.725  -2.752   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.405  -1.246   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.419  -3.783   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.060  -0.770   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.060   0.770   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -0.099  -5.289   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    8                                                       
CONECT    3    4    6                                                       
CONECT    4    3    9                                                       
CONECT    5    6    7                                                       
CONECT    6    3    5    8                                                  
CONECT    7    1    5   10                                                  
CONECT    8    2    6    9                                                  
CONECT    9    4    8                                                       
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0059805 (5-Hydroxyindole)

COMPND    HMDB0059805
HETATM    1  O1  UNL     1       3.169  -1.021  -0.176  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.901  -0.441  -0.159  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.714   0.908  -0.393  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.468   1.500  -0.381  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.662   0.733  -0.125  1.00  0.00           C  
HETATM    6  N1  UNL     1      -1.971   1.044  -0.053  1.00  0.00           N  
HETATM    7  C5  UNL     1      -2.638  -0.093   0.226  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.746  -1.133   0.332  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.482  -0.620   0.111  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.778  -1.198   0.094  1.00  0.00           C  
HETATM   11  H1  UNL     1       3.699  -1.063   0.683  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.590   1.511  -0.593  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.334   2.568  -0.567  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.405   1.979  -0.185  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.711  -0.238   0.359  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.931  -2.178   0.546  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.894  -2.257   0.281  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3    3   10
CONECT    3    4   12
CONECT    4    5    5   13
CONECT    5    6    9
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10
CONECT   10   17
END
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SMILES for HMDB0059805 (5-Hydroxyindole)

OC1=CC2=C(NC=C2)C=C1
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INCHI for HMDB0059805 (5-Hydroxyindole)

InChI=1S/C8H7NO/c10-7-1-2-8-6(5-7)3-4-9-8/h1-5,9-10H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Hydroxy-1H-indoleChEBI
indol-5-OlChEBI
Chemical FormulaC8H7NO
Average Molecular Weight133.1473
Monoisotopic Molecular Weight133.052763851
IUPAC Name1H-indol-5-ol
Traditional Name5-hydroxyindol
CAS Registry NumberNot Available
SMILES
OC1=CC2=C(NC=C2)C=C1
InChI Identifier
InChI=1S/C8H7NO/c10-7-1-2-8-6(5-7)3-4-9-8/h1-5,9-10H
InChI KeyLMIQERWZRIFWNZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassHydroxyindoles
Direct ParentHydroxyindoles
Alternative Parents
Substituents
  • Hydroxyindole
  • Indole
  • 1-hydroxy-2-unsubstituted benzenoid
  • Benzenoid
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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 Locations
  • Blood
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothHemodialysis patients with colon details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not AvailableHemodialysis patients without colon. details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDCPD-16174
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound16054
PDB IDNot Available
ChEBI ID89649
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. Aronov PA, Luo FJ, Plummer NS, Quan Z, Holmes S, Hostetter TH, Meyer TW: Colonic contribution to uremic solutes. J Am Soc Nephrol. 2011 Sep;22(9):1769-76. doi: 10.1681/ASN.2010121220. Epub 2011 Jul 22. [PubMed:21784895 ]
  2. Phua LC, Koh PK, Cheah PY, Ho HK, Chan EC: Global gas chromatography/time-of-flight mass spectrometry (GC/TOFMS)-based metabonomic profiling of lyophilized human feces. J Chromatogr B Analyt Technol Biomed Life Sci. 2013 Oct 15;937:103-13. doi: 10.1016/j.jchromb.2013.08.025. Epub 2013 Aug 26. [PubMed:24029555 ]
  3. Ashcroft GW, Eccleston D, Crawford TB: 5-hydroxyindole metabolism in rat brain. A study of intermediate metabolism using the technique of tryptophan loading. I. Methods. J Neurochem. 1965 Jun;12(6):483-92. [PubMed:5294372 ]
  4. Eccleston D, Ashcroft GW, Crawford TB: 5-hydroxyindole metabolism in rat brain. A study of intermediate metabolism using the technique of tryptophan loading. II. Applications and drug studies. J Neurochem. 1965 Jun;12(6):493-503. [PubMed:5294373 ]