Hmdb loader

Showing metabocard for 2-Hydroxybenzyl alcohol (HMDB0059709)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-01-09 12:11:21 UTC
Update Date2023-02-21 17:29:13 UTC
HMDB IDHMDB0059709
Secondary Accession Numbers
  • HMDB59709
Metabolite Identification
Common Name2-Hydroxybenzyl alcohol
Description2-Hydroxybenzyl alcohol, also known as 2-(hydroxymethyl)phenol or saligenin, belongs to the class of organic compounds known as benzyl alcohols. These are organic compounds containing the phenylmethanol substructure. 2-Hydroxybenzyl alcohol is an extremely weak basic (essentially neutral) compound (based on its pKa). 2-Hydroxybenzyl alcohol exists in all living organisms, ranging from bacteria to humans. Outside of the human body, 2-Hydroxybenzyl alcohol has been detected, but not quantified in, several different foods, such as evening primroses, corns, carobs, java plums, and peppermints. This could make 2-hydroxybenzyl alcohol a potential biomarker for the consumption of these foods. A hydroxybenzyl alcohol that is phenol substituted by a hydroxymethyl group at C-2.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059709 (2-Hydroxybenzyl alcohol)

2-Hydroxybenzyl alcohol
  Mrv0541 01091312042D          

  9  9  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0059709 (2-Hydroxybenzyl alcohol)

HMDB0059709
     RDKit          3D
2-Hydroxybenzyl alcohol
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.5488    0.5535    0.4438 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9296   -0.2946   -0.4958 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4535   -0.2806   -0.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2926   -1.4278   -0.0619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3606    0.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2752   -0.1186    0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5494    1.0351    0.1527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025    0.9267   -0.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5964    2.0592   -0.2039 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2714    0.1335    0.9556 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3457   -1.3261   -0.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1805   -0.0840   -1.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1695   -2.4186   -0.1407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2772   -2.2868    0.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3471   -0.0979    0.4420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9832    2.0234    0.2475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1062    2.9643   -0.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  9 17  1  0
M  END
Download

3D SDF for HMDB0059709 (2-Hydroxybenzyl alcohol)

2-Hydroxybenzyl alcohol
  Mrv0541 01091312042D          

  9  9  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059709

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1=C(O)C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H8O2/c8-5-6-3-1-2-4-7(6)9/h1-4,8-9H,5H2

> <INCHI_KEY>
CQRYARSYNCAZFO-UHFFFAOYSA-N

> <FORMULA>
C7H8O2

> <MOLECULAR_WEIGHT>
124.1372

> <EXACT_MASS>
124.0524295

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
12.727707853675977

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)phenol

> <ALOGPS_LOGP>
0.40

> <JCHEM_LOGP>
0.9023307269999997

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.107805100271282

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.92081391652063

> <JCHEM_PKA_STRONGEST_BASIC>
-2.921396336543979

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
34.8548

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
saligenin

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0059709 (2-Hydroxybenzyl alcohol)

HMDB0059709
     RDKit          3D
2-Hydroxybenzyl alcohol
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.5488    0.5535    0.4438 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9296   -0.2946   -0.4958 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4535   -0.2806   -0.1849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2926   -1.4278   -0.0619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3606    0.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2752   -0.1186    0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5494    1.0351    0.1527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025    0.9267   -0.0722 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5964    2.0592   -0.2039 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2714    0.1335    0.9556 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3457   -1.3261   -0.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1805   -0.0840   -1.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1695   -2.4186   -0.1407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2772   -2.2868    0.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3471   -0.0979    0.4420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9832    2.0234    0.2475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1062    2.9643   -0.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  9 17  1  0
M  END
Download

PDB for HMDB0059709 (2-Hydroxybenzyl alcohol)

HEADER    PROTEIN                                 09-JAN-13   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2-Hydroxybenzyl alcohol                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JAN-13         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    3                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for HMDB0059709 (2-Hydroxybenzyl alcohol)

COMPND    HMDB0059709
HETATM    1  O1  UNL     1       2.549   0.554   0.444  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.930  -0.295  -0.496  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.453  -0.281  -0.185  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.293  -1.428  -0.062  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.674  -1.361   0.173  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.275  -0.119   0.274  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.549   1.035   0.153  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.202   0.927  -0.072  1.00  0.00           C  
HETATM    9  O2  UNL     1       0.596   2.059  -0.204  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.271   0.133   0.956  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.346  -1.326  -0.179  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.180  -0.084  -1.513  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.170  -2.419  -0.141  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.277  -2.287   0.257  1.00  0.00           H  
HETATM   15  H6  UNL     1      -3.347  -0.098   0.442  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.983   2.023   0.248  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.106   2.964  -0.094  1.00  0.00           H  
CONECT    1    2   10
CONECT    2    3   11   12
CONECT    3    4    4    8
CONECT    4    5   13
CONECT    5    6    6   14
CONECT    6    7   15
CONECT    7    8    8   16
CONECT    8    9
CONECT    9   17
END
Download

SMILES for HMDB0059709 (2-Hydroxybenzyl alcohol)

OCC1=C(O)C=CC=C1
Download

INCHI for HMDB0059709 (2-Hydroxybenzyl alcohol)

InChI=1S/C7H8O2/c8-5-6-3-1-2-4-7(6)9/h1-4,8-9H,5H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-(Hydroxymethyl)phenolChEBI
SaligeninChEBI
2-MonomethylolphenolHMDB
O-Hydroxybenzyl alcoholHMDB
Salicyl alcohol, monosodium saltHMDB
Salicyl alcohol, disodium saltHMDB
2-Methylol phenolHMDB
Salicyl alcohol, (ar)-isomerHMDB
2-Hydroxybenzyl alcoholChEBI
Salicyl alcoholMeSH
Chemical FormulaC7H8O2
Average Molecular Weight124.1372
Monoisotopic Molecular Weight124.0524295
IUPAC Name2-(hydroxymethyl)phenol
Traditional Namesaligenin
CAS Registry Number90-01-7
SMILES
OCC1=C(O)C=CC=C1
InChI Identifier
InChI=1S/C7H8O2/c8-5-6-3-1-2-4-7(6)9/h1-4,8-9H,5H2
InChI KeyCQRYARSYNCAZFO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzyl alcohols. These are organic compounds containing the phenylmethanol substructure.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzyl alcohols
Direct ParentBenzyl alcohols
Alternative Parents
Substituents
  • Benzyl alcohol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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 IDFDB031162
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02323
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSalicyl alcohol
METLIN IDNot Available
PubChem Compound5146
PDB IDNot Available
ChEBI ID16464
Food Biomarker OntologyNot Available
VMH ID2HYMEPH
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]