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Showing NP-Card for Saligenin (NP0002906)

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Record Information
Version1.0
Created at2020-11-23 19:43:19 UTC
Updated at2021-08-19 23:59:31 UTC
NP-MRD IDNP0002906
Secondary Accession NumbersNone
Natural Product Identification
Common NameSaligenin
Provided ByBMRBBMRB logo
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 exists in all living organisms, ranging from bacteria to humans. 2-Hydroxybenzyl alcohol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Saligenin is found in Anthriscus sylvestris, Festuca rubra, Gardenia jasminoides, Populus laurifolia, Populus tremula, Salix alba, Salix caprea and Salix myrsinifolia. It was first documented in 2008 (PMID: 17984079). Based on a literature review a significant number of articles have been published on 2-Hydroxybenzyl alcohol (PMID: 22770225) (PMID: 25010147) (PMID: 34151556) (PMID: 32706303).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002906 (Saligenin)


     RDKit          2D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -3.3977    0.0387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8978    0.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3979    0.0720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3377    1.3793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8376    1.3959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6019    0.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -1.2020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3665   -1.2186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3690   -2.5259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1621    1.3293    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9144    1.5553    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8811   -1.4446    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4267    2.6699    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5731    2.7032    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1018    0.1220    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6308   -2.4926    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8689   -2.5426    0.0000 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  1
  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 MOL for NP0002906 (Saligenin)

NP0002906
     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.8371   -0.4134   -0.7136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9758   -0.3464    0.4066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5210   -0.3544    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2756   -1.4400   -0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6559   -1.2389   -0.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2997   -0.0049   -0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4764    1.0848    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1113    0.9069    0.1726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7570    2.0047    0.4223 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3999    0.2044   -1.4189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2586    0.4076    1.1121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1711   -1.4143    0.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2111   -2.4009   -0.2202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2975   -2.0787   -0.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3492    0.0601   -0.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9279    2.1011    0.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2618    2.9222    0.4211 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 NP0002906 (Saligenin)


     RDKit          2D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -3.3977    0.0387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8978    0.0554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3979    0.0720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3377    1.3793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8376    1.3959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6019    0.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -1.2020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3665   -1.2186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3690   -2.5259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1621    1.3293    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9144    1.5553    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8811   -1.4446    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4267    2.6699    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5731    2.7032    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1018    0.1220    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6308   -2.4926    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8689   -2.5426    0.0000 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  1
  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
> <DATABASE_ID>
NP0002906

> <DATABASE_NAME>
NP-MRD

> <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 NP0002906 (Saligenin)

NP0002906
     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.8371   -0.4134   -0.7136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9758   -0.3464    0.4066 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5210   -0.3544    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2756   -1.4400   -0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6559   -1.2389   -0.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2997   -0.0049   -0.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4764    1.0848    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1113    0.9069    0.1726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7570    2.0047    0.4223 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3999    0.2044   -1.4189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2586    0.4076    1.1121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1711   -1.4143    0.9151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2111   -2.4009   -0.2202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2975   -2.0787   -0.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3492    0.0601   -0.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9279    2.1011    0.1099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2618    2.9222    0.4211 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 NP0002906 (Saligenin)

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 NP0002906 (Saligenin)

COMPND    NP0002906
HETATM    1  O1  UNL     1      -2.837  -0.413  -0.714  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.976  -0.346   0.407  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.521  -0.354   0.102  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.276  -1.440  -0.119  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.656  -1.239  -0.252  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.300  -0.005  -0.181  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.476   1.085   0.036  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.111   0.907   0.173  1.00  0.00           C  
HETATM    9  O2  UNL     1      -0.757   2.005   0.422  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.400   0.204  -1.419  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.259   0.408   1.112  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.171  -1.414   0.915  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.211  -2.401  -0.220  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.298  -2.079  -0.459  1.00  0.00           H  
HETATM   15  H6  UNL     1       3.349   0.060  -0.335  1.00  0.00           H  
HETATM   16  H7  UNL     1       1.928   2.101   0.110  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.262   2.922   0.421  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 NP0002906 (Saligenin)

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

INCHI for NP0002906 (Saligenin)

InChI=1S/C7H8O2/c8-5-6-3-1-2-4-7(6)9/h1-4,8-9H,5H2
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View in JSmol
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
Salicyl alcoholHMDB
2-Hydroxybenzyl alcoholChEBI
Chemical FormulaC7H8O2
Average Mass124.1372 Da
Monoisotopic Mass124.05243 Da
IUPAC Name2-(hydroxymethyl)phenol
Traditional Namesaligenin
CAS Registry NumberNot Available
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anthriscus sylvestrisLOTUS Database
Festuca rubraLOTUS Database
Gardenia jasminoidesLOTUS Database
Populus laurifoliaLOTUS Database
Populus tremulaLOTUS Database
Salix albaLOTUS Database
Salix capreaLOTUS Database
Salix myrsinifoliaLOTUS Database
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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAromatic homomonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting Point87.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point238.60 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility63000 mg/L @ 22 °C (exp)The Good Scents Company Information System
LogP0.730The Good Scents Company Information System
Predicted Properties
PropertyValueSource
logP0.4ALOGPS
logP0.9ChemAxon
logS-0.26ALOGPS
pKa (Strongest Acidic)9.92ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity34.85 m³·mol⁻¹ChemAxon
Polarizability12.73 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0059709
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031162
KNApSAcK IDNot Available
Chemspider ID4962
KEGG Compound IDC02323
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSalicyl alcohol
METLIN IDNot Available
PubChem Compound5146
PDB IDNot Available
ChEBI ID16464
Good Scents IDrw1176731
References
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 ]
  2. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
  3. Kumar S, Singh SK, Calabrese C, Maris A, Melandri S, Das A: Structure of saligenin: microwave, UV and IR spectroscopy studies in a supersonic jet combined with quantum chemistry calculations. Phys Chem Chem Phys. 2014 Aug 28;16(32):17163-71. doi: 10.1039/c4cp01693a. [PubMed:25010147 ]
  4. Pandey AM, Digrawal NK, Mohanta N, Jamdade AB, Chaudhari MB, Bisht GS, Gnanaprakasam B: Catalytic Acceptorless Dehydrogenation of Amino Alcohols and 2-Hydroxybenzyl Alcohols for Annulation Reaction under Neutral Conditions. J Org Chem. 2021 Jul 2;86(13):8805-8828. doi: 10.1021/acs.joc.1c00714. Epub 2021 Jun 21. [PubMed:34151556 ]
  5. Eckardt M, Benisch R, Simat TJ: Characterisation, release and migration of phenolic compounds from resoles used in polyester-phenol coatings intended for food contact materials. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2020 Oct;37(10):1791-1810. doi: 10.1080/19440049.2020.1782480. Epub 2020 Jul 24. [PubMed:32706303 ]