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Showing metabocard for (S)-4-Hydroxymandelonitrile (HMDB0060318)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:53:18 UTC
Update Date2023-02-21 17:29:51 UTC
HMDB IDHMDB0060318
Secondary Accession Numbers
  • HMDB60318
Metabolite Identification
Common Name(S)-4-Hydroxymandelonitrile
Description(S)-4-Hydroxymandelonitrile belongs to the class of organic compounds known as 1-hydroxy-2-unsubstituted benzenoids. These are phenols that are unsubstituted at the 2-position (S)-4-Hydroxymandelonitrile is an extremely weak basic (essentially neutral) compound (based on its pKa) (S)-4-Hydroxymandelonitrile exists in all living organisms, ranging from bacteria to humans. Outside of the human body, (S)-4-Hydroxymandelonitrile has been detected, but not quantified in, several different foods, such as common thymes, grapefruit/pummelo hybrids, celeriacs, nopals, and apples. This could make (S)-4-hydroxymandelonitrile a potential biomarker for the consumption of these foods. A 4-hydroxymandelonitrile that has (S)-configuration.
Structure
Data?1677000591
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

  Mrv1652306262017482D          

 11 11  0  0  0  0            999 V2000
10000.0295 9999.7818    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.7437 9999.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.029510000.6074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.5694 9999.3689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1686 9998.1305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3137 9999.3690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5994 9999.7814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8848 9999.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8848 9998.5440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5993 9998.1315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3137 9998.5441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  6  0  0  0
  2  4  3  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
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11  6  1  0  0  0  0
  1  6  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

HMDB0060318
     RDKit          3D
(S)-4-Hydroxymandelonitrile
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.3359   -1.7267   -0.1969 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7643   -0.7835    0.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0433    0.4336    0.4726 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5355    1.4959   -0.2672 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5936    0.2164    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1087   -1.0557    0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2299   -1.3104   -0.2256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432   -0.2765   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4980   -0.4979   -0.5023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6528    0.9960   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3178    1.2504    0.1815 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2279    0.6772    1.5466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4689    1.3779   -1.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8224   -1.8837    0.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6179   -2.3116   -0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1104   -0.6660    0.3032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3829    1.8087   -0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0525    2.2560    0.3433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 11  5  1  0
  3 12  1  1
  4 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
 10 17  1  0
 11 18  1  0
M  END
Download

3D SDF for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

  Mrv1652306262017482D          

 11 11  0  0  0  0            999 V2000
10000.0295 9999.7818    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.7437 9999.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.029510000.6074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.5694 9999.3689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1686 9998.1305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3137 9999.3690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5994 9999.7814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8848 9999.3689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8848 9998.5440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5993 9998.1315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3137 9998.5441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  6  0  0  0
  2  4  3  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
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11  6  1  0  0  0  0
  1  6  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060318

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@H](C#N)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H/t8-/m1/s1

> <INCHI_KEY>
HOOOPXDSCKBLFG-MRVPVSSYSA-N

> <FORMULA>
C8H7NO2

> <MOLECULAR_WEIGHT>
149.1467

> <EXACT_MASS>
149.047678473

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.527119351226446

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxy-2-(4-hydroxyphenyl)acetonitrile

> <ALOGPS_LOGP>
0.73

> <JCHEM_LOGP>
0.6502191896666667

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.969083556572523

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.455437104895557

> <JCHEM_PKA_STRONGEST_BASIC>
-4.195778758403649

> <JCHEM_POLAR_SURFACE_AREA>
64.25

> <JCHEM_REFRACTIVITY>
39.664

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.37e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-4-hydroxymandelonitrile

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

HMDB0060318
     RDKit          3D
(S)-4-Hydroxymandelonitrile
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.3359   -1.7267   -0.1969 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7643   -0.7835    0.1058 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0433    0.4336    0.4726 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5355    1.4959   -0.2672 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5936    0.2164    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1087   -1.0557    0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2299   -1.3104   -0.2256 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1432   -0.2765   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4980   -0.4979   -0.5023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6528    0.9960   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3178    1.2504    0.1815 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2279    0.6772    1.5466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4689    1.3779   -1.2360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8224   -1.8837    0.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6179   -2.3116   -0.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1104   -0.6660    0.3032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3829    1.8087   -0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0525    2.2560    0.3433 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 11  5  1  0
  3 12  1  1
  4 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
 10 17  1  0
 11 18  1  0
M  END
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PDB for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

HEADER    PROTEIN                                 26-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-JUN-20         0                                  
HETATM    1  C   UNK     0    8666.7228666.259   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8668.0558665.489   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8666.7228667.801   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0    8669.5968665.489   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0    8661.3818663.177   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8665.3868665.489   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8664.0528666.259   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8662.7188665.489   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8662.7188663.949   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8664.0528663.179   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8665.3868663.949   0.000  0.00  0.00           C+0
CONECT    1    2    3    6                                                  
CONECT    2    1    4                                                       
CONECT    3    1                                                            
CONECT    4    2                                                            
CONECT    5    9                                                            
CONECT    6    7   11    1                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10    5                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

COMPND    HMDB0060318
HETATM    1  N1  UNL     1       3.336  -1.727  -0.197  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.764  -0.783   0.106  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.043   0.434   0.473  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.535   1.496  -0.267  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.594   0.216   0.220  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.109  -1.056   0.013  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.230  -1.310  -0.226  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.143  -0.277  -0.265  1.00  0.00           C  
HETATM    9  O2  UNL     1      -3.498  -0.498  -0.502  1.00  0.00           O  
HETATM   10  C7  UNL     1      -1.653   0.996  -0.056  1.00  0.00           C  
HETATM   11  C8  UNL     1      -0.318   1.250   0.182  1.00  0.00           C  
HETATM   12  H1  UNL     1       2.228   0.677   1.547  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.469   1.378  -1.236  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.822  -1.884   0.041  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.618  -2.312  -0.390  1.00  0.00           H  
HETATM   16  H5  UNL     1      -4.110  -0.666   0.303  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.383   1.809  -0.089  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.053   2.256   0.343  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    5   12
CONECT    4   13
CONECT    5    6    6   11
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   10
CONECT    9   16
CONECT   10   11   11   17
CONECT   11   18
END
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SMILES for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

O[C@H](C#N)C1=CC=C(O)C=C1
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INCHI for HMDB0060318 ((S)-4-Hydroxymandelonitrile)

InChI=1S/C8H7NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H/t8-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(2s)-2-Hydroxy-2-(4-hydroxyphenyl)acetonitrileHMDB
(S)-4-HydroxymandelonitrileHMDB
(alphaS)-alpha,4-DihydroxybenzeneacetonitrileHMDB
(p-Hydroxyphenyl)glycolonitrileHMDB
(αS)-α,4-DihydroxybenzeneacetonitrileHMDB
2-Hydroxy-2-(4-hydroxyphenyl)acetonitrileHMDB
4-HydroxymandelonitrileHMDB
alpha,4-DihydroxybenzeneacetonitrileHMDB
p-HydroxymandelonitrileHMDB
α,4-DihydroxybenzeneacetonitrileHMDB
Chemical FormulaC8H7NO2
Average Molecular Weight149.1467
Monoisotopic Molecular Weight149.047678473
IUPAC Name(2S)-2-hydroxy-2-(4-hydroxyphenyl)acetonitrile
Traditional Name(S)-4-hydroxymandelonitrile
CAS Registry Number71807-09-5
SMILES
O[C@H](C#N)C1=CC=C(O)C=C1
InChI Identifier
InChI=1S/C8H7NO2/c9-5-8(11)6-1-3-7(10)4-2-6/h1-4,8,10-11H/t8-/m1/s1
InChI KeyHOOOPXDSCKBLFG-MRVPVSSYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1-hydroxy-2-unsubstituted benzenoids. These are phenols that are unsubstituted at the 2-position.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub Class1-hydroxy-2-unsubstituted benzenoids
Direct Parent1-hydroxy-2-unsubstituted benzenoids
Alternative Parents
Substituents
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocyclic benzene moiety
  • Cyanohydrin
  • Secondary alcohol
  • Alpha-hydroxynitrile
  • Carbonitrile
  • Nitrile
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic alcohol
  • Hydrocarbon derivative
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic 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 IDDB03430
Phenol Explorer Compound IDNot Available
FooDB IDFDB030165
KNApSAcK IDNot Available
Chemspider ID389105
KEGG Compound IDC03742
BioCyc IDCPD-648
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440104
PDB IDNot Available
ChEBI ID16660
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

Enzyme Details
1. Cytosolic beta-glucosidase
General function:
Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:
Glycosidase probably involved in the intestinal absorption and metabolism of dietary flavonoid glycosides. Able to hydrolyze a broad variety of glycosides including phytoestrogens, flavonols, flavones, flavanones and cyanogens. Possesses beta-glycosylceramidase activity and may be involved in a nonlysosomal catabolic pathway of glycosylceramide.
Gene Name:
GBA3
Uniprot ID:
Q9H227
Molecular weight:
Not Available
Reactions
Dhurrin + Water → (S)-4-Hydroxymandelonitrile + D-Glucosedetails