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Showing metabocard for Mandelonitrile (HMDB0060486)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:24:17 UTC
Update Date2022-03-07 03:17:45 UTC
HMDB IDHMDB0060486
Secondary Accession Numbers
  • HMDB60486
Metabolite Identification
Common NameMandelonitrile
DescriptionMandelonitrile belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene. Mandelonitrile is an extremely weak basic (essentially neutral) compound (based on its pKa). Mandelonitrile exists in all living organisms, ranging from bacteria to humans.
Structure
Data?1563866066
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060486 (Mandelonitrile)

  Mrv0541 05161318242D          

 10 10  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  3  0  0  0  0
  8 10  1  6  0  0  0
M  END
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3D MOL for HMDB0060486 (Mandelonitrile)

HMDB0060486
     RDKit          3D
Mandelonitrile
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.1618    1.6039   -2.4053 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0160    0.9751   -1.4323 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8237    0.2066   -0.2109 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5159   -1.0005   -0.2599 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3818    0.0414    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2865    0.8411    0.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6353    0.7102    1.1514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3750   -0.2298    0.4612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7233   -1.0327   -0.4588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3780   -0.8905   -0.6719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2455    0.7842    0.6271 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7846   -1.3247    0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2467    1.6007    1.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1635    1.3426    1.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4395   -0.3325    0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3159   -1.7789   -1.0052 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1410   -1.5160   -1.3916 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
  9 10  2  0
 10  5  1  0
  3 11  1  1
  4 12  1  0
  6 13  1  0
  7 14  1  0
  8 15  1  0
  9 16  1  0
 10 17  1  0
M  END
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3D SDF for HMDB0060486 (Mandelonitrile)

  Mrv0541 05161318242D          

 10 10  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   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
    0.0000    0.0000    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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  7  4  2  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  3  0  0  0  0
  8 10  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0060486

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8,10H/t8-/m0/s1

> <INCHI_KEY>
NNICRUQPODTGRU-QMMMGPOBSA-N

> <FORMULA>
C8H7NO

> <MOLECULAR_WEIGHT>
133.1473

> <EXACT_MASS>
133.052763851

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
13.5517896289222

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-2-phenylacetonitrile

> <ALOGPS_LOGP>
0.68

> <JCHEM_LOGP>
0.9537845113333332

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.666910761057423

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.795695242182852

> <JCHEM_PKA_STRONGEST_BASIC>
-4.200129584931049

> <JCHEM_POLAR_SURFACE_AREA>
44.019999999999996

> <JCHEM_REFRACTIVITY>
37.6831

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-mandelonitrile

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0060486 (Mandelonitrile)

HMDB0060486
     RDKit          3D
Mandelonitrile
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.1618    1.6039   -2.4053 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0160    0.9751   -1.4323 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8237    0.2066   -0.2109 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5159   -1.0005   -0.2599 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3818    0.0414    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2865    0.8411    0.9268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6353    0.7102    1.1514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3750   -0.2298    0.4612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7233   -1.0327   -0.4588 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3780   -0.8905   -0.6719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2455    0.7842    0.6271 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7846   -1.3247    0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2467    1.6007    1.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1635    1.3426    1.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4395   -0.3325    0.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3159   -1.7789   -1.0052 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1410   -1.5160   -1.3916 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
  9 10  2  0
 10  5  1  0
  3 11  1  1
  4 12  1  0
  6 13  1  0
  7 14  1  0
  8 15  1  0
  9 16  1  0
 10 17  1  0
M  END
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PDB for HMDB0060486 (Mandelonitrile)

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   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  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.334   5.390   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    7                                                       
CONECT    5    3    7                                                       
CONECT    6    8    9                                                       
CONECT    7    4    5    8                                                  
CONECT    8    6    7   10                                                  
CONECT    9    6                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0060486 (Mandelonitrile)

COMPND    HMDB0060486
HETATM    1  N1  UNL     1       2.162   1.604  -2.405  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.016   0.975  -1.432  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.824   0.207  -0.211  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.516  -1.001  -0.260  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.382   0.041   0.006  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.286   0.841   0.927  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.635   0.710   1.151  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.375  -0.230   0.461  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.723  -1.033  -0.459  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.378  -0.891  -0.672  1.00  0.00           C  
HETATM   11  H1  UNL     1       2.245   0.784   0.627  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.785  -1.325   0.644  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.247   1.601   1.501  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.163   1.343   1.880  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.439  -0.333   0.639  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.316  -1.779  -1.005  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.141  -1.516  -1.392  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    5   11
CONECT    4   12
CONECT    5    6    6   10
CONECT    6    7   13
CONECT    7    8    8   14
CONECT    8    9   15
CONECT    9   10   10   16
CONECT   10   17
END
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SMILES for HMDB0060486 (Mandelonitrile)

O[C@@H](C#N)C1=CC=CC=C1
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INCHI for HMDB0060486 (Mandelonitrile)

InChI=1S/C8H7NO/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8,10H/t8-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(+)-MandelonitrileChEBI
(R)-(+)-MandelonitrileChEBI
D-MandelonitrileChEBI
Benzaldehyde cyanohydrinKegg
(R)-MandelonitrileKegg
Chemical FormulaC8H7NO
Average Molecular Weight133.1473
Monoisotopic Molecular Weight133.052763851
IUPAC Name(2R)-2-hydroxy-2-phenylacetonitrile
Traditional Name(-)-mandelonitrile
CAS Registry NumberNot Available
SMILES
O[C@@H](C#N)C1=CC=CC=C1
InChI Identifier
InChI=1S/C8H7NO/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8,10H/t8-/m0/s1
InChI KeyNNICRUQPODTGRU-QMMMGPOBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassNot Available
Direct ParentBenzene and substituted derivatives
Alternative Parents
Substituents
  • Monocyclic benzene moiety
  • Alpha-hydroxynitrile
  • Secondary alcohol
  • Cyanohydrin
  • Nitrile
  • Carbonitrile
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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 Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+MetCCS_train_pos128.87130932474
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00561
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMandelonitrile
METLIN IDNot Available
PubChem Compound9548674
PDB IDNot Available
ChEBI ID18450
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
Prunasin + Water → Mandelonitrile + D-Glucosedetails