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Showing metabocard for 3-Hydroxypropionitrile (HMDB0245904)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:57:08 UTC
Update Date2021-09-26 22:54:38 UTC
HMDB IDHMDB0245904
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Hydroxypropionitrile
Description3-Hydroxypropionitrile, also known as hydracrylonitrile or 2-cyanoethanol, belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N. Based on a literature review very few articles have been published on 3-Hydroxypropionitrile. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-hydroxypropionitrile is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Hydroxypropionitrile is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245904 (3-Hydroxypropionitrile)


  Mrv0541 02241205232D          

  5  4  0  0  0  0            999 V2000
    2.8875   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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  1  0  0  0  0
  4  5  3  0  0  0  0
M  END
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3D MOL for HMDB0245904 (3-Hydroxypropionitrile)

HMDB0245904
     RDKit          3D
3-Hydroxypropionitrile
 10  9  0  0  0  0  0  0  0  0999 V2000
    2.3505   -1.1453   -0.0478 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5196   -0.3363    0.0587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4995    0.6905    0.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8666    0.1503   -0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530   -0.9294    0.5721 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7557    1.5777   -0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559    1.0160    1.2554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7321   -0.2089   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    0.9728   -0.1741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2295   -1.7873    0.0884 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
  4  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
  4  9  1  0
  5 10  1  0
M  END
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3D SDF for HMDB0245904 (3-Hydroxypropionitrile)


  Mrv0541 02241205232D          

  5  4  0  0  0  0            999 V2000
    2.8875   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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  1  0  0  0  0
  4  5  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245904

> <DATABASE_NAME>
hmdb

> <SMILES>
OCCC#N

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO/c4-2-1-3-5/h5H,1,3H2

> <INCHI_KEY>
WSGYTJNNHPZFKR-UHFFFAOYSA-N

> <FORMULA>
C3H5NO

> <MOLECULAR_WEIGHT>
71.0779

> <EXACT_MASS>
71.037113787

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
7.080180097045148

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxypropanenitrile

> <ALOGPS_LOGP>
-0.98

> <JCHEM_LOGP>
-0.7456321573333334

> <ALOGPS_LOGS>
-0.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.190845055785811

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7153243725992864

> <JCHEM_POLAR_SURFACE_AREA>
44.019999999999996

> <JCHEM_REFRACTIVITY>
18.0246

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.00e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethylene cyanohydrin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0245904 (3-Hydroxypropionitrile)

HMDB0245904
     RDKit          3D
3-Hydroxypropionitrile
 10  9  0  0  0  0  0  0  0  0999 V2000
    2.3505   -1.1453   -0.0478 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5196   -0.3363    0.0587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4995    0.6905    0.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8666    0.1503   -0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1530   -0.9294    0.5721 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7557    1.5777   -0.4051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559    1.0160    1.2554 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7321   -0.2089   -1.2944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6000    0.9728   -0.1741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2295   -1.7873    0.0884 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
  4  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
  4  9  1  0
  5 10  1  0
M  END
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PDB for HMDB0245904 (3-Hydroxypropionitrile)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       5.390  -1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0245904 (3-Hydroxypropionitrile)

COMPND    HMDB0245904
HETATM    1  N1  UNL     1       2.350  -1.145  -0.048  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.520  -0.336   0.059  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.500   0.691   0.196  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.867   0.150  -0.249  1.00  0.00           C  
HETATM    5  O1  UNL     1      -1.153  -0.929   0.572  1.00  0.00           O  
HETATM    6  H1  UNL     1       0.756   1.578  -0.405  1.00  0.00           H  
HETATM    7  H2  UNL     1       0.456   1.016   1.255  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.732  -0.209  -1.294  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.600   0.973  -0.174  1.00  0.00           H  
HETATM   10  H5  UNL     1      -1.229  -1.787   0.088  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    6    7
CONECT    4    5    8    9
CONECT    5   10
END
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SMILES for HMDB0245904 (3-Hydroxypropionitrile)

OCCC#N
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INCHI for HMDB0245904 (3-Hydroxypropionitrile)

InChI=1S/C3H5NO/c4-2-1-3-5/h5H,1,3H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
HydracrylonitrileHMDB
2-CyanoethanolHMDB
Chemical FormulaC3H5NO
Average Molecular Weight71.0779
Monoisotopic Molecular Weight71.037113787
IUPAC Name3-hydroxypropanenitrile
Traditional Nameethylene cyanohydrin
CAS Registry NumberNot Available
SMILES
OCCC#N
InChI Identifier
InChI=1S/C3H5NO/c4-2-1-3-5/h5H,1,3H2
InChI KeyWSGYTJNNHPZFKR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassOrganic cyanides
Direct ParentNitriles
Alternative Parents
Substituents
  • Nitrile
  • Carbonitrile
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
PropertyValueSource
logP-0.98ALOGPS
logP-0.75ChemAxon
logS-0.38ALOGPS
pKa (Strongest Acidic)15.19ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area44.02 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity18.02 m³·mol⁻¹ChemAxon
Polarizability7.08 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+118.78230932474
DeepCCS[M-H]-116.96630932474
DeepCCS[M-2H]-152.28330932474
DeepCCS[M+Na]+125.97430932474
AllCCS[M+H]+121.632859911
AllCCS[M+H-H2O]+117.132859911
AllCCS[M+NH4]+125.832859911
AllCCS[M+Na]+127.032859911
AllCCS[M-H]-130.332859911
AllCCS[M+Na-2H]-135.832859911
AllCCS[M+HCOO]-141.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-HydroxypropionitrileOCCC#N1352.6Standard polar33892256
3-HydroxypropionitrileOCCC#N754.8Standard non polar33892256
3-HydroxypropionitrileOCCC#N809.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxypropionitrile GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fdo-9000000000-a8f372ef6a7d2293b54f2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxypropionitrile GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxypropionitrile GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxypropionitrile GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-001l-9000000000-878dfd598b53796d83a02014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 10V, Positive-QTOFsplash10-0uk9-9000000000-ae7067f66ed62aade3652016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 20V, Positive-QTOFsplash10-0zfr-9000000000-03520f0fcdf9107cc6f32016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 40V, Positive-QTOFsplash10-0udi-9000000000-8a732f8543d9490db4ed2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 10V, Negative-QTOFsplash10-00di-9000000000-eeb06115583fbfe5b4ee2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 20V, Negative-QTOFsplash10-00dl-9000000000-180cdf02c78243071e482016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 40V, Negative-QTOFsplash10-0f6x-9000000000-7032b2a47ede7c93ea402016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 10V, Positive-QTOFsplash10-0uk9-9000000000-a5d46343d7ebc5d1d4202021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 20V, Positive-QTOFsplash10-0f6x-9000000000-d0690699f0c674dfd3d52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 40V, Positive-QTOFsplash10-0udi-9000000000-c01df908bca422df0ba62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 10V, Negative-QTOFsplash10-00di-9000000000-824624715e96152c7f472021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 20V, Negative-QTOFsplash10-0fk9-9000000000-3d6a9c731d30e82a79ff2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxypropionitrile 40V, Negative-QTOFsplash10-0f6x-9000000000-17ed7b6746e948d38b9f2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
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 ID7720
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound8011
PDB IDNot Available
ChEBI IDNot Available
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]