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Showing metabocard for Cyanoacetic acid (HMDB0250607)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:42:00 UTC
Update Date2021-09-26 23:02:10 UTC
HMDB IDHMDB0250607
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyanoacetic acid
DescriptionCyanoacetic acid, also known as acide cyanacetique or cyanessigsaeure, belongs to the class of organic compounds known as carboxylic acids. Carboxylic acids are compounds containing a carboxylic acid group with the formula -C(=O)OH. Based on a literature review very few articles have been published on Cyanoacetic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyanoacetic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyanoacetic acid 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 HMDB0250607 (Cyanoacetic acid)


  Mrv0541 02241204072D          

  6  5  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   -1.4289    0.0000 O   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  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  3  0  0  0  0
M  END
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3D MOL for HMDB0250607 (Cyanoacetic acid)

HMDB0250607
     RDKit          3D
Cyanoacetic acid
  9  8  0  0  0  0  0  0  0  0999 V2000
   -2.6689    0.9502    0.1458 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6983    0.3411   -0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4687   -0.4143   -0.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7001    0.1994    0.4034 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823    1.2458    1.0605 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9694   -0.3129    0.3454 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3094   -0.4983   -1.3727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6632   -1.4505    0.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6567   -0.0605   -0.3624 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  2  0
  4  6  1  0
  3  7  1  0
  3  8  1  0
  6  9  1  0
M  END
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3D SDF for HMDB0250607 (Cyanoacetic acid)


  Mrv0541 02241204072D          

  6  5  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   -1.4289    0.0000 O   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  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250607

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CC#N

> <INCHI_IDENTIFIER>
InChI=1S/C3H3NO2/c4-2-1-3(5)6/h1H2,(H,5,6)

> <INCHI_KEY>
MLIREBYILWEBDM-UHFFFAOYSA-N

> <FORMULA>
C3H3NO2

> <MOLECULAR_WEIGHT>
85.0614

> <EXACT_MASS>
85.016378345

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
7.076710009604815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-cyanoacetic acid

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-0.27316840166666667

> <ALOGPS_LOGS>
-0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.03566294428715

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.061521760815647

> <JCHEM_POLAR_SURFACE_AREA>
61.089999999999996

> <JCHEM_REFRACTIVITY>
17.9671

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyanoacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0250607 (Cyanoacetic acid)

HMDB0250607
     RDKit          3D
Cyanoacetic acid
  9  8  0  0  0  0  0  0  0  0999 V2000
   -2.6689    0.9502    0.1458 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6983    0.3411   -0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4687   -0.4143   -0.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7001    0.1994    0.4034 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823    1.2458    1.0605 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9694   -0.3129    0.3454 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3094   -0.4983   -1.3727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6632   -1.4505    0.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6567   -0.0605   -0.3624 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  2  0
  4  6  1  0
  3  7  1  0
  3  8  1  0
  6  9  1  0
M  END
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PDB for HMDB0250607 (Cyanoacetic acid)

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  O   UNK     0       3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0250607 (Cyanoacetic acid)

COMPND    HMDB0250607
HETATM    1  N1  UNL     1      -2.669   0.950   0.146  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.698   0.341  -0.045  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.469  -0.414  -0.276  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.700   0.199   0.403  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.482   1.246   1.061  1.00  0.00           O  
HETATM    6  O2  UNL     1       1.969  -0.313   0.345  1.00  0.00           O  
HETATM    7  H1  UNL     1      -0.309  -0.498  -1.373  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.663  -1.451   0.101  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.657  -0.060  -0.362  1.00  0.00           H  
CONECT    1    2    2    2
CONECT    2    3
CONECT    3    4    7    8
CONECT    4    5    5    6
CONECT    6    9
END
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SMILES for HMDB0250607 (Cyanoacetic acid)

OC(=O)CC#N
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INCHI for HMDB0250607 (Cyanoacetic acid)

InChI=1S/C3H3NO2/c4-2-1-3(5)6/h1H2,(H,5,6)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Acide cyanacetiqueChEBI
CyanessigsaeureChEBI
Cyanoethanoic acidChEBI
Malonic acid mononitrileChEBI
Malonic mononitrileChEBI
CyanoethanoateGenerator
Malonate mononitrileGenerator
CyanoacetateGenerator
Cyanoacetic acid, copper (+2) saltMeSH
Chemical FormulaC3H3NO2
Average Molecular Weight85.0614
Monoisotopic Molecular Weight85.016378345
IUPAC Name2-cyanoacetic acid
Traditional Namecyanoacetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CC#N
InChI Identifier
InChI=1S/C3H3NO2/c4-2-1-3(5)6/h1H2,(H,5,6)
InChI KeyMLIREBYILWEBDM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboxylic acids. Carboxylic acids are compounds containing a carboxylic acid group with the formula -C(=O)OH.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acids
Direct ParentCarboxylic acids
Alternative Parents
Substituents
  • Nitrile
  • Carbonitrile
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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 PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.46ALOGPS
logP-0.27ChemAxon
logS-0.59ALOGPS
pKa (Strongest Acidic)2.06ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area61.09 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity17.97 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]+121.76130932474
DeepCCS[M-H]-119.66830932474
DeepCCS[M-2H]-155.52130932474
DeepCCS[M+Na]+129.94230932474
AllCCS[M+H]+122.932859911
AllCCS[M+H-H2O]+118.432859911
AllCCS[M+NH4]+127.032859911
AllCCS[M+Na]+128.232859911
AllCCS[M-H]-122.632859911
AllCCS[M+Na-2H]-127.232859911
AllCCS[M+HCOO]-132.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.3148 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.32 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid941.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid376.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid111.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid278.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid82.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid289.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid326.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)351.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid643.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid155.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid855.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid246.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid309.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate738.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA281.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water340.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Cyanoacetic acidOC(=O)CC#N1604.5Standard polar33892256
Cyanoacetic acidOC(=O)CC#N891.6Standard non polar33892256
Cyanoacetic acidOC(=O)CC#N994.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyanoacetic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-000f-9000000000-6b401feb90f6f6b4047d2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyanoacetic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyanoacetic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyanoacetic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-0006-9000000000-625b04c92965c0eb781e2014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 10V, Positive-QTOFsplash10-00kr-9000000000-93c80d4036524536e1d12016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 20V, Positive-QTOFsplash10-014u-9000000000-2dd6a191af9174b67a6b2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 40V, Positive-QTOFsplash10-0006-9000000000-609dc576b5e44de6bf342016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 10V, Negative-QTOFsplash10-001i-9000000000-39644a63ece11adf03932016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 20V, Negative-QTOFsplash10-000x-9000000000-caefeee74c057eea868e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 40V, Negative-QTOFsplash10-0006-9000000000-0bb0273844c43773a12a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 10V, Positive-QTOFsplash10-0006-9000000000-b950b4f5752d2d0b41f62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 20V, Positive-QTOFsplash10-0006-9000000000-042ab9174696882de89d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 40V, Positive-QTOFsplash10-0006-9000000000-042ab9174696882de89d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 10V, Negative-QTOFsplash10-001i-9000000000-ddd7e9bf339cc5fe149a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 20V, Negative-QTOFsplash10-0159-9000000000-f9bdf530fd37a20242172021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyanoacetic acid 40V, Negative-QTOFsplash10-014i-9000000000-44a1e7b463fca49556fc2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
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 ID9357
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyanoacetic acid
METLIN IDNot Available
PubChem Compound9740
PDB IDNot Available
ChEBI ID51889
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 ]