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Showing metabocard for Succinamic acid (HMDB0258538)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:09:58 UTC
Update Date2021-09-26 23:15:30 UTC
HMDB IDHMDB0258538
Secondary Accession NumbersNone
Metabolite Identification
Common NameSuccinamic acid
Descriptionsuccinamic acid, also known as succinamate, belongs to the class of organic compounds known as straight chain fatty acids. These are fatty acids with a straight aliphatic chain. Based on a literature review very few articles have been published on succinamic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Succinamic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Succinamic 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 HMDB0258538 (Succinamic acid)


  Mrv1533004231520122D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   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  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0258538 (Succinamic acid)

HMDB0258538
     RDKit          3D
Succinamic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.8467    0.1962    0.2437 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822   -0.4181    0.1367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -1.6435   -0.0557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3683    0.4140    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8461   -0.4468    0.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1008    0.3239    0.2200 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0614    1.5567    0.4129 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3245   -0.3017    0.1114 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1628    0.6162    1.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4668    0.2243   -0.5820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842    0.9774    1.2118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3575    1.1376   -0.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8419   -1.2892    0.8557 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7576   -0.9557   -0.8936 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6981   -0.3914   -0.8463 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0258538 (Succinamic acid)


  Mrv1533004231520122D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   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  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258538

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(=O)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H7NO3/c5-3(6)1-2-4(7)8/h1-2H2,(H2,5,6)(H,7,8)

> <INCHI_KEY>
JDVPQXZIJDEHAN-UHFFFAOYSA-N

> <FORMULA>
C4H7NO3

> <MOLECULAR_WEIGHT>
117.104

> <EXACT_MASS>
117.042593089

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.567561172189238

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-carbamoylpropanoic acid

> <ALOGPS_LOGP>
-1.32

> <JCHEM_LOGP>
-1.205425581

> <ALOGPS_LOGS>
0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.070962652115863

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.191030771966093

> <JCHEM_PKA_STRONGEST_BASIC>
-2.000867834620418

> <JCHEM_POLAR_SURFACE_AREA>
80.39

> <JCHEM_REFRACTIVITY>
25.359199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-carbamoylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0258538 (Succinamic acid)

HMDB0258538
     RDKit          3D
Succinamic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.8467    0.1962    0.2437 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822   -0.4181    0.1367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -1.6435   -0.0557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3683    0.4140    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8461   -0.4468    0.1107 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1008    0.3239    0.2200 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0614    1.5567    0.4129 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3245   -0.3017    0.1114 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1628    0.6162    1.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4668    0.2243   -0.5820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842    0.9774    1.2118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3575    1.1376   -0.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8419   -1.2892    0.8557 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7576   -0.9557   -0.8936 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6981   -0.3914   -0.8463 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0258538 (Succinamic acid)

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0258538 (Succinamic acid)

COMPND    HMDB0258538
HETATM    1  N1  UNL     1      -2.847   0.196   0.244  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.582  -0.418   0.137  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.462  -1.643  -0.056  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.368   0.414   0.256  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.846  -0.447   0.111  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.101   0.324   0.220  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.061   1.557   0.413  1.00  0.00           O  
HETATM    8  O3  UNL     1       3.324  -0.302   0.111  1.00  0.00           O  
HETATM    9  H1  UNL     1      -3.163   0.616   1.127  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.467   0.224  -0.582  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.384   0.977   1.212  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.358   1.138  -0.601  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.842  -1.289   0.856  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.758  -0.956  -0.894  1.00  0.00           H  
HETATM   15  H7  UNL     1       3.698  -0.391  -0.846  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    3    4
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6    7    7    8
CONECT    8   15
END
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SMILES for HMDB0258538 (Succinamic acid)

NC(=O)CCC(O)=O
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INCHI for HMDB0258538 (Succinamic acid)

InChI=1S/C4H7NO3/c5-3(6)1-2-4(7)8/h1-2H2,(H2,5,6)(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Succinic acid monoamideChEBI
Succinate monoamideGenerator
SuccinamateGenerator
Chemical FormulaC4H7NO3
Average Molecular Weight117.104
Monoisotopic Molecular Weight117.042593089
IUPAC Name3-carbamoylpropanoic acid
Traditional Name3-carbamoylpropanoic acid
CAS Registry NumberNot Available
SMILES
NC(=O)CCC(O)=O
InChI Identifier
InChI=1S/C4H7NO3/c5-3(6)1-2-4(7)8/h1-2H2,(H2,5,6)(H,7,8)
InChI KeyJDVPQXZIJDEHAN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as straight chain fatty acids. These are fatty acids with a straight aliphatic chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentStraight chain fatty acids
Alternative Parents
Substituents
  • Fatty amide
  • Straight chain fatty acid
  • Carboxamide group
  • Primary carboxylic acid amide
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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-1.3ALOGPS
logP-1.2ChemAxon
logS0.17ALOGPS
pKa (Strongest Acidic)4.19ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area80.39 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity25.36 m³·mol⁻¹ChemAxon
Polarizability10.57 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]+124.2330932474
DeepCCS[M-H]-121.45230932474
DeepCCS[M-2H]-157.82830932474
DeepCCS[M+Na]+132.73630932474
AllCCS[M+H]+127.932859911
AllCCS[M+H-H2O]+123.732859911
AllCCS[M+NH4]+131.832859911
AllCCS[M+Na]+133.032859911
AllCCS[M-H]-123.432859911
AllCCS[M+Na-2H]-126.632859911
AllCCS[M+HCOO]-130.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Succinamic acidNC(=O)CCC(O)=O1831.0Standard polar33892256
Succinamic acidNC(=O)CCC(O)=O1157.5Standard non polar33892256
Succinamic acidNC(=O)CCC(O)=O1459.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Succinamic acid,2TMS,isomer #1C[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C1431.6Semi standard non polar33892256
Succinamic acid,2TMS,isomer #1C[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C1448.3Standard non polar33892256
Succinamic acid,2TMS,isomer #1C[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C1709.0Standard polar33892256
Succinamic acid,2TMS,isomer #2C[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C1572.6Semi standard non polar33892256
Succinamic acid,2TMS,isomer #2C[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C1556.2Standard non polar33892256
Succinamic acid,2TMS,isomer #2C[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C1912.3Standard polar33892256
Succinamic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C)[Si](C)(C)C1529.5Semi standard non polar33892256
Succinamic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C)[Si](C)(C)C1533.9Standard non polar33892256
Succinamic acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C)[Si](C)(C)C1605.9Standard polar33892256
Succinamic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C(C)(C)C1870.6Semi standard non polar33892256
Succinamic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C(C)(C)C1845.7Standard non polar33892256
Succinamic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NC(=O)CCC(=O)O[Si](C)(C)C(C)(C)C1903.0Standard polar33892256
Succinamic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C(C)(C)C1996.4Semi standard non polar33892256
Succinamic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C(C)(C)C1935.4Standard non polar33892256
Succinamic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(C(=O)CCC(=O)O)[Si](C)(C)C(C)(C)C1976.5Standard polar33892256
Succinamic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2194.7Semi standard non polar33892256
Succinamic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2164.8Standard non polar33892256
Succinamic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CCC(=O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C1974.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-006x-9000000000-234804c949dec6eb48912021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Succinamic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart 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 ID12005
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID50398
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 ]