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Showing NP-Card for Malonic semialdehyde (NP0091128)

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Record Information
Version2.0
Created at2022-05-11 18:31:27 UTC
Updated at2022-05-11 18:31:27 UTC
NP-MRD IDNP0091128
Secondary Accession NumbersNone
Natural Product Identification
Common NameMalonic semialdehyde
DescriptionMalonic semialdehyde belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group. Malonic semialdehyde is an extremely weak basic (essentially neutral) compound (based on its pKa). Malonic semialdehyde exists in all living organisms, ranging from bacteria to humans. Malonic semialdehyde and L-glutamic acid can be biosynthesized from β-alanine and oxoglutaric acid through its interaction with the enzyme 4-aminobutyrate aminotransferase, mitochondrial. Malonic semialdehyde is found in Trypanosoma brucei. In humans, malonic semialdehyde is involved in beta-alanine metabolism.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0091128 (Malonic semialdehyde)


  Mrv0541 02241201192D          

  6  5  0  0  0  0            999 V2000
   -0.1207   -0.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8344    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  2  0  0  0  0
M  END
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3D MOL for NP0091128 (Malonic semialdehyde)

     RDKit          3D

 10  9  0  0  0  0  0  0  0  0999 V2000
    1.8210   -1.2299    0.6218 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5758   -0.0632    0.3316 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1915    0.4507    0.2302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093   -0.6087    0.5192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4926   -1.7854    0.8106 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1484   -0.2603    0.4586 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3788    0.6392    0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0312    0.8780   -0.7846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0076    1.2799    0.9468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4780    0.6999    0.4700 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  4  1  0
  4  5  2  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  6 10  1  0
  3  8  1  0
  3  9  1  0
  2  7  1  0
M  END
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3D SDF for NP0091128 (Malonic semialdehyde)


  Mrv0541 02241201192D          

  6  5  0  0  0  0            999 V2000
   -0.1207   -0.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8344    0.0690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3102   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.8930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482   -0.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0091128

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)

> <INCHI_KEY>
OAKURXIZZOAYBC-UHFFFAOYSA-N

> <FORMULA>
C3H4O3

> <MOLECULAR_WEIGHT>
88.0621

> <EXACT_MASS>
88.016043994

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
7.274262978216537

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxopropanoic acid

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-0.48973352066666664

> <ALOGPS_LOGS>
0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.702401134335275

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7620503977209387

> <JCHEM_PKA_STRONGEST_BASIC>
-7.174413486324497

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
18.062400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.51e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-oxopropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0091128 (Malonic semialdehyde)

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PDB for NP0091128 (Malonic semialdehyde)
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  C   UNK     0      -0.225  -0.644   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.113   0.129   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.558   0.129   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.446  -0.644   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.113   1.667   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -2.890  -0.644   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5                                                  
CONECT    3    1    6                                                       
CONECT    4    2                                                            
CONECT    5    2                                                            
CONECT    6    3                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END

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3D PDB for NP0091128 (Malonic semialdehyde)
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SMILES for NP0091128 (Malonic semialdehyde)
OC(=O)CC=O
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INCHI for NP0091128 (Malonic semialdehyde)
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)
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View in JSmol
Synonyms
ValueSource
Malonate semialdehydeKegg
Malonic acid semialdehydeGenerator
Formylacetic acidChEBI
FormylacetateGenerator
3-OxopropanoateHMDB
3-Oxopropanoic acidHMDB
3-Oxopropionic acidHMDB
Formyl acetateHMDB
Formyl acetic acidHMDB
Malonaldehydic acidHMDB
Malonic semialdehyde sodium saltMeSH, HMDB
Chemical FormulaC3H4O3
Average Mass88.0621 Da
Monoisotopic Mass88.01604 Da
IUPAC Name3-oxopropanoic acid
Traditional Name3-oxopropanoic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CC=O
InChI Identifier
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)
InChI KeyOAKURXIZZOAYBC-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct Parent1,3-dicarbonyl compounds  
Alternative Parents
Substituents
  • 1,3-dicarbonyl compound
    • 

  • Alpha-hydrogen aldehyde
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Short-chain aldehyde
    • 

  • Aldehyde
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.69ALOGPS
logP-0.49ChemAxon
logS0.46ALOGPS
pKa (Strongest Acidic)3.76ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity18.06 m³·mol⁻¹ChemAxon
Polarizability7.27 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011111  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB027893  
KNApSAcK IDNot Available
Chemspider ID845  
KEGG Compound IDC00222  
BioCyc IDMALONATE-S-ALD  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound868  
PDB IDNot Available
ChEBI ID17960  
Good Scents IDNot Available
References
General ReferencesNot Available