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Showing NP-Card for 2,4-Dihydroxybutanoic acid (NP0083422)

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Record Information
Version2.0
Created at2022-04-29 04:28:33 UTC
Updated at2022-04-29 04:28:33 UTC
NP-MRD IDNP0083422
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,4-Dihydroxybutanoic acid
Description2,4-Dihydroxybutanoic acid, also known as 2,4-dihydroxybutyrate or 3-deoxytetronate, belongs to the class of organic compounds known as short-chain hydroxy acids and derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms. 2,4-Dihydroxybutanoic acid is found in Arabidopsis thaliana, Homo sapiens (Urine) and Lotus corniculatus. 2,4-Dihydroxybutanoic acid was first documented in 1987 (PMID: 3126356). 2,4-Dihydroxybutanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083422 (2,4-Dihydroxybutanoic acid)

3-Deoxytetronic acid  .mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    0.0000 O   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
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
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3D MOL for NP0083422 (2,4-Dihydroxybutanoic acid)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
    2.7206    0.6938   -0.6346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8874    0.2353    0.1886 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3753   -0.5163    1.2452 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4383    0.5105    0.0023 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2460    1.2782   -1.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2869   -0.8086   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7725   -0.6673   -0.1905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3244    0.0426    0.8891 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2848   -0.3016    1.6609 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1021    1.1173    0.8826 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3754    2.2174   -0.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0800   -1.3411   -0.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0835   -1.4108    0.8562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0962   -0.2501   -1.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2069   -1.6874   -0.1283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7395    0.8879    0.5961 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8 16  1  0
  7 14  1  0
  7 15  1  0
  6 12  1  0
  6 13  1  0
  4 10  1  1
  5 11  1  0
  3  9  1  0
M  END
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3D SDF for NP0083422 (2,4-Dihydroxybutanoic acid)

3-Deoxytetronic acid  .mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    0.0000 O   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
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083422

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCC(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)

> <INCHI_KEY>
UFYGCFHQAXXBCF-UHFFFAOYSA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.1039

> <EXACT_MASS>
120.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
10.933480891022622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,4-dihydroxybutanoic acid

> <ALOGPS_LOGP>
-1.46

> <JCHEM_LOGP>
-1.458779745666667

> <ALOGPS_LOGS>
0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.20091433487325

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.669896389811606

> <JCHEM_PKA_STRONGEST_BASIC>
-2.418943130539679

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
25.2489

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.00e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,4-dihydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0083422 (2,4-Dihydroxybutanoic acid)

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PDB for NP0083422 (2,4-Dihydroxybutanoic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Deoxytetronic acid  .mol                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.001   1.925   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.334  -0.385   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -3.334   0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.667  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    7                                                       
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    4                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0083422 (2,4-Dihydroxybutanoic acid)
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SMILES for NP0083422 (2,4-Dihydroxybutanoic acid)
OCCC(O)C(O)=O
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INCHI for NP0083422 (2,4-Dihydroxybutanoic acid)
InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)
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Synonyms
ValueSource
2,4-Dihydroxybutyric acidChEBI
2,4-DihydroxybutyrateGenerator
2,4-DihydroxybutanoateGenerator
2,4-Dihydroxy-butyrateHMDB
2,4-Dihydroxy-butyric acidHMDB
3-DeoxytetronateHMDB
3-Deoxytetronic acidHMDB
2,4-Dihydroxy-butanoateHMDB
Chemical FormulaC4H8O4
Average Mass120.1039 Da
Monoisotopic Mass120.04226 Da
IUPAC Name2,4-dihydroxybutanoic acid
Traditional Name2,4-dihydroxybutyric acid
CAS Registry NumberNot Available
SMILES
OCCC(O)C(O)=O
InChI Identifier
InChI=1S/C4H8O4/c5-2-1-3(6)4(7)8/h3,5-6H,1-2H2,(H,7,8)
InChI KeyUFYGCFHQAXXBCF-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
Arabidopsis thalianaLOTUS Database
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
Homo sapiens (Urine)Animalia
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Lotus corniculatusLOTUS Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain hydroxy acids and derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassShort-chain hydroxy acids and derivatives  
Direct ParentShort-chain hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Short-chain hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Monosaccharide
    • 

  • Fatty acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.5ALOGPS
logP-1.5ChemAxon
logS0.77ALOGPS
pKa (Strongest Acidic)3.67ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity25.25 m³·mol⁻¹ChemAxon
Polarizability10.93 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000360  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021980  
KNApSAcK IDNot Available
Chemspider ID167259  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5349  
PubChem Compound192742  
PDB IDNot Available
ChEBI ID86348  
Good Scents IDNot Available
References
General References
  1. Brown GK, Cromby CH, Manning NJ, Pollitt RJ: Urinary organic acids in succinic semialdehyde dehydrogenase deficiency: evidence of alpha-oxidation of 4-hydroxybutyric acid, interaction of succinic semialdehyde with pyruvate dehydrogenase and possible secondary inhibition of mitochondrial beta-oxidation. J Inherit Metab Dis. 1987;10(4):367-75. [PubMed:3126356  ]