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Showing NP-Card for 2-Deoxytetronic acid (NP0083440)

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Record Information
Version2.0
Created at2022-04-29 04:29:11 UTC
Updated at2022-04-29 04:29:11 UTC
NP-MRD IDNP0083440
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Deoxytetronic acid
Description(S)-3,4-Dihydroxybutyric acid, also known as (S)-3,4-dihydroxybutanoate or 2-deoxytetronate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom (S)-3,4-Dihydroxybutyric acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3,4-Dihydroxybutyric acid is a normal human urinary metabolite that is excreted in increased concentration in patients with succinic semialdehyde dehydrogenase (SSADH) deficiency. The compound is also detectable in blood. The renal clearance of this compound is roughly equal that of creatinine (S)-3,4-Dihydroxybutyric acid, with regard to humans, has been linked to the inborn metabolic disorder succinic semialdehyde dehydrogenase deficiency. 2-Deoxytetronic acid is found in Crocus sativus, Homo sapiens (Urine) and Triticum aestivum . 2-Deoxytetronic acid was first documented in 1975 (PMID: 1167165). Normal adults excrete 0.37 +/- 0.15 (SD) mmoles of 3,4-dihydroxybutyrate per 24 hr (PMID: 3191387) (PMID: 6720928) (PMID: 25177334).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083440 (2-Deoxytetronic acid)

3,4-Dihydroxybutyric acid.mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    0.7134    0.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7156    0.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7112    1.0341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4268   -1.0341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7177    1.0303    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
  3  8  1  0  0  0  0
M  END
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3D MOL for NP0083440 (2-Deoxytetronic acid)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
    1.8944    1.7171    0.1576 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9292    0.4700    0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1762   -0.1375    0.0935 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7303   -0.3689   -0.0344 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5500    0.4064   -0.0419 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7976    1.1201    1.1018 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6847   -0.6235   -0.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8893    0.0723   -0.2397 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3914   -0.9528   -0.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7930   -0.9054   -1.0124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7710   -1.1426    0.7491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5478    1.0814   -0.9190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2645    0.8751    1.8800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6384   -1.2995    0.7027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5397   -1.2025   -1.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7733    0.8901   -0.7866 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  5  1  0
  5  6  1  0
  5  4  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
  5 12  1  6
  6 13  1  0
  4 10  1  0
  4 11  1  0
  3  9  1  0
M  END
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3D SDF for NP0083440 (2-Deoxytetronic acid)

3,4-Dihydroxybutyric acid.mol
  Mrv0541 02231218282D          

  8  7  0  0  0  0            999 V2000
    0.7134    0.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7156    0.2053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7112    1.0341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4268   -1.0341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7177    1.0303    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
  3  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083440

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
DZAIOXUZHHTJKN-UHFFFAOYSA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.1039

> <EXACT_MASS>
120.042258744

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
10.9061022959665

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxybutanoic acid

> <ALOGPS_LOGP>
-1.54

> <JCHEM_LOGP>
-1.433915966

> <ALOGPS_LOGS>
0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.288104053178337

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.086188822234564

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9449499833882467

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
25.0078

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.32e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydroxybutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0083440 (2-Deoxytetronic acid)

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PDB for NP0083440 (2-Deoxytetronic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3,4-Dihydroxybutyric acid.mol                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.332   0.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -0.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.336   0.383   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -0.390   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.328   1.930   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.667  -0.376   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.663  -1.930   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.340   1.923   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    7                                                       
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    4                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0083440 (2-Deoxytetronic acid)
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SMILES for NP0083440 (2-Deoxytetronic acid)
OCC(O)CC(O)=O
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INCHI for NP0083440 (2-Deoxytetronic acid)
InChI=1S/C4H8O4/c5-2-3(6)1-4(7)8/h3,5-6H,1-2H2,(H,7,8)
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View in JSmol
Synonyms
ValueSource
(S)-3,4-DihydroxybutyrateGenerator
(S)-3,4-Dihydroxy-butyric acidHMDB
(S)-3,4-DihydroxybutanoateHMDB
(S)-3,4-Dihydroxybutanoic acidHMDB
2-DeoxytetronateHMDB
2-Deoxytetronic acidHMDB
3,4-DihydroxybutanoateHMDB
3,4-Dihydroxybutanoic acidHMDB
3,4-Dihydroxybutanoic acid, (S)-isomerHMDB
3,4-Dihydroxybutanoic acid, monosodium saltHMDB
Chemical FormulaC4H8O4
Average Mass120.1039 Da
Monoisotopic Mass120.04226 Da
IUPAC Name3,4-dihydroxybutanoic acid
Traditional Name3,4-dihydroxybutanoic acid
CAS Registry NumberNot Available
SMILES
OCC(O)CC(O)=O
InChI Identifier
InChI=1S/C4H8O4/c5-2-3(6)1-4(7)8/h3,5-6H,1-2H2,(H,7,8)
InChI KeyDZAIOXUZHHTJKN-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
Crocus sativusLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiens (Urine)Animalia
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
Triticum aestivumPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassBeta hydroxy acids and derivatives  
Direct ParentBeta hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Short-chain hydroxy acid
    • 

  • Fatty acid
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • 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-1.4ChemAxon
logS0.84ALOGPS
pKa (Strongest Acidic)4.09ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity25.01 m³·mol⁻¹ChemAxon
Polarizability10.91 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000337  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021961  
KNApSAcK IDNot Available
Chemspider ID133026  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound150929  
PDB IDNot Available
ChEBI ID86371  
Good Scents IDNot Available
References
General References
  1. Fell V, Lee CR, Pollitt RJ: The occurrence of (S)-3,4-dihydroxybutyrate in human blood and urine. Biochem Med. 1975 May;13(1):40-5. doi: 10.1016/0006-2944(75)90138-6. [PubMed:1167165  ] 
  2. Minami T, Oomura Y, Nabekura J, Fukuda A: Direct effects of 3,4-dihydroxybutanoic acid gamma-lactone and 2,4,5-trihydroxypentanoic acid gamma-lactone on lateral and ventromedial hypothalamic neurons. Brain Res. 1988 Oct 18;462(2):258-64. doi: 10.1016/0006-8993(88)90554-9. [PubMed:3191387  ] 
  3. Shimizu N, Oomura Y, Sakata T: Modulation of feeding by endogenous sugar acids acting as hunger or satiety factors. Am J Physiol. 1984 Apr;246(4 Pt 2):R542-50. doi: 10.1152/ajpregu.1984.246.4.R542. [PubMed:6720928  ] 
  4. Mousavi M, Jonsson P, Antti H, Adolfsson R, Nordin A, Bergdahl J, Eriksson K, Moritz T, Nilsson LG, Nyberg L: Serum metabolomic biomarkers of dementia. Dement Geriatr Cogn Dis Extra. 2014 Jul 11;4(2):252-62. doi: 10.1159/000364816. eCollection 2014 May. [PubMed:25177334  ]