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Showing NP-Card for (s)-3,4-dihydroxybutyric acid (NP0315908)

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Record Information
Version2.0
Created at2022-09-11 14:46:40 UTC
Updated at2022-09-11 14:46:40 UTC
NP-MRD IDNP0315908
Secondary Accession NumbersNone
Natural Product Identification
Common Name(s)-3,4-dihydroxybutyric acid
Description3S,4-dihydroxy-butyric acid, also known as (S)-3,4-dhba, 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 found in Crocus sativus. Based on a literature review very few articles have been published on 3s,4-dihydroxy-butyric acid.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0315908 ((s)-3,4-dihydroxybutyric acid)


  Mrv1652309112216462D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 O   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  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for NP0315908 ((s)-3,4-dihydroxybutyric acid)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
    1.1897   -1.1664   -1.5092 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4156   -0.1755   -0.7996 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5570   -0.0720   -0.0318 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4412    0.9436   -0.7628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4669    0.7440    0.4629 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3903    0.7409    1.5803 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1846   -0.5747    0.3427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0535   -0.5879   -0.7524 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0944    0.7752    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0010    1.8954   -0.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1954    0.9349   -1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1716    1.5762    0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0186    1.3192    2.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6823   -0.8316    1.3016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4478   -1.4004    0.1423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9058   -0.1370   -0.5227 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  1
  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 NP0315908 ((s)-3,4-dihydroxybutyric acid)


  Mrv1652309112216462D          

  8  7  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 O   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  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0315908

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](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)/t3-/m0/s1

> <INCHI_KEY>
DZAIOXUZHHTJKN-VKHMYHEASA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.104

> <EXACT_MASS>
120.042258738

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.903667256121105

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3,4-dihydroxybutanoic acid

> <JCHEM_LOGP>
-1.433915966

> <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>
77.75999999999999

> <JCHEM_REFRACTIVITY>
25.0078

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(S)-3,4-dihydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0315908 ((s)-3,4-dihydroxybutyric acid)

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PDB for NP0315908 ((s)-3,4-dihydroxybutyric acid)
HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+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  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   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    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0315908 ((s)-3,4-dihydroxybutyric acid)
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SMILES for NP0315908 ((s)-3,4-dihydroxybutyric acid)
OC[C@@H](O)CC(O)=O
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INCHI for NP0315908 ((s)-3,4-dihydroxybutyric acid)
InChI=1S/C4H8O4/c5-2-3(6)1-4(7)8/h3,5-6H,1-2H2,(H,7,8)/t3-/m0/s1
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Synonyms
ValueSource
3S,4-Dihydroxy-butyrateGenerator
(S)-3,4-DHBAMeSH
(S)-3,4-Dihydroxybutyric acidMeSH
Chemical FormulaC4H8O4
Average Mass120.1040 Da
Monoisotopic Mass120.04226 Da
IUPAC Name(3S)-3,4-dihydroxybutanoic acid
Traditional Name(S)-3,4-dihydroxybutyric acid
CAS Registry NumberNot Available
SMILES
OC[C@@H](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)/t3-/m0/s1
InChI KeyDZAIOXUZHHTJKN-VKHMYHEASA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Crocus sativusLOTUS Database
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-1.4ChemAxon
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
Polarizability10.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9095744  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10920498  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]