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Showing NP-Card for (R)-3-Hydroxybutyric acid (NP0000416)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:15:19 UTC
NP-MRD IDNP0000416
Secondary Accession NumbersNone
Natural Product Identification
Common Name(R)-3-Hydroxybutyric acid
Description(R)-3-Hydroxybutyric acid is a butyric acid substituted with a hydroxyl group in the beta or 3 position. 3-Hydroxybutyric acid, or beta-hydroxybutyrate, is involved in the synthesis and degradation of ketone bodies. Like the other ketone bodies (acetoacetate and acetone), levels of beta-hydroxybutyrate are raised in the blood and urine in ketosis. Beta-hydroxybutyrate is a typical partial-degradation product of branched-chain amino acids (primarily valine) released from muscle for hepatic and renal gluconeogenesis This acid is metabolized by 3-hydroxybutyrate dehydrogenase (catalyzes the oxidation of D-3-hydroxybutyrate to form acetoacetate, using NAD+ as an electron acceptor). The enzyme functions in nervous tissues and muscles, enabling the use of circulating hydroxybutyrate as a fuel. In the liver mitochondrial matrix, the enzyme can also catalyze the reverse reaction, a step in ketogenesis. 3-Hydroxybutyric acid is a chiral compound having two enantiomers, D-3-hydroxybutyric acid and L-3-hydroxybutyric acid. In humans, beta-hydroxybutyrate is synthesized in the liver from acetyl-CoA, and can be used as an energy source by the brain when blood glucose is low. It can also be used for the synthesis of biodegradable plastics (Wikipedia).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000416 ((R)-3-Hydroxybutyric acid)


  Mrv1652303252017492D          

  7  6  0  0  0  0            999 V2000
   12.3700  -12.1081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5121  -12.1081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2266  -10.8705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6556  -11.6956    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.9411  -12.1081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6556  -10.8705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2266  -11.6956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  1  0  0  0
M  END
Download

3D MOL for NP0000416 ((R)-3-Hydroxybutyric acid)

HMDB0000011
     RDKit          3D
3-Hydroxybutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.7425   -0.4236    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7444    0.6456    0.0230 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4149    1.3086    1.2191 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5104    0.2340   -0.6764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3087   -0.7914   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7814   -1.8855    0.3046 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6465   -0.5912    0.3127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6225    0.0533    0.7702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0681   -0.8741   -0.6781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3154   -1.2104    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2441    1.4129   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3665    0.8920    1.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1227    1.1704   -0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2318   -0.1403   -1.7054 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1839    0.1997   -0.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for NP0000416 ((R)-3-Hydroxybutyric acid)


  Mrv1652303252017492D          

  7  6  0  0  0  0            999 V2000
   12.3700  -12.1081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5121  -12.1081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2266  -10.8705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6556  -11.6956    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.9411  -12.1081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6556  -10.8705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2266  -11.6956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  7  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0000416

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1

> <INCHI_KEY>
WHBMMWSBFZVSSR-GSVOUGTGSA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.1045

> <EXACT_MASS>
104.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.959788970081753

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-hydroxybutanoic acid

> <ALOGPS_LOGP>
-0.50

> <JCHEM_LOGP>
-0.38700599933333335

> <ALOGPS_LOGS>
0.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.695695082377142

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.406291419798768

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6205133689113183

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
23.464100000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-3-hydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000416 ((R)-3-Hydroxybutyric acid)

HMDB0000011
     RDKit          3D
3-Hydroxybutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.7425   -0.4236    0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7444    0.6456    0.0230 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4149    1.3086    1.2191 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5104    0.2340   -0.6764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3087   -0.7914   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7814   -1.8855    0.3046 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6465   -0.5912    0.3127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6225    0.0533    0.7702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0681   -0.8741   -0.6781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3154   -1.2104    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2441    1.4129   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3665    0.8920    1.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1227    1.1704   -0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2318   -0.1403   -1.7054 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1839    0.1997   -0.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for NP0000416 ((R)-3-Hydroxybutyric acid)

HEADER    PROTEIN                                 25-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAR-20         0                                  
HETATM    1  O   UNK     0      23.091 -22.602   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      17.756 -22.602   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      19.090 -20.292   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      21.757 -21.832   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.423 -22.602   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.757 -20.292   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      19.090 -21.832   0.000  0.00  0.00           C+0
CONECT    1    4                                                            
CONECT    2    7                                                            
CONECT    3    7                                                            
CONECT    4    5    1    6                                                  
CONECT    5    4    7                                                       
CONECT    6    4                                                            
CONECT    7    2    3    5                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0000416 ((R)-3-Hydroxybutyric acid)

COMPND    HMDB0000011
HETATM    1  C1  UNL     1      -1.743  -0.424   0.266  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.744   0.646   0.023  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.415   1.309   1.219  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.510   0.234  -0.676  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.309  -0.791  -0.002  1.00  0.00           C  
HETATM    6  O2  UNL     1       0.781  -1.886   0.305  1.00  0.00           O  
HETATM    7  O3  UNL     1       2.647  -0.591   0.313  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.623   0.053   0.770  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.068  -0.874  -0.678  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.315  -1.210   0.917  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.244   1.413  -0.651  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.366   0.892   1.669  1.00  0.00           H  
HETATM   13  H6  UNL     1       1.123   1.170  -0.816  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.232  -0.140  -1.705  1.00  0.00           H  
HETATM   15  H8  UNL     1       3.184   0.200  -0.051  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4   11
CONECT    3   12
CONECT    4    5   13   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for NP0000416 ((R)-3-Hydroxybutyric acid)

C[C@@H](O)CC(O)=O
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INCHI for NP0000416 ((R)-3-Hydroxybutyric acid)

InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(R)-(-)-beta-Hydroxybutyric acidChEBI
(R)-3-Hydroxybutanoic acidChEBI
3-D-Hydroxybutyric acidChEBI
D-3-Hydroxybutyric acidChEBI
(R)-3-Hydroxybutyric acidKegg
D-beta-Hydroxybutyric acidKegg
(R)-(-)-b-HydroxybutyrateGenerator
(R)-(-)-b-Hydroxybutyric acidGenerator
(R)-(-)-beta-HydroxybutyrateGenerator
(R)-(-)-Β-hydroxybutyrateGenerator
(R)-(-)-Β-hydroxybutyric acidGenerator
(R)-3-HydroxybutanoateGenerator
3-D-HydroxybutyrateGenerator
D-3-HydroxybutyrateGenerator
(R)-3-HydroxybutyrateGenerator
D-b-HydroxybutyrateGenerator
D-b-Hydroxybutyric acidGenerator
D-beta-HydroxybutyrateGenerator
D-Β-hydroxybutyrateGenerator
D-Β-hydroxybutyric acidGenerator
3-HydroxybutyrateGenerator
3-delta-HydroxybutyrateHMDB
3-delta-Hydroxybutyric acidHMDB
BHIBHMDB
D-(-)-3-HydroxybutyrateHMDB
delta-(-)-3-HydroxybutyrateHMDB
delta-3-HydroxybutyrateHMDB
delta-3-Hydroxybutyric acidHMDB
delta-beta-HydroxybutyrateHMDB
3R-Hydroxy-butanoateHMDB
(-)-3-Hydroxy-N-butyric acidHMDB
(-)-3-Hydroxybutyric acidHMDB
(3R)-3-Hydroxybutanoic acidHMDB
(3R)-3-Hydroxybutyric acidHMDB
(3R)-HydroxybutyrateHMDB
(R)-(-)-3-Hydroxybutyric acidHMDB
(R)-beta-Hydroxybutanoic acidHMDB
(R)-beta-Hydroxybutyric acidHMDB
(R)-Β-hydroxybutanoic acidHMDB
(R)-Β-hydroxybutyric acidHMDB
3-Hydroxy-N-butyric acidHMDB
3-Hydroxybutanoic acidHMDB
3R-Hydroxybutanoic acidHMDB
D-(-)-3-Hydroxybutanoic acidHMDB
D-(-)-3-Hydroxybutyric acidHMDB
D-(-)-beta-Hydroxybutyric acidHMDB
D-(-)-Β-hydroxybutyric acidHMDB
beta-Hydroxy-N-butyric acidHMDB
beta-Hydroxybutanoic acidHMDB
beta-Hydroxybutyric acidHMDB
Β-hydroxy-N-butyric acidHMDB
Β-hydroxybutanoic acidHMDB
Β-hydroxybutyric acidHMDB
3-Hydroxybutyric acidHMDB
Chemical FormulaC4H8O3
Average Mass104.1045 Da
Monoisotopic Mass104.04734 Da
IUPAC Name(3R)-3-hydroxybutanoic acid
Traditional Name(-)-3-hydroxybutyric acid
CAS Registry Number625-72-9
SMILES
C[C@@H](O)CC(O)=O
InChI Identifier
InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
InChI KeyWHBMMWSBFZVSSR-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Annulohypoxylon truncatumLOTUS Database
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
Streptomyces griseorubiginosusLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS Database
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK 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
  • Short-chain hydroxy acid
  • Beta-hydroxy acid
  • Fatty acid
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point49 - 50 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility539 g/LALOGPS
logP-0.5ALOGPS
logP-0.39ChemAxon
logS0.71ALOGPS
pKa (Strongest Acidic)4.41ChemAxon
pKa (Strongest Basic)-2.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity23.46 m³·mol⁻¹ChemAxon
Polarizability9.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000011
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021869
KNApSAcK IDC00052123
Chemspider ID83181
KEGG Compound IDC01089
BioCyc IDCPD-335
BiGG ID36784
Wikipedia LinkBeta-Hydroxybutyric_acid
METLIN IDNot Available
PubChem Compound92135
PDB IDNot Available
ChEBI ID17066
Good Scents IDNot Available
References
General References
  1. Pan JW, Telang FW, Lee JH, de Graaf RA, Rothman DL, Stein DT, Hetherington HP: Measurement of beta-hydroxybutyrate in acute hyperketonemia in human brain. J Neurochem. 2001 Nov;79(3):539-44. [PubMed:11701757 ]
  2. Raunio RP, Leivo PV, Kuusinen AM: Bioluminescent assay of D-3-hydroxybutyrate in serum. J Biolumin Chemilumin. 1986 Jun;1(1):11-4. [PubMed:3503522 ]
  3. Schulz S, Toft S: Identification of a sex pheromone from a spider. Science. 1993 Jun 11;260(5114):1635-7. doi: 10.1126/science.260.5114.1635. [PubMed:17810206 ]
  4. (). Bernardi, R. et al., Chem. Commun., 1984, 460, (resoln). .
  5. (). Encyclopedia of Food and Color Additives, (ed. Burdock, G.A.), CRC Press, 1997, 994-995, (Et ester). .
  6. (). Fenaroli's Handbook of Flavor Ingredients, 3rd edn., (ed. Burdock, G.A.), CRC Press, 1995, 1, 238, (Et ester). .
  7. (). Forsyth, W.G.C. et al., Nature (London), 1958, 182, 800, (isol). .
  8. (). Gottschalk, G. et al., Nature (London), 1965, 205, 308. .
  9. (). Krajewski, D. et al., Phytochemistry, 1997, 45, 1627, (ester glucosides). .
  10. (). Levene, P.A. et al., J. Biol. Chem., 1926, 68, 418, (abs config). .
  11. (). Lewis, R.J., Sax's Dangerous Properties of Industrial Materials, 8th edn., Van Nostrand Reinhold, 1992, MEF500 MKP250. .
  12. (). Marchessault, R.H. et al., Makromol. Chem., Macromol. Symp., 1988, 19, 235, (rev, polymers). .
  13. (). Muller, H.-M. et al., Angew. Chem., Int. Ed., 1993, 32, 477, (rev, polymer). .
  14. (). Org. Synth., 1993, 71, 39, (synth, acid, Meester, pmr, ir). .
  15. (). Quang DN, Hashimoto T, Toyota M, Asakawa Y. Occurrence of a high concentration of spider pheromones in the ascomycete fungus Hypoxylon truncatum. J Nat Prod. 2003 Dec;66(12):1613-4.. .
  16. (). Schulz S, Toft S. Identification of a sex pheromone from a spider. Science. 1993 Jun 11;260(5114):1635-7.. .
  17. (). Seebach, D. et al., Helv. Chim. Acta, 1982, 65, 495-503, (esters, synth). .
  18. (). Seebach, D. et al., Helv. Chim. Acta, 1988, 71, 155, (synth, dimer). .
  19. (). Wipf, B. et al., Helv. Chim. Acta, 1983, 66, 485. .