Np mrd loader

Showing NP-Card for (R)-3-Hydroxyisobutyric acid (NP0000656)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:17:14 UTC
NP-MRD IDNP0000656
Secondary Accession NumbersNone
Natural Product Identification
Common Name(R)-3-Hydroxyisobutyric acid
DescriptionThe chiral metabolites 3-hydroxyisobutyric acid (HIBA) and 3-aminoisobutyric acid (AIBA) are intermediates in the pathways of l-valine and thymine and play an important role in the diagnosis of the very rare inherited metabolic diseases 3-hydroxyisobutyric aciduria (OMIM 236795 ) and methylmalonic semialdehyde dehydrogenase deficiency (OMIM 603178 ). (PMID 10686279 ).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000656 ((R)-3-Hydroxyisobutyric acid)


  Mrv1652307101917012D          

  7  6  0  0  1  0            999 V2000
   18.9558   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0981   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -2.9330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.1704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2413   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.9954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  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
  4  6  1  1  0  0  0
  4  7  1  0  0  0  0
M  END
Download

3D MOL for NP0000656 ((R)-3-Hydroxyisobutyric acid)

HMDB0000336
     RDKit          3D
(R)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    0.3802    1.5829    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2283    0.1864   -0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2372   -0.2358   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.1965    0.9586 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0044   -0.7387    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514   -0.3339    1.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0443   -2.1164    0.0836 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4103    1.9279   -0.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    1.5638    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3086    2.3115   -0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5463    0.1549   -1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8364    0.5362   -0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3684   -1.2241   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9172   -1.0332    1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7525   -2.3850   -0.6026 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for NP0000656 ((R)-3-Hydroxyisobutyric acid)


  Mrv1652307101917012D          

  7  6  0  0  1  0            999 V2000
   18.9558   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0981   -4.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -2.9330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.1704    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2413   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5268   -4.9954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8124   -3.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  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
  4  6  1  1  0  0  0
  4  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000656

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
DBXBTMSZEOQQDU-GSVOUGTGSA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.1045

> <EXACT_MASS>
104.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.982094489313155

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-3-hydroxy-2-methylpropanoic acid

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-0.26059474566666674

> <ALOGPS_LOGS>
0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.518589741896943

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.365338407814565

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6927927583619056

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
23.6198

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.71e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-3-hydroxyisobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000656 ((R)-3-Hydroxyisobutyric acid)

HMDB0000336
     RDKit          3D
(R)-3-Hydroxyisobutyric acid
 15 14  0  0  0  0  0  0  0  0999 V2000
    0.3802    1.5829    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2283    0.1864   -0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2372   -0.2358   -0.3864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.1965    0.9586 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0044   -0.7387    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6514   -0.3339    1.3708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0443   -2.1164    0.0836 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4103    1.9279   -0.1327 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171    1.5638    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3086    2.3115   -0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5463    0.1549   -1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8364    0.5362   -0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3684   -1.2241   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9172   -1.0332    1.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7525   -2.3850   -0.6026 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  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
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

PDB for NP0000656 ((R)-3-Hydroxyisobutyric acid)

HEADER    PROTEIN                                 10-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JUL-19         0                                  
HETATM    1  O   UNK     0      35.384  -7.785   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.050  -7.785   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.383  -5.475   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      32.717  -7.785   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      34.050  -7.015   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      32.717  -9.325   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      31.383  -7.015   0.000  0.00  0.00           C+0
CONECT    1    5                                                            
CONECT    2    7                                                            
CONECT    3    7                                                            
CONECT    4    5    6    7                                                  
CONECT    5    1    4                                                       
CONECT    6    4                                                            
CONECT    7    2    3    4                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
Download

3D PDB for NP0000656 ((R)-3-Hydroxyisobutyric acid)

COMPND    HMDB0000336
HETATM    1  C1  UNL     1       0.380   1.583   0.071  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.228   0.186  -0.486  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.237  -0.236  -0.386  1.00  0.00           C  
HETATM    4  O1  UNL     1      -1.567  -0.196   0.959  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.004  -0.739   0.368  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.651  -0.334   1.371  1.00  0.00           O  
HETATM    7  O3  UNL     1       1.044  -2.116   0.084  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.410   1.928  -0.133  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.217   1.564   1.155  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.309   2.311  -0.404  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.546   0.155  -1.539  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.836   0.536  -0.923  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.368  -1.224  -0.849  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.917  -1.033   1.315  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.752  -2.385  -0.603  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    5   11
CONECT    3    4   12   13
CONECT    4   14
CONECT    5    6    6    7
CONECT    7   15
END
Download

SMILES for NP0000656 ((R)-3-Hydroxyisobutyric acid)

C[C@H](CO)C(O)=O
Download

INCHI for NP0000656 ((R)-3-Hydroxyisobutyric acid)

InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
Download
View in JSmol
Synonyms
ValueSource
(R)-3-HydroxyisobutyrateGenerator
(R)-3-Hydroxy-2-methylpropionateHMDB
(R)-3-Hydroxy-2-methylpropionic acidHMDB
2-Methyl-(R)-hydracrylateHMDB
2-Methyl-(R)-hydracrylic acidHMDB
3-Hydroxy-2-methylpropionateHMDB
D-(-)-3-HydroxyisobutyrateHMDB
D-(-)-3-Hydroxyisobutyric acidHMDB
D-b-HydroxyisobutyrateHMDB
D-b-Hydroxyisobutyric acidHMDB
delta-(-)-3-HydroxyisobutyrateHMDB
delta-(-)-3-Hydroxyisobutyric acidHMDB
delta-beta-HydroxyisobutyrateHMDB
delta-beta-Hydroxyisobutyric acidHMDB
R-b-HydroxyisobutyrateHMDB
R-b-Hydroxyisobutyric acidHMDB
R-beta-HydroxyisobutyrateHMDB
R-beta-Hydroxyisobutyric acidHMDB
3R-Hydroxy-isobutyrateHMDB
(2R)-3-Hydroxy-2-methylpropanoic acidHMDB
(2R)-3-Hydroxy-2-methylpropionic acidHMDB
(R)-3-Hydroxy-2-methyl-propanoic acidHMDB
(R)-3-Hydroxy-2-methyl-propionic acidHMDB
(R)-3-Hydroxy-2-methylpropanoic acidHMDB
(±)-3-hydroxy-2-methylpropanoic acidHMDB
(±)-3-hydroxy-2-methylpropionic acidHMDB
2-(Hydroxymethyl)propanoic acidHMDB
2-(Hydroxymethyl)propionic acidHMDB
2-Methyl-3-hydroxypropanoic acidHMDB
2-Methyl-3-hydroxypropionic acidHMDB
3-HIBAHMDB
3-Hydroxy-2-methylpropanoic acidHMDB
3-Hydroxy-2-methylpropionic acidHMDB
3-Hydroxyisobutyric acidHMDB
D-beta-Hydroxyisobutyric acidHMDB
D-Β-hydroxyisobutyric acidHMDB
DL-3-Hydroxyisobutyric acidHMDB
R-3-Hydroxyisobutyric acidHMDB
R-Β-hydroxyisobutyric acidHMDB
beta-Hydroxyisobutyric acidHMDB
Β-hydroxyisobutyric acidHMDB
3-Hydroxy-2-isobutyrateHMDB
3-Hydroxy-2-isobutyric acidHMDB
(R)-3-Hydroxyisobutyric acidHMDB
Chemical FormulaC4H8O3
Average Mass104.1045 Da
Monoisotopic Mass104.04734 Da
IUPAC Name(2R)-3-hydroxy-2-methylpropanoic acid
Traditional Name(R)-3-hydroxyisobutyric acid
CAS Registry Number1910-47-0
SMILES
C[C@H](CO)C(O)=O
InChI Identifier
InChI=1S/C4H8O3/c1-3(2-5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
InChI KeyDBXBTMSZEOQQDU-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 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
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
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
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility571 g/LALOGPS
logP-0.47ALOGPS
logP-0.26ChemAxon
logS0.74ALOGPS
pKa (Strongest Acidic)4.37ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity23.62 m³·mol⁻¹ChemAxon
Polarizability9.98 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000336
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021960
KNApSAcK IDNot Available
Chemspider ID9392288
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11217234
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Podebrad F, Heil M, Beck T, Mosandl A, Sewell AC, Bohles H: Stereodifferentiation of 3-hydroxyisobutyric- and 3-aminoisobutyric acid in human urine by enantioselective multidimensional capillary gas chromatography-mass spectrometry. Clin Chim Acta. 2000 Feb 25;292(1-2):93-105. [PubMed:10686279 ]
  2. Gray RG, Pollitt RJ, Webley J: Methylmalonic semialdehyde dehydrogenase deficiency: demonstration of defective valine and beta-alanine metabolism and reduced malonic semialdehyde dehydrogenase activity in cultured fibroblasts. Biochem Med Metab Biol. 1987 Aug;38(1):121-4. [PubMed:3117077 ]
  3. Roe CR, Struys E, Kok RM, Roe DS, Harris RA, Jakobs C: Methylmalonic semialdehyde dehydrogenase deficiency: psychomotor delay and methylmalonic aciduria without metabolic decompensation. Mol Genet Metab. 1998 Sep;65(1):35-43. [PubMed:9787093 ]
  4. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  5. Authors unspecified: Cancer Therapy Interactions With Foods and Dietary Supplements (PDQ(R)): Patient Version. 2002. [PubMed:34403226 ]
  6. Srikalaivani R, Singh A, Vijayan M, Surolia A: Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase. Biochem J. 2018 Aug 14;475(15):2457-2471. doi: 10.1042/BCJ20180271. [PubMed:29959185 ]
  7. Sun L, Xie B, Zhang Q, Wang Y, Wang X, Gao B, Liu M, Wang M: Biomarkers identification by a combined clinical and metabonomics analysis in Henoch-Schonlein purpura nephritis children. Oncotarget. 2017 Nov 24;8(69):114239-114250. doi: 10.18632/oncotarget.23207. eCollection 2017 Dec 26. [PubMed:29371982 ]