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Showing NP-Card for (2r,3r)-3-hydroxy-2-methylbutanoic acid (NP0254810)

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Record Information
Version1.0
Created at2022-09-07 19:05:17 UTC
Updated at2022-09-07 19:05:18 UTC
NP-MRD IDNP0254810
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3r)-3-hydroxy-2-methylbutanoic acid
Description3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid, also known as [S-(R,R)]-3-hydroxy-2-methyl-butanoate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 3-Hydroxy-2-methyl-butanoic acid (HMBA)is a normal urinary metabolite involved in the isoleucine catabolism, as well as presumably b-oxidation of fatty acids and ketogenesis, excreted in abnormally high amounts in beta-ketothiolase deficiency. 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. (2r,3r)-3-hydroxy-2-methylbutanoic acid is found in Cuscuta chinensis. It was first documented in 2000 (PMID: 11122323). Differences in the enantiomeric ratio of HMBA may originate from the enantioselectivity of different enzyme systems (PMID 10755375 ) (PMID: 10755375).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)

3-hydroxy-2-methyl-[S-(R,R)]-Butanoic acid.mol
  Mrv0541 02231218302D          

  8  7  0  0  0  0            999 V2000
    0.7145   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2062    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
  2  7  1  1  0  0  0
  3  8  1  1  0  0  0
M  END
Download

3D MOL for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.9868   -0.5915   -0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9138    0.4436   -0.1854 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3350    1.6440    0.3588 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3711    0.0499    0.4989 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9347   -1.2438   -0.0724 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3845    1.1024    0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1131    2.1235   -0.3992 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6663    0.9325    0.8298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5524   -0.4420    0.9095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7391   -0.3965   -0.8597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5958   -1.6234   -0.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6759    0.5854   -1.2700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5831    1.4801    1.2993 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2064   -0.1363    1.5861 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8430   -1.2672   -1.1711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3688   -2.0954    0.3733 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0114   -1.3171    0.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4825    0.7518    0.2562 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
  4  6  1  0
  6  8  1  0
  6  7  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  6
  3 13  1  0
  4 14  1  1
  5 15  1  0
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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3D SDF for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)

3-hydroxy-2-methyl-[S-(R,R)]-Butanoic acid.mol
  Mrv0541 02231218302D          

  8  7  0  0  0  0            999 V2000
    0.7145   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2062    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
  2  7  1  1  0  0  0
  3  8  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0254810

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t3-,4-/m1/s1

> <INCHI_KEY>
VEXDRERIMPLZLU-QWWZWVQMSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.801239239149535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-3-hydroxy-2-methylbutanoic acid

> <ALOGPS_LOGP>
-0.13

> <JCHEM_LOGP>
0.1559802790000001

> <ALOGPS_LOGS>
0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.303379950745505

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.513689206767185

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7866129389831196

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
28.038600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.36e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-3-hydroxy-2-methylbutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)

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PDB for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-hydroxy-2-methyl-[S-(R,R)]-Butanoic acid.mol    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -1.925   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667   0.385   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.334  -1.925   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000   1.925   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.667   0.385   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3                                                            
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)
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SMILES for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)
C[C@@H](O)[C@@H](C)C(O)=O
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INCHI for NP0254810 ((2r,3r)-3-hydroxy-2-methylbutanoic acid)
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t3-,4-/m1/s1
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View in JSmol
Synonyms
ValueSource
3-Hydroxy-2-methyl-[S-(R,R)]-butanoateGenerator
3-Hydroxy-2-methyl-[S-(r*,r*)]-butanoateHMDB
3-Hydroxy-2-methyl-[S-(r*,r*)]-butanoic acidHMDB
[S-(R,R)]-3-Hydroxy-2-methyl-butanoateHMDB
[S-(R,R)]-3-Hydroxy-2-methyl-butanoic acidHMDB
Chemical FormulaC5H10O3
Average Mass118.1311 Da
Monoisotopic Mass118.06299 Da
IUPAC Name(2R,3R)-3-hydroxy-2-methylbutanoic acid
Traditional Name(2R,3R)-3-hydroxy-2-methylbutanoic acid
CAS Registry NumberNot Available
SMILES
C[C@@H](O)[C@@H](C)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t3-,4-/m1/s1
InChI KeyVEXDRERIMPLZLU-QWWZWVQMSA-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
Cuscuta chinensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentHydroxy fatty acids  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Methyl-branched fatty acid
    • 

  • Hydroxy acid
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-0.13ALOGPS
logP0.16ChemAxon
logS0.45ALOGPS
pKa (Strongest Acidic)4.51ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.04 m³·mol⁻¹ChemAxon
Polarizability11.8 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000410  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022026  
KNApSAcK IDNot Available
Chemspider ID13628080  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5399  
PubChem Compound12313369  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Herrmann W, Schorr H, Bodis M, Knapp JP, Muller A, Stein G, Geisel J: Role of homocysteine, cystathionine and methylmalonic acid measurement for diagnosis of vitamin deficiency in high-aged subjects. Eur J Clin Invest. 2000 Dec;30(12):1083-9. [PubMed:11122323  ] 
  2. Heil M, Podebrad F, Prado E, Beck T, Mosand A, Sewell AC, Bohles H, Lehnert W: Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting. J Chromatogr B Biomed Sci Appl. 2000 Mar 10;739(2):313-24. [PubMed:10755375  ] 
  3. LOTUS database [Link]