Showing NP-Card for (S)-(+)-2-Hydroxy-3-methylbutyric acid (NP0002797)

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Record Information
Version2.0
Created at2020-11-23 19:40:41 UTC
Updated at2021-08-12 19:52:10 UTC
NP-MRD IDNP0002797
Secondary Accession NumbersNone
Natural Product Identification
Common Name(S)-(+)-2-Hydroxy-3-methylbutyric acid
Provided ByBMRBBMRB logo
Description2-Hydroxy-3-methylbutyric acid, also known as a-hydroxyisovaleric acid or 2-oxyisovalerate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 2-Hydroxy-3-methylbutyric acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (S)-(+)-2-Hydroxy-3-methylbutyric acid was first documented in 2011 (PMID: 21516781). Based on a literature review very few articles have been published on 2-Hydroxy-3-methylbutyric acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

     RDKit          2D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.3909    0.6765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2730   -0.3237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2731   -1.4416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7272    0.7942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3907    1.7944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8451   -0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192   -1.7006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2702    0.2622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5198   -0.3112    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0189    1.3815    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5088    1.6766    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7147   -1.4526    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -0.5852    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1552   -2.4417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2732   -2.5595    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7273    1.9121    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0835    3.2626    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3881   -0.7380    0.0000 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  7  2  0
  6  8  1  0
  1  9  1  6
  1 10  1  0
  1 11  1  0
  2 12  1  1
  3 13  1  6
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  8 18  1  0
M  END
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3D MOL for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

NP0002797
     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.7114   -0.8735    0.5111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    0.1847    0.4797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0648    1.3013   -0.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6499   -0.4792    0.0070 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9543   -1.5019    0.9213 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7807    0.4338   -0.1339 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7115    1.4143   -0.9031 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9386    0.2201    0.5840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4549   -0.6959   -0.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2873   -1.8882    0.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2059   -0.8181    1.4953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4252    0.5927    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5657    1.2010   -1.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7884    2.3033    0.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1683    1.2848   -0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4581   -0.9566   -0.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3466   -1.0675    1.7237 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4489   -0.6553    0.4199 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  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  6
  5 17  1  0
  8 18  1  0
M  END
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3D SDF for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

     RDKit          2D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.3909    0.6765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2730   -0.3237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2731   -1.4416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7272    0.7942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3907    1.7944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8451   -0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192   -1.7006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2702    0.2622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5198   -0.3112    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0189    1.3815    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5088    1.6766    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7147   -1.4526    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -0.5852    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1552   -2.4417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2732   -2.5595    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7273    1.9121    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0835    3.2626    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3881   -0.7380    0.0000 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  7  2  0
  6  8  1  0
  1  9  1  6
  1 10  1  0
  1 11  1  0
  2 12  1  1
  3 13  1  6
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  8 18  1  0
M  END
> <DATABASE_ID>
NP0002797

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t4-/m0/s1

> <INCHI_KEY>
NGEWQZIDQIYUNV-BYPYZUCNSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.132

> <EXACT_MASS>
118.062994182

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.776164381367607

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxy-3-methylbutanoic acid

> <ALOGPS_LOGP>
0.10

> <JCHEM_LOGP>
0.4156657033333334

> <ALOGPS_LOGS>
0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.053181861607996

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.138361788089717

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8921886131871277

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
27.8354

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.15e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-hydroxyisovaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

NP0002797
     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.7114   -0.8735    0.5111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6168    0.1847    0.4797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0648    1.3013   -0.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6499   -0.4792    0.0070 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9543   -1.5019    0.9213 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7807    0.4338   -0.1339 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7115    1.4143   -0.9031 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9386    0.2201    0.5840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4549   -0.6959   -0.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2873   -1.8882    0.4160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2059   -0.8181    1.4953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4252    0.5927    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5657    1.2010   -1.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7884    2.3033    0.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1683    1.2848   -0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4581   -0.9566   -0.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3466   -1.0675    1.7237 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4489   -0.6553    0.4199 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  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  6
  5 17  1  0
  8 18  1  0
M  END
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PDB for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

HEADER    PROTEIN                                 01-OCT-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-OCT-16         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  H   UNK     0       0.770   1.334   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    3                                                            
CONECT    3    1    2    4                                                  
CONECT    4    3    5    6    9                                             
CONECT    5    4    7    8                                                  
CONECT    6    4                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

COMPND    NP0002797
HETATM    1  C1  UNL     1      -1.711  -0.873   0.511  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.617   0.185   0.480  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.065   1.301  -0.404  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.650  -0.479   0.007  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.954  -1.502   0.921  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.781   0.434  -0.134  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.712   1.414  -0.903  1.00  0.00           O  
HETATM    8  O3  UNL     1       2.939   0.220   0.584  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.455  -0.696  -0.302  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.287  -1.888   0.416  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.206  -0.818   1.495  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.425   0.593   1.494  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.566   1.201  -1.386  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.788   2.303   0.006  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.168   1.285  -0.560  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.458  -0.957  -0.989  1.00  0.00           H  
HETATM   17  H9  UNL     1       1.347  -1.068   1.724  1.00  0.00           H  
HETATM   18  H10 UNL     1       3.449  -0.655   0.420  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4   12
CONECT    3   13   14   15
CONECT    4    5    6   16
CONECT    5   17
CONECT    6    7    7    8
CONECT    8   18
END
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SMILES for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

[H][C@](O)(C(C)C)C(O)=O
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INCHI for NP0002797 ((S)-(+)-2-Hydroxy-3-methylbutyric acid)

InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t4-/m0/s1
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View in JSmol
Synonyms
Chemical FormulaC5H10O3
Average Mass118.1320 Da
Monoisotopic Mass118.06299 Da
IUPAC Name(2S)-2-hydroxy-3-methylbutanoic acid
Traditional Nameα-hydroxyisovaleric acid
CAS Registry NumberNot Available
SMILES
[H][C@](O)(C(C)C)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-3(2)4(6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t4-/m0/s1
InChI KeyNGEWQZIDQIYUNV-BYPYZUCNSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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 ParentsNot Available
SubstituentsNot Available
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
logP0.1ALOGPS
logP0.42ChemAxon
logS0.26ALOGPS
pKa (Strongest Acidic)4.14ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity27.84 m³·mol⁻¹ChemAxon
Polarizability11.78 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062584
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID745606
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID60631
Good Scents IDNot Available
References
General References
  1. Beloborodova NV, Bairamov IT, Olenin AIu, Fedotcheva NI: [Exometabolites of some anaerobic microorganisms of human microflora]. Biomed Khim. 2011 Jan-Feb;57(1):95-105. doi: 10.18097/pbmc20115701095. [PubMed:21516781 ]